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New MIT study identifies the most effective words used in meetings.
Words have power, especially in meetings. A new study from MIT's Sloan School of Management finds that saying "yeah", "give", "start" and even "meeting" can boost a person's persuasive powers among co-workers.
Statisticians Cynthia Rudin and Been Kim studied 95 meetings for the vocabulary used in proposals that were accepted by the group. They concluded that the most persuasive words are those that build consensus.
"Yeah" signals agreement with a previous idea, the authors posit. Using the word "start" in sentences like "I think we should start with the basics" is useful for building early alliances early; group participants want to appear interested in being productive. The word "give" indicates some benefit to the group. (As in, "This would give us market share.") The word can also suggest that an idea is based on prior knowledge. For example: "Given speech recognition, I think you should go for the less fancy chip."
Image via Monkey Business Images/Shutterstock.com
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Our CityGroups are the essence of who we are as a church. Community, spiritual formation, congregational care, service to our city... it all comes from these monthly groups. You can expect to share joy, laughter, to read and pray through the scriptures, and to strategize how to serve the community.
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Earlier Event: December 4Rio Vista CityGroup
Later Event: December 12Coral Ridge CityGroup

subset: commoncrawl


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4 arrested; reports cite possible tie to Hoffman drugs
Four people have been arrested in Manhattan and are being questioned in connection to potentially selling drugs to late actor Philip Seymour Hoffman, CBS News and the New York Daily News are reporting.
Police raided a Chinatown apartment at about 7 p.m. and took the four people into custody, the DailyNews reports.
The New York Times reports search warrants were executed in three apartments and that the four arrested were found with 350 bags of heroin.
The four were arrested at 302 Mott St. in Manhattan and taken into custody during the execution of a search warrant, Det. Brian Sessa of NYPD said early Wednesday. Drugs were found at the location, Sessa said.
When asked if the arrests were connected to Hoffman's death, Sessa said, "Not that we're aware of."
Three men and one woman were being questioned, CNN reports. The New York Postnamed the four people being questioned, all of whom in the story appear to deny any links to Hoffman or selling heroin.
The 46-year-old actor was found Sunday lying on the bathroom floor of his Greenwich Village apartment with a syringe in his arm.
Investigators found about 50 envelopes of what they believe is heroin, along with used syringes, prescription drugs and empty bags, according CNN and NBC, which cited unnamed law enforcement sources.
STORY:Hoffman death puts focus on heroin's comeback
MORE:Philip Seymour Hoffman autopsy results expected soon
VOICES:'Heroin abuse looks like my dad'
Investigators also found addiction treatment medication, blood pressure medication and a muscle relaxant, according to NBC News and CNN.
No traces of the powerful pain reliever fentanyl was found in the heroin, a police source told the DailyNews. Heroin laced with fentanyl has killed more than 20 people in Pennsylvania, the DailyNews reports.
A private funeral for Hoffman will be held Friday in New York City. Plans also are underway for a memorial service in New York later in the month, Hoffman representative Karen Samfilippo said in a statement obtained by USA TODAY.
Hoffman was last seen alive Saturday night and his body was removed from the apartment on Sunday night.
Hoffman has three children with Mimi O'Donnell, a costume designer.
Broadway theaters plan to dim their marquee lights for one minute starting at 7:45 p.m. Wednesday in Hoffman's memory.
Contributing: Donna Freydkin


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The 6 Second Abs machine is one in a long line of ab exercisers that became popular a few years back on late night TV.
The philosophy behind 6 Second Abs is simple. They provide a machine that they say will allow you to perform the perfect crunch. There are 3 clicks of down force and 3 clicks of up force.
So does the 6 Second Abs machine work? Sure, you can do a crunch. But the name is misleading as hell. The "6 Seconds" they refer to is the amount of time it takes to perform one rep, not to get great abs (like you'd fall for that anyway)…
6 Second Abs Manufacturer Claims:
Perfect Form – Maintain the proper form for a more effective crunch while in a comfortable, seated position.
Perfect Tempo – Audible clicks guide you through a perfect crunch lasting 6 seconds.
The Right Resistance – 5 adjustable resistance levels, from approximately 15 to 55 pounds.
I have a problem with the 6 Second Abs claims. There is no guarantee that you will be in perfect form, perfect tempo or get the right resistance.
For starters, most people that use an ab machine have crappy form, this fact isn't helped by the unusual motion of this machine either.
Then there's the tempo. 6 Seconds Abs is making a big leap of faith if they think people won't try to go fast to get the exercise session over with.
Then there's the resistance, sure it's good to add resistance to your ab workout but the resistance bands work only marginally well at best.
To round out this review, 6 Second Abs also includes a diet and exercise guide, and a couple of workout videos.
If their machine works so great and will give you rock hard abs, what the hell do you need all that other stuff? I let you think up your own answer to that…


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21 August 2012 at 3.56pm | Comment on this article
When an MP in the 1990s described the homeless as "the people you step over coming out of the Opera House", Matt Peacock was inspired to change that perception. He formed the charity Streetwise Opera and, earlier this summer, people who have experienced homelessness performed at the Royal Opera House. The festival, With One Voice, was sold out and streamed live online.
Part of the London 2012 Festival, the event was the first time that homeless people have been invited to take part in an Olympic celebration. "The Olympics is usually a time when the homeless are forgotten", Matt told us, "and, in the worst cases, are moved off the streets."
The chance to perform had a positive effect on Streetwise Opera's participants' lives. For many of them, this was their first public performance. "Everyone was excited and so keen to show a different side of homelessness, one of achievement rather than need. The feedback we've had has been extraordinary, many saying that it was the best experience of their lives," said Matt.
One participant, Patrick, began attending opera workshops in Nottingham in 2010. Reflecting on With One Voice, he said, "Everyone noticed the change in me since coming to Streetwise Opera – my partner, my kids, my friends. I was using heroin for 25 years and, for the first time, I can look my kids in the eye."
Streetwise Opera is keen to make this year's event an Olympic tradition: it is trying to persuade Rio to organize something similar for homeless or disadvantaged people during its Games in 2016. You can support Streetwise Opera's bid by signing a petition that will go to the IOC and the Rio 2016 committee.


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Choosing the Right Beer for a Recipe
With the wide array of styles available, you need to make a choice about which beer to use in a recipe. Although the everyday, light-bodied, commercial lagers generally do fine, they obviously don't add as much flavor as other styles. Consider the following factors when choosing a cooking beer:
Color: Beers brewed with a large percentage of dark grain, such as Stout and Porter, are likely to transpose their color to your meal — not an appetizing hue for fettuccine Alfredo or scrambled eggs.
Level of sweetness (maltiness) versus level of bitterness (hoppiness and grain astringency): Malt is by far the predominant beer taste in a recipe, but bitterness can take over easily because beer's bitterness increases with reduction (that is, the decrease in volume caused by boiling). Add bitter beer later in a recipe, or if a beer is being cooked for a while, choose a maltier beer style. In general, go with a mild beer rather than a bold one and avoid highly hopped beers, such as some Pale Ales. Sweeter, heavier beers should be reserved for dessert mixes and glazes.
As the water and alcohol boil off, both the sweet and bitter flavors of the beer intensify.
Unusual flavors: Keep in mind that beers are now available in a wide variety of styles, many with flavors that aren't traditionally associated with beer. You may encounter fruited beers, chocolate beers, sour beers, and smoked beers. It's not that these flavored beers don't present lots of culinary possibilities in their own right; they're just not meant for use in the average recipe.
Unless you're well versed in beer styles and know what to expect from each, you'll find the pale but tasty Munich Helles (pale Munich-style lager) well suited to cross-culinary usage.
Beware of the many recipes floating around out there that call for just plain beer as an ingredient, without specifying a particular brand or style. This generalization is evidence of the simplistic and uninformed mentality that a beer is a beer is a beer. Given the great diversity in beer today, using the wrong style can be a recipe for a disastrous meal. On the other hand, if the errant recipe author is from the United States, you can probably assume that a pale, commercial lager is the intended style.


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Hot off the Press
Specialty-Alloy Processor Adds Turret Head Slitter
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Thursday, September 5, 2013
United Performance Metals (UPM), Hamilton, OH, has added an 18-in. turret head slitter to its production facility, capable of slitting coiled stock from 0.020 to 0.125 in. thick. Compared to existing slitters, UPM expects the new machine to reduce setup times, increase line speeds and optimize operator efficiency. The slitter boasts a pressure bar system that eliminates scratching and minimizes camber, and an interchangeable rewind drum. UPM processes stainless-steel, nickel-, cobalt-, aluminum- and titanium-based alloys in sheet, coil, plate and bar; www.upmet.com/.
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It's funny how nobody notices all the good things you do until you don't do them.
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I noticed you are not noticing me.
To make a mistake is human, but to blame it on someone else, that's even more human.
It's true that we don't know what we've got until we lose it, but it's also true that we don't know what we've been missing until it arrives.
You're born free, then you're taxed to death.
If you don't succeed at first, hide all evidence that you tried.
The probability of meeting someone you know increases a hundredfold when you're with someone you're not supposed to be seen with.
Don't ask me anything, and I won't tell you any lies.
You know when you put a stick in water and it looks bent? That's why I never take baths.
Don't be stupid, it might make you famous.
A joke is a very serious thing.
If there is a wrong way to do something, then someone will do it.
Insanity: doing the same thing over and over again and expecting different results.
We have to do the impossible, but it is possible.
If you think nothing is impossible, try slamming a revolving door.
If what you've done is stupid but it works, then it really isn't that stupid at all.
If a philosopher answers your question, you will no longer understand what you asked in the first place.
When someone doesn't like something, it's often because they're not familiar with it, or they're too familiar with it.
Everyone wants your happiness. Don't let them take it!!
How can you make sure you never miss your target? Shoot first, and whatever you hit, call it the target.
Never test how deep the water is with both feet.
It's not important to win, it's important to make the other guy lose.
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Two days before Thanksgiving, the Indianapolis School Board will make a decision sure to heat up discussion around the turkey in just about every home with young children. That's when board members will vote on whether to adopt year-round classes.
If the board approves the measure, Indianapolis pupils would go to school in cycles of eight to 10 weeks, with three to five weeks off after each, throughout the year. That would put them among the growing number of children around the nation who are going to school on so-called balanced schedules.
Indianapolis Superintendent Eugene White said the schedule would add 20 class days every year, giving pupils more time to learn and shorter periods away from the classroom to forget what they've studied. For both teachers and students, the shorter but more frequent breaks will "give them some kind of relief and (allow them to) come back more invigorated," he said.
That's important in a district criticized for low standardized-test scores and high dropout rates, said board member Annie Roof, because "what we are doing isn't working."
An msnbc.com-NBC News special report
Alex Johnson is a reporter for msnbc.com. The following NBC stations contributed to this report: KARE of Minneapolis, Minn.; KSNV of Las Vegas; WETM of Elmira, N.Y.; WMAQ of Chicago; WNYT of Albany, N.Y.; WPSD of Paducah, Ky.; and WTHR of Indianapolis.
• Follow Alex Johnson on Facebook
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10 percent by 2012?
If the board approves, Indianapolis will hop on a bandwagon that's quietly rolling across the education landscape.
Ten years ago, according to Education Department statistics, about 1.5 million public school children went to class on a "balanced schedule" — usually shorthanded as YRE, for "year-round education."
Six years ago, that number was up to 2 million. By 2008, nearly 2.5 million pupils were on a YRE plan.
Hoffman withdrew $1,200 hours before death: sources
Philip Seymour Hoffman withdrew a total of $1,200 from an ATM at a supermarket near his New York City apartment the night before he was found lifeless in his bathroom with a syringe still in his left arm, sources told NBC News.
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- Hoffman withdrew $1,200 hours before death: sources
That's the last year for which official figures are available, but since then, some of the nation's biggest districts have adopted or expanded YRE in their facilities, notably the Chicago Public Schools, and others — including Houston and Indianapolis — could join them next year.
By 2012, education groups estimate, more than 5 million pupils — about 10 percent of all children enrolled in American public schools — could be going to school year-round.
In Chicago, the drive to adopt YRE was championed by Arne Duncan during his term as the school system's chief executive. Duncan is now President Barack Obama's education secretary, and his boss is behind the campaign for year-round learning.
"The idea of a longer school year, I think, makes sense," Obama said in an interview last month on NBC's TODAY. "Students are losing a lot of what they learn during the school year during the summer."
The phenomenon is called "spring slide," a term coined by Doris R. Entwisle, Karl L. Alexander and Linda Steffel Olson of Johns Hopkins University in Baltimore, who have tracked Baltimore schoolchildren since 1982 and have been publishing their findings since 1997.
Challenging some prevalent assumptions, they reported in 2007 that children from lower socioeconomic backgrounds make just as much progress during the academic year as better-off children. On standardized reading comprehension tests, students improved by about 195 points regardless which socioeconomic background they come from, low, middle or high, the researchers found.
Where does the summer break come from?
Year-round school isn't a new idea. Newark, N.J., schools went year-round back in 1912, chipping away at a summer break tradition that is commonly — and perhaps wrongly — attributed to the so-called agrarian calendar. In fact, historians and economists disagree on whether farming had anything to do with the gradual institution of the June-to-September summer vacation.
William A. Fischel, an economics professor at Dartmouth College, points out that in most American regions, planting usually took place in early to mid-spring — before school traditionally lets out — and that harvesting usually occurred in the mid- to late fall — after school traditionally starts.
Fischel points to widespread literature of the time strongly suggesting that children commonly went to school in June, July and August in the 19th century, before the idea of formally grading children by age and achievement began emerging.
• You can read the abstract of Fischel's 2006 paper here
Once grading based on age became common, school calendars had to be coordinated, because Americans were highly mobile people in the 19th century, ever pushing the country toward the Pacific Ocean and plopping their children into new schools. And before paved roads, if you wanted to pack up the family belongings and point the mule west, you most likely did it in the summer — when the weather made traveling easier.
But in the summer months, kids in the top third economically kept gaining, picking up on average 46.6 points on the reading test. It was a dramatically different story for the less-privileged two-thirds: Kids the middle group gained about 4.5 points on average, while those in the bottom third lost 1.9 points. (Other research has shown similar, though less dramatic, trends in math and science.)
'We don't have them here enough'
Put another way, well-off children — those with access to tutoring and academic camps and travel — keep learning when school's out for the summer, while those without such advantages tread water or even sink.
"Society can't keep saying to schools 'have every kid perform better' when we don't have them here enough," said Charlie Kyte, president of the Minnesota Association of School Administrators. A few Minnesota districts have adopted balanced calendars, and many others are studying the idea.
In Indianapolis, the difference is clear in the small number of schools that are already year-round, said Margaret Silk, a fourth-grade teacher at one of them, Ernie Pyle Elementary School. There, 70 percent of students from low-income families pass their state assessment tests, higher than the Indiana average for all students and well above the average for lower-income students.
Silk said that under the traditional calendar, it took six weeks of reviewing the previous year's lessons just to get her students back up to speed.
"In this calendar, oh, my goodness, (it takes) maybe two weeks at most," she said.
• Vote: Do you support a longer school year?
• Read more reports on Education Nation
Natasha Flowers, an assistant education professor at Indiana University-Purdue University Indianapolis, said the year-round classes make a significant difference to children who are at the most risk — those from families that "don't have resources to do lots of academic enriching during the summer."
That's especially important as the federal No Child Left Behind program requires kids to master more material by the time they graduate. Educators like Mike Ginalski, superintendent of schools in Corning, N.Y., say it's getting harder to "cram all of the curriculum in basically a nine- to 10-month period of time."
"There are children that can always benefit from more time and more support that they receive daily in school," Ginalski said.
So why isn't year-round education taking root even faster?
For one thing, it's not just pupils who don't like the idea of sitting in class all day in the middle of summer. Public opinion polling has consistently shown that a majority of American adults oppose mandatory summer classes, too.
The most recent poll, by Rasmussen Reports in July, found that adults opposed a year-round calendar by 63 percent to 31 percent — about the same ratio as other surveys taken in recent years. (The Rasmussen poll reported a margin of sampling error of 3 percentage points.)
Most popular
But the big objection boils down to this:
"Show me the money," Randy J. Greene, superintendent of schools in Paducah, Ky., said when the idea was raised there after Obama's comments last month.
Year-round buses and lunches and after-school tutoring programs cost more, Greene said, and parents are already unhappy about a 4 percent increase in property taxes to cover the $300,000 cut in state funding that hit the district this year.
The cost concern is playing out differently in Las Vegas, where the Clark County School Board — facing a $30 million shortfall in its budget thanks to reduced state funding and declining property tax revenue — voted in April to abandon a year-round calendar and return to the traditional three-month summer break. The new calendar was projected to save the district about $13.8 million.
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Marcie McDonald, principal of Squires Elementary School, said she understood that the board had to try to balance its smaller budget. But she said doing so would come at a real cost.
Ninety-two percent of McDonald's pupils are Latino, and for two-thirds of them, English is their second language.
"Our little ones are learning language," McDonald said. "They go home and listen to their primary language of their home for three months and come back. And having not used English for three months — that poses another concern or problem."
Follow Alex Johnson on Facebook| Follow Alex Johnson on Twitter
© 2013 msnbc.com Reprints


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I hope this is it. I hope it gets to production in 2018.
It'll Be Revealed Soon, At Least In Concept Form
According to Japan's Best Car magazine, the Supra could make its debut as a concept car at the Tokyo Motor Show in October. Apparently, it'll share the stage with a version of the little, rear-drive S-FR Concept first shown at Tokyo in 2015, and intriguingly, some sort of sporty Corolla concept.


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After School Special Backpack Charm
Backpack Charm
Ages 6-10
Add personal appeal to a book bag or backpack with a fun backpack charm.
BONUS! Download the instructions to make a cute bookmark and pencil case.
Download the backpack charm patterns. Or instruct the child to draw a simple shape that's no larger than 5" square, such as an apple, cat or heart. Cut out the pattern along the lines.
Cut one shape from each felt square.
Thread the needle with six strands of embroidery floss; knot the ends. Hand stitch the desired embellishments to one shape right side. For example, if using the featured cat shape, stitch an eye on the head and a collar and bell at the neck. Or cut out fabric scraps to stitch on the apple.
Align the two shapes with wrong sides together; pin, and then backstitch the perimeter, leaving a 1" opening. Gently stuff with fiberfill. Hand stitch the opening closed.
Hand stitch the ribbon or rickrack lower-edge center to the charm upper-edge center (1). Tie the ends together.
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Make Your Stay Super
Free WiFi for convenience and guest receptions for your enjoyment
Wake up to a free 8-item SuperStart breakfast. We have free WiFi, guest laundry and large-vehicle parking with outdoor electrical outlets. Enjoy our guest reception at select times, with free snacks and beer.
Things to Do
Experience family fun and outdoor recreation at nearby parks
Take the short drive to Wylie Park, which has go-karts, mini-golf, bumper boats, hiking, or biking. Storybook Land has a fun medieval castle and nursery rhyme displays. Fish, boat, or hunt some of the best pheasant in the country. If you golf, hit the links at Lee Municipal Park Golf Course. Northern State University is two miles away.
Meetings and Events at Our Super 8
With 900 square feet of event space, our hotel features 1 meeting room. Plan your next meeting or special event with us. We also arrange great rates for groups — large or small.


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Reviewed By William P (Mount Vernon, TX) Reviewed for a 1938 Buick Special —4/12/2018 4:58 PM
Used these on a street rod with 350 sbc 300 HP show car. Sounds good at idle and wakes up when you romp on it. They almost eliminated a drone problem.Just loud enough to let everyone know the car is not a wimp. Would definitely buy again.


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Skin (Rosacea) Kit #2: Arnica, Willowherb Serum, Herbal Nova, Liquid Silk & Shammy
We searched high and low for ingredients, studied them, tested them and then produced a line of highly effective products for the most sensitive skin types in the world. We have many rosacea and sensitive skin customers using these wonderful products. If you have sensitive, rosacea, post surgery or acne skin that cannot tolerate regular skin care products, this is your answer. While our packaging is simple, our ingredients and quality is outstanding.
This 5 piece kit will save you 20% off of purchasing these products separately.
Arnica Wash:
Light, gel/lotion low foaming cleanser made for highly sensitive, very dry, or post surgery skin types. Arnica repairs, calms, heals bruising and wounds to the skin; Aloe Leaf Gel is soothing and cooling; Angelica Soothes and repairs; Echinacea (cone flower) is anti-microbial as well as anti-aging. Absolutely NO irritation or left over oily residue from this miraculous cleanser. No oil, perfumes, fragrance, dyes or alcohols. This mild, non-sensitizing, low foaming facial wash easily removes makeup and other residue which can add to skins sensitivity. Sames great product, now in new packaging! ($26.95)
Willowherb Soothing Serum:
This ultra cooling, soothing gel by Skin Rx contains Canadian willowherb, which is clinically proven to calm redness and irritation while acting as an anti-bacterial agent as well. Vitamin K is added for it's blood clotting ability, thus aids in healing and calming capillaries/blood vessels that have enlarged or burst. Vitamin K is great for darkness under the eyes. Also contains Ginko Biloba, aloe and Hyaluronic Gel. Use this serum 2-3 times a day as needed. No oil, perfumes, fragrance, dyes or irritating alcohols. A Great moisturizer for oily skin, ($30.95)
Herbal Nova Creme:
Richly hydrating cream with natural ingredients to drench your skin in moisture (non-oily). Contains whole aloe, ceramides, Hyaluronic Acid (maximum water hydrator), Echinaecea, Cornflower, Soy, Meadowfoam Oil, Squalane Oil, Vitamins E, C, A. Excellent for the driest of skin. ($29.95)
Liquid Silk:
Plant extract oils and phospholipids make this silky serum a must have for dry skin. Apply it under or over your moisturizer for a "rose petal" feel to the skin. Make-up goes on smooth and skin looks radiant. Protects dry skin all day from moisture loss. Wheat germ oil soothes irritated skin, especially in the case of eczema, aids wound healing and is known to have a favorable effect on scar tissue.Paraben free.($24.95)
PVA Shammy:
Ultra soft, smooth and spongy texture, thin 9" x 9" cloth that lasts and lasts for years. Cleanse the skin with this cloth instead of harsh washcloths. Gentle on sensitive skin. Cleans great around the eyes and for removing eye make-up thoroughly. Great for babies too! ($8.00)
This is a great kit for anybody, you don't need to have sensitive or rosacea skin, you just need to want to keep your skin looking great. Priced separately this kit would be $120.80, but you save over to 20% purchasing it in this convenient package.
More Information:
- View Ingredients
- Directions for Use
Works Well With:
- Aloe Soothing Masque 2 oz


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Summary: Antitoxin component of bacterial toxin-antitoxin system, MqsA
Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.
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Toxin-antitoxin system Edit Wikipedia article
A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a protein 'poison' and a corresponding 'antidote'. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).[2][3] Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies.[4][5]
Toxin-antitoxin systems are typically classified according to how the antitoxin neutralises the toxin. In a Type I toxin-antitoxin system, the translation of messenger RNA (mRNA) that encodes the toxin is inhibited by the binding of a small non-coding RNA antitoxin to the mRNA. The protein toxin in a type II system is inhibited post-translationally by the binding of another protein antitoxin. Type III toxin-antitoxin systems consist of a small RNA that binds directly to the toxin protein.[6] There are also types IV-VI, which are less common.[7] Toxin-antitoxin genes are often transferred through horizontal gene transfer[8][9] and are associated with pathogenic bacteria, having been found on plasmids conferring antibiotic resistance and virulence.[1]
Chromosomal toxin-antitoxin systems also exist, some of which perform cell functions such as responding to stresses, causing cell cycle arrest and bringing about programmed cell death.[1][10] In evolutionary terms, toxin-antitoxin systems can be considered selfish DNA in that the purpose of the systems are to replicate, regardless of whether they benefit the host organism or not. Some have proposed adaptive theories to explain the evolution of toxin-antitoxin systems; for example, chromosomal toxin-antitoxin systems could have evolved to prevent the inheritance of large deletions of the host genome.[11] Toxin-antitoxin systems have several biotechnological applications, such as a method of maintaining plasmids in cell lines, targets for antibiotics, and as positive selection vectors.[12]
Evolutionary advantage
Plasmid stabilising toxin-antitoxin systems have been used as examples of selfish DNA as part of the gene centered view of evolution. It has been theorised that toxin-antitoxin loci serve only to maintain their own DNA, at the expense of the host organism.[1] Other theories propose the systems have evolved to increase the fitness of plasmids in competition with other plasmids.[13] Thus, the toxin-antitoxin system confers an advantage to the host DNA by eliminating competing plasmids in cell progeny. This theory was corroborated through computer modelling.[14] This does not, however, explain the presence of toxin-antitoxin systems on chromosomes.
Chromosomal toxin-antitoxin systems have a number of adaptive theories explaining their success at natural selection. The simplest explanation of their existence on chromosomes is that they prevent harmful large deletions of the cell's genome, though arguably deletions of large coding regions are fatal to a daughter cell regardless.[11] MazEF, a toxin-antitoxin locus found in E. coli and other bacteria, induces programmed cell death in response to starvation, specifically a lack of amino acids.[17] This releases the cell's contents for absorption by neighbouring cells, potentially preventing the death of close relatives, and thereby increasing the inclusive fitness of the cell that perished. This is an example of altruism and how bacterial colonies resemble multicellular organisms.[14] However, the "mazEF mediated PCD" is largely refuted by several studies.[18][19][20]
Another theory states that chromosomal toxin-antitoxin systems are designed to be bacteriostatic rather than bactericidal.[21] RelE, for example, is a global inhibitor of translation during nutrient stress, and its expression reduces the chance of starvation by lowering the cell's nutrient requirements.[22] A homologue of mazF toxin called mazF-mx is essential for fruiting body formation in Myxococcus xanthus.[23] When nutrients become limiting in this swarming bacteria, a group of 50,000 cells converge into a fruiting body structure.[24] The maxF-mx toxin is a component of this nutrient-stress pathway; it enables a percentage of cells within the fruiting body to form myxospores. It has been suggested that M. xanthus has hijacked the toxin-antitoxin system, replacing the antitoxin with its own molecular control to regulate its development.[23]
It has also been proposed that chromosomal copies of plasmid toxin-antitoxin systems may serve as anti-addiction modules – a method of omitting a plasmid from progeny without suffering the effects of the toxin.[9] An example of this is an antitoxin on the Erwinia chrysanthemi genome that counteracts the toxic activity of an F plasmid toxin counterpart.[25]
Nine possible functions of toxin-antitoxin systems have been proposed. These are:[26][27]
- Junk – they have been acquired from plasmids and retained due to their addictive nature.
- Stabilisation of genomic parasites – chromosomal remnants from transposons and bacteriophages.
- Selfish alleles – non-addictive alleles are unable to replace addictive alleles during recombination but the opposite is able to occur.
- Gene regulation – some toxins act as a means of general repression of gene expression[28] while others are more specific.[29]
- Growth control – bacteriostatic toxins, as mentioned above, restrict growth rather than killing the host cell.[21]
- Persisters – some bacterial populations contain a sub-population of 'persisters' that are slow-growing, hardy individuals, which potentially insure the population against catastrophic loss.[30] At least with regard to endoribonuclease encoding Type II TA systems, their role in persistence is highly debated.[31] What has been demonstrated by experiments and modelling [32] is that an imbalance between the level of toxin and its antitoxin, either by mutations [33][34] or by overexpression[35] results in high persistence.
- Programmed cell arrest and the preservation of the commons – the altruistic explanation as demonstrated by MazEF, detailed above.
- Programmed cell death – similar to the above function, although individuals must have variable stress survival level to prevent entire population destruction.
- Antiphage mechanism – when bacteriophage interrupt the host cell's transcription and translation, a toxin-antitoxin system may be activated that limits the phage's replication.[36][37]
An experiment where five TA systems were deleted from a strain of E. coli found no evidence that the TA systems conferred an advantage to the host. This result casts doubt on the growth control and programmed cell death hypotheses.[38] As of the existing knowledge in 2017, the chromosomal Type II TA systems are horizontally propagating selfish DNA which may have played a role in antiaddiction to TA encoding plasmids.[9][27]
System types
Type I
Type I toxin-antitoxin systems rely on the base-pairing of complementary antitoxin RNA with the toxin's mRNA. Translation of the mRNA is then inhibited either by degradation via RNase III or by occluding the Shine-Dalgarno sequence or ribosome binding site. Often the toxin and antitoxin are encoded on opposite strands of DNA. The 5' or 3' overlapping region between the two genes is the area involved in complementary base-pairing, usually with between 19–23 contiguous base pairs.[39]
Toxins of type I systems are small, hydrophobic proteins that confer toxicity by damaging cell membranes.[1] Few intracellular targets of type I toxins have been identified, possibly due to the difficult nature of analysing proteins that are poisonous to their bacterial hosts.[10]
Type I systems sometimes include a third component. In the case of the well-characterised hok/sok system, in addition to the hok toxin and sok antitoxin, there is a third gene, called mok. This open reading frame almost entirely overlaps that of the toxin, and the translation of the toxin is dependent on the translation of this third component.[3] Thus the binding of antitoxin to toxin is sometimes a simplification, and the antitoxin in fact binds a third RNA, which then affects toxin translation.[39]
Example systems
|The original and best-understood type I toxin-antitoxin system (pictured), which stabilises plasmids in a number of gram-negative bacteria
|The first type I system to be identified in gram-positive bacteria
|Responds to DNA damage
|A chromosomal system in Enterobacteriaceae
|A hok/sok homologue, which also stabilises the F plasmid
|Discovered in E. coli intergenic regions, the antitoxin was originally named QUAD RNA
|Ensures the inheritance of the skin element during sporulation in Bacillus subtilis
|A chromosomal system induced as an SOS response
|A system identified in Xanthomonas campestris with erratic phylogenetic distribution.
See also
Type II
Type II toxin-antitoxin systems are generally better-understood than type I.[39] In this system a labile protein antitoxin tightly binds and inhibits the activity of a stable toxin.[10] The largest family of type II toxin-antitoxin systems is vapBC,[47] which has been found through bioinformatics searches to represent between 37 and 42% of all predicted type II loci.[15][16]
Type II systems are organised in operons with the antitoxin protein typically being located upstream of the toxin, which helps to prevent expression of the toxin without the antitoxin[48]. The proteins are typically around 100 amino acids in length,[39] and exhibit toxicity in a number of ways: CcdB protein, for example, affects DNA gyrase by poisoning DNA topoisomerase II[49] whereas MazF protein is a toxic endoribonuclease that cleaves cellular mRNAs at specific sequence motifs.[50] The most common toxic activity is the protein acting as an endonuclease, also known as an interferase.[51][52]
A third protein can sometimes be involved in type II toxin-antitoxin systems.[53] In the case of the aforementioned MazEF addiction module, in addition to the toxin and antitoxin there is a regulatory protein involved called MazG. MazG protein interacts with E. coli's Era GTPase and is described as a 'nucleoside triphosphate pyrophosphohydrolase,'[54] which hydrolyses nucleoside triphosphates to monophosphates. Later research showed that MazG is transcribed in the same polycistronic mRNA as MazE and MazF, and that MazG bound the MazF toxin to further inhibit its activity.[55]
Unlike the aforementioned toxin-antitoxin systems, DarTG is a considered a type II system, in which both the toxin and the antitoxin have enzymatic activity. The DarG antitoxin does not inhibit the DarT toxin, which modifies DNA by ADP-ribosylating specific sequence motifs, but instead removes the toxic modification caused by the toxin and therefore DarTG could be considered a type IV system.[56]
Example systems
|Found on the F plasmid of Escherichia coli
|Found in multiple copies in Caulobacter crescentus
|Found in E. coli and in chromosomes of other bacteria
|A system induced by the SOS response to DNA damage in E. coli
|Found in archaea and bacteria
|Stabilises the R1 plasmid and is related to the CcdB/A system
|Found mostly in Gram-positive bacteria
|Found in archaea and bacteria
Type III
|ToxN, type III toxin-antitoxin system
Type III toxin-antitoxin systems rely on direct interaction between a toxic protein and an RNA antitoxin. The toxic effects of the protein are neutralised by the RNA gene.[6] One example is the ToxIN system from the bacterial plant pathogen Erwinia carotovora. The toxic ToxN protein is approximately 170 amino acids long and has been shown to be toxic to E. coli. The toxic activity of ToxN is inhibited by ToxI RNA, an RNA with 5.5 direct repeats of a 36 nucleotide motif (AGGTGATTTGCTACCTTTAAGTGCAGCTAGAAATTC).[60][61] Crystallographic analysis of ToxIN has found that ToxN inhibition requires the formation of a trimeric ToxIN complex, whereby three ToxI monomers bind three ToxN monomers; the complex is held together by extensive protein-RNA interactions.[62]
Type IV
Type IV toxin-antitoxin systems are similar to type II systems, because they consist of two proteins. Unlike type II systems, the antitoxin in type IV toxin-antitoxin systems counteracts the activity of the toxin, and the two proteins do not directly interact.[63]
Type V
GhoT/GhoS is a type V toxin-antitoxin system, in which the antitoxin (GhoS) cleaves the ghoT mRNA. This system is regulated by the type II system, MsqR/MsqA.[64]
Type VI
SocAB is a type VI toxin-antitoxin system that was discovered in Caulobacter crescentus. The antitoxin, SocA, promotes degradation of the toxin, SocB, by the protease ClpXP.[65]
Biotechnological applications
The biotechnological applications of toxin-antitoxin systems have begun to be realised by several biotechnology organisations.[12][21] A primary usage is in maintaining plasmids in a large bacterial cell culture. In an experiment examining the effectiveness of the hok/sok locus, it was found that segregational stability of an inserted plasmid expressing beta-galactosidase was increased by between 8 and 22 times compared to a control culture lacking a toxin-antitoxin system.[66][67] In large-scale microorganism processes such as fermentation, progeny cells lacking the plasmid insert often have a higher fitness than those who inherit the plasmid and can outcompete the desirable microorganisms. A toxin-antitoxin system maintains the plasmid thereby maintaining the efficiency of the industrial process.[12]
Additionally, toxin-antitoxin systems may be a future target for antibiotics. Inducing suicide modules against pathogens could help combat the growing problem of multi-drug resistance.[68]
Ensuring a plasmid accepts an insert is a common problem of DNA cloning. Toxin-antitoxin systems can be used to positively select for only those cells that have taken up a plasmid containing the inserted gene of interest, screening out those that lack the inserted gene. An example of this application comes from CcdB-encoded toxin, which has been incorporated into plasmid vectors.[69] The gene of interest is then targeted to recombine into the CcdB locus, inactivating the transcription of the toxic protein. Thus, cells containing the plasmid but not the insert perish due to the toxic effects of CcdB protein, and only those that incorporate the insert survive.[12]
Another example application involves both the CcdB toxin and CcdA antitoxin. CcdB is found in recombinant bacterial genomes and an inactivated version of CcdA is inserted into a linearised plasmid vector. A short extra sequence is added to the gene of interest that activates the antitoxin when the insertion occurs. This method ensures orientation-specific gene insertion.[69]
Genetically modified organisms must be contained in a pre-defined area during research.[68] Toxin-antitoxin systems can cause cell suicide in certain conditions, such as a lack of a lab-specific growth medium they would not encounter outside of the controlled laboratory set-up.[21][70]
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- ^ a b Jankevicius G, Ariza A, Ahel M, Ahel I (December 2016). "The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA". Molecular Cell. 64 (6): 1109–1116. doi:10.1016/j.molcel.2016.11.014. PMC 5179494 . PMID 27939941.
- ^ Fiebig A, Castro Rojas CM, Siegal-Gaskins D, Crosson S (July 2010). "Interaction specificity, toxicity and regulation of a paralogous set of ParE/RelE-family toxin-antitoxin systems". Molecular Microbiology. 77 (1): 236–51. doi:10.1111/j.1365-2958.2010.07207.x. PMC 2907451 . PMID 20487277. (subscription required)
- ^ Jørgensen MG, Pandey DP, Jaskolska M, Gerdes K (February 2009). "HicA of Escherichia coli defines a novel family of translation-independent mRNA interferases in bacteria and archaea". Journal of Bacteriology. 191 (4): 1191–9. doi:10.1128/JB.01013-08. PMC 2631989 . PMID 19060138.
- ^ Mutschler H, Meinhart A (December 2011). "ε/ζ systems: their role in resistance, virulence, and their potential for antibiotic development". Journal of Molecular Medicine. 89 (12): 1183–94. doi:10.1007/s00109-011-0797-4. PMC 3218275 . PMID 21822621.
- ^ Fineran PC, Blower TR, Foulds IJ, Humphreys DP, Lilley KS, Salmond GP (January 2009). "The phage abortive infection system, ToxIN, functions as a protein-RNA toxin-antitoxin pair". Proceedings of the National Academy of Sciences of the United States of America. 106 (3): 894–9. doi:10.1073/pnas.0808832106. PMC 2630095 . PMID 19124776.
- ^ Blower TR, Fineran PC, Johnson MJ, Toth IK, Humphreys DP, Salmond GP (October 2009). "Mutagenesis and functional characterization of the RNA and protein components of the toxIN abortive infection and toxin-antitoxin locus of Erwinia". Journal of Bacteriology. 191 (19): 6029–39. doi:10.1128/JB.00720-09. PMC 2747886 . PMID 19633081.
- ^ Blower TR, Pei XY, Short FL, Fineran PC, Humphreys DP, Luisi BF, Salmond GP (February 2011). "A processed noncoding RNA regulates an altruistic bacterial antiviral system". Nature Structural & Molecular Biology. 18 (2): 185–90. doi:10.1038/nsmb.1981. PMC 4612426 . PMID 21240270.
- ^ Brown JM, Shaw KJ (November 2003). "A novel family of Escherichia coli toxin-antitoxin gene pairs". Journal of Bacteriology. 185 (22): 6600–8. doi:10.1128/jb.185.22.6600-6608.2003. PMC 262102 . PMID 14594833.
- ^ Wang X, Lord DM, Hong SH, Peti W, Benedik MJ, Page R, Wood TK (June 2013). "Type II toxin/antitoxin MqsR/MqsA controls type V toxin/antitoxin GhoT/GhoS". Environmental Microbiology. 15 (6): 1734–44. doi:10.1111/1462-2920.12063. PMC 3620836 . PMID 23289863.
- ^ Aakre CD, Phung TN, Huang D, Laub MT (December 2013). "A bacterial toxin inhibits DNA replication elongation through a direct interaction with the β sliding clamp". Molecular Cell. 52 (5): 617–28. doi:10.1016/j.molcel.2013.10.014. PMC 3918436 . PMID 24239291.
- ^ Wu K, Jahng D, Wood TK (1994). "Temperature and growth rate effects on the hok/sok killer locus for enhanced plasmid stability". Biotechnology Progress. 10 (6): 621–9. doi:10.1021/bp00030a600. PMID 7765697.
- ^ Pecota DC, Kim CS, Wu K, Gerdes K, Wood TK (May 1997). "Combining the hok/sok, parDE, and pnd postsegregational killer loci to enhance plasmid stability". Applied and Environmental Microbiology. 63 (5): 1917–24. PMC 168483 . PMID 9143123.
- ^ a b Gerdes K, Christensen SK, Løbner-Olesen A (May 2005). "Prokaryotic toxin-antitoxin stress response loci". Nature Reviews. Microbiology. 3 (5): 371–82. doi:10.1038/nrmicro1147. PMID 15864262.
- ^ a b Bernard P, Gabant P, Bahassi EM, Couturier M (October 1994). "Positive-selection vectors using the F plasmid ccdB killer gene". Gene. 148 (1): 71–4. doi:10.1016/0378-1119(94)90235-6. PMID 7926841.
- ^ Torres B, Jaenecke S, Timmis KN, García JL, Díaz E (December 2003). "A dual lethal system to enhance containment of recombinant micro-organisms". Microbiology. 149 (Pt 12): 3595–601. doi:10.1099/mic.0.26618-0. PMID 14663091.
Further reading
- Wen J, Won D, Fozo EM (February 2014). "The ZorO-OrzO type I toxin-antitoxin locus: repression by the OrzO antitoxin". Nucleic Acids Research. 42 (3): 1930–46. doi:10.1093/nar/gkt1018. PMC 3919570 . PMID 24203704.
External links
- RASTA – Rapid Automated Scan for Toxins and Antitoxins in Bacteria
This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Antitoxin component of bacterial toxin-antitoxin system, MqsA Provide feedback
MqsA_antitoxin is a family of prokaryotic proteins that act as antidotes to the mRNA interferase MqsR. It has a zinc-binding at the very N-terminus indicating its DNA-binding capacity. MqsR is the gene most highly upregulated in E. Colo MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells [2] and it plays an essential role in biofilm regulation [3] and cell signalling [4]. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2 complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterised bacterial toxins [1].
Literature references
Brown BL, Grigoriu S, Kim Y, Arruda JM, Davenport A, Wood TK, Peti W, Page R;, PLoS Pathog. 2009;5:e1000706.: Three dimensional structure of the MqsR:MqsA complex: a novel TA pair comprised of a toxin homologous to RelE and an antitoxin with unique properties. PUBMED:20041169 EPMC:20041169
Shah D, Zhang Z, Khodursky A, Kaldalu N, Kurg K, Lewis K;, BMC Microbiol. 2006;6:53.: Persisters: a distinct physiological state of E. coli. PUBMED:16768798 EPMC:16768798
Gonzalez Barrios AF, Zuo R, Hashimoto Y, Yang L, Bentley WE, Wood TK;, J Bacteriol. 2006;188:305-316.: Autoinducer 2 controls biofilm formation in Escherichia coli through a novel motility quorum-sensing regulator (MqsR, B3022). PUBMED:16352847 EPMC:16352847
Ren D, Bedzyk LA, Thomas SM, Ye RW, Wood TK;, Appl Microbiol Biotechnol. 2004;64:515-524.: Gene expression in Escherichia coli biofilms. PUBMED:14727089 EPMC:14727089
Internal database links
|BetR HTH_11 HTH_19 HTH_23 HTH_24 HTH_25 HTH_26 HTH_28 HTH_3 HTH_31 HTH_37 HTH_Crp_2 Phage_CI_repr Sigma70_r4 YdaS_antitoxin YokU
|Similarity to PfamA using HHSearch:
This tab holds annotation information from the InterPro database.
InterPro entry IPR032758
This is a family of prokaryotic proteins that are the antitoxin components of the toxin-antitoxin (TA) modules. Proteins in this entry include MqsA from Escherichia coli and HigA-2 from Vibrio cholerae serotype O1. MqsA acts as antidote to the mRNA interferase MqsR [PUBMED:24212724], while HigA-2 counteracts the effect of the HigB-2 toxin [PUBMED:17020579].
MqsA has a zinc-binding at the very N terminus indicating its DNA-binding capacity. MqsR is a family of bacterial toxins that act as an mRNA interferase. The mqsR gene is the gene most highly upregulated in E. coli persister cells [PUBMED:16768798] and the MgsR protein plays an essential role in biofilm regulation [PUBMED:16352847] and cell signalling [PUBMED:14727089]. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterised bacterial toxins [PUBMED:20041169].
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- a link to the page in the Pfam site showing information about the sequence that the graphic describes
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
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Pfam Clan
This family is a member of clan HTH (CL0123), which has the following description:
This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif.
The clan contains the following 340 members:AbiEi_3_N AbiEi_4 ANAPC2 AphA_like Arg_repressor ARID ArsR B-block_TFIIIC B5 Bac_DnaA_C Baculo_PEP_N BetR BHD_3 BLACT_WH Bot1p BrkDBD BsuBI_PstI_RE_N C_LFY_FLO CaiF_GrlA CarD_CdnL_TRCF CDC27 Cdc6_C Cdh1_DBD_1 CDT1 CDT1_C CENP-B_N Costars CPSase_L_D3 Cro Crp CSN4_RPN5_eIF3a CSN8_PSD8_EIF3K CtsR Cullin_Nedd8 CUT CUTL CvfB_WH DBD_HTH DDRGK DEP Dimerisation Dimerisation2 DNA_meth_N DpnI_C DprA_WH DsrC DsrD DUF1016_N DUF1133 DUF1153 DUF1323 DUF134 DUF1441 DUF1492 DUF1495 DUF1670 DUF1804 DUF1819 DUF1836 DUF1870 DUF2089 DUF2250 DUF2316 DUF2513 DUF2582 DUF3116 DUF3253 DUF3853 DUF3860 DUF3908 DUF433 DUF4364 DUF4423 DUF4447 DUF480 DUF4817 DUF5635 DUF573 DUF722 DUF739 DUF742 DUF977 E2F_TDP EAP30 eIF-5_eIF-2B ELL ESCRT-II Ets EutK_C Exc F-112 FaeA Fe_dep_repr_C Fe_dep_repress FeoC FokI_C FokI_N Forkhead FtsK_gamma FUR GcrA GerE GntR GP3_package HARE-HTH HemN_C HNF-1_N Homeobox_KN Homeodomain Homez HPD HrcA_DNA-bdg HSF_DNA-bind HTH_1 HTH_10 HTH_11 HTH_12 HTH_13 HTH_15 HTH_16 HTH_17 HTH_18 HTH_19 HTH_20 HTH_21 HTH_22 HTH_23 HTH_24 HTH_25 HTH_26 HTH_27 HTH_28 HTH_29 HTH_3 HTH_30 HTH_31 HTH_32 HTH_33 HTH_34 HTH_35 HTH_36 HTH_37 HTH_38 HTH_39 HTH_40 HTH_41 HTH_42 HTH_43 HTH_45 HTH_46 HTH_47 HTH_48 HTH_49 HTH_5 HTH_50 HTH_51 HTH_52 HTH_53 HTH_54 HTH_55 HTH_56 HTH_57 HTH_6 HTH_7 HTH_8 HTH_9 HTH_ABP1_N HTH_AraC HTH_AsnC-type HTH_CodY HTH_Crp_2 HTH_DeoR HTH_IclR HTH_Mga HTH_micro HTH_OrfB_IS605 HTH_ParB HTH_psq HTH_Tnp_1 HTH_Tnp_1_2 HTH_Tnp_4 HTH_Tnp_IS1 HTH_Tnp_IS630 HTH_Tnp_ISL3 HTH_Tnp_Mu_1 HTH_Tnp_Mu_2 HTH_Tnp_Tc3_1 HTH_Tnp_Tc3_2 HTH_Tnp_Tc5 HTH_WhiA HxlR IBD IF2_N IRF KicB KilA-N Kin17_mid KORA KorB La LacI LexA_DNA_bind Linker_histone LZ_Tnp_IS481 MADF_DNA_bdg MAGE MarR MarR_2 MerR MerR-DNA-bind MerR_1 MerR_2 Mga Mnd1 MogR_DNAbind Mor MotA_activ MqsA_antitoxin MRP-L20 MukE Myb_DNA-bind_2 Myb_DNA-bind_3 Myb_DNA-bind_4 Myb_DNA-bind_5 Myb_DNA-bind_6 Myb_DNA-bind_7 Myb_DNA-binding Neugrin NFRKB_winged NOD2_WH NUMOD1 ORC_WH_C OST-HTH P22_Cro PaaX PadR PapB PAX PCI Penicillinase_R Phage_AlpA Phage_antitermQ Phage_CI_repr Phage_CII Phage_NinH Phage_Nu1 Phage_rep_O Phage_rep_org_N Phage_terminase PheRS_DBD1 PheRS_DBD2 PheRS_DBD3 Pou Pox_D5 PqqD PRC2_HTH_1 PUFD PuR_N Put_DNA-bind_N Raf1_HTH Rap1-DNA-bind Rep_3 RepA_C RepA_N RepC RepL Replic_Relax RFX_DNA_binding Ribosomal_S18 Ribosomal_S19e Ribosomal_S25 Rio2_N RNA_pol_Rpc34 RNA_pol_Rpc82 RNase_H2-Ydr279 ROQ_II RP-C RPA RPA_C RQC Rrf2 RTP RuvB_C S10_plectin SAC3_GANP SANT_DAMP1_like SatD SelB-wing_1 SelB-wing_2 SelB-wing_3 SgrR_N Sigma54_CBD Sigma54_DBD Sigma70_ECF Sigma70_ner Sigma70_r2 Sigma70_r3 Sigma70_r4 Sigma70_r4_2 Ski_Sno SLIDE Slx4 SMC_Nse1 SMC_ScpB SoPB_HTH SpoIIID SRP19 SRP_SPB STN1_2 Sulfolobus_pRN Sun2_CC2 Suv3_N Swi6_N SWIRM Tau95 TBPIP TEA Terminase_5 TetR_N TFA2_Winged_2 TFIIE_alpha TFIIE_beta TFIIF_alpha TFIIF_beta Tn7_Tnp_TnsA_C Tn916-Xis TraI_2_C Trans_reg_C TrfA TrmB tRNA_bind_2 tRNA_bind_3 Trp_repressor UPF0122 UPF0175 Vir_act_alpha_C YdaS_antitoxin YjcQ YokU z-alpha
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
Alignment types
We make a range of alignments for each Pfam-A family:
- seed
- the curated alignment from which the HMM for the family is built
- full
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- UniProt
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- meta
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- jalview
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- PP/Heatmap
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
- Selex
- Stockholm
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
View options
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
|Representative proteomes
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
Download options
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
|Representative proteomes
|Raw Stockholm
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Seed source:
|Previous IDs:
|Sequence Ontology:
|Coggill P
|Number in seed:
|Number in full:
|Average length of the domain:
|112.90 aa
|Average identity of full alignment:
|23 %
|Average coverage of the sequence by the domain:
|70.10 %
HMM information
|HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Model details:
|Model length:
|Family (HMM) version:
|download the raw HMM for this family
Species distribution
Sunburst controlsHide
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Colour assignments
|Other sequences
|Unclassified sequence
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
- superkingdom
- kingdom
- phylum
- class
- order
- family
- genus
- species
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
Tree controlsHide
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Selected sequences
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- graphically
- as an alignment
- sequence accessions
- sequences in FASTA format
The tree shows the occurrence of this domain across different species. More...
Species trees
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
Interactive tree
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the MqsA_antitoxin domain has been found. There are 19 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
Loading structure mapping...


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text:
Listening/looking/reading and Patience
edited April 2012 in Non-Animal Collective Discussion
As a result of thinking about Danse Manatee a bit earlier, I thought about the problem of patience and works of art and returning to the source. Now, maybe, maybe, one can take a look at a painting or sculpture and say "I don't like it." It's possible to do this with a film, too, I suppose (depending on the film) (uh, "depending on the street!" inappropriate pointless reference there that's only funny to me most likely). However, I wonder if the same should be said about music? Would I have given Danse a second chance if I didn't know who was behind it, if I didn't anticipate its eventual blossoming? I wonder. Yet I knew, or thought I knew, and so returned to it again and again, and it became something more each time. This makes me question all of my quick judgments on anything: how can I read a poem ONCE and declare it good or bad? For instance, I question my reading of, say, a longish literary work after a single reading and my judgement or enjoyment (or lack) thereof. Are things supposed to be enjoyed only once? Imagine listening to Person Pitch one time! Revolver one time! Hell, I don't know: Merriweather one time, The Lonesome Crowded West only once (I'm being revealing by my examples here I guess) any musical composition one time and one time only! And then never again! Nabokov said "All reading is rereading" but damn it there's no time! So I wonder: are literary works (or films or enter-your-choice-of-art-here) to be returned to again again--like albums? Damn it--this goes back to the "there's a shitload of great things out there ready to be discovered but only a finite lifetime to enjoy them" argument, which to me is a horrible prospect. So, I don't want to stick with things that will remain dross when precious things are out there awaiting my discovery. The main questions here, I suppose, are when should we have patience with works of art? When shouldn't we? When do you? When don't you?
For me, I enjoy some songs or albums as soon as I hear them. Some examples of this are summertime clothes, fireworks, brother sport, etc. I didn't need any patience to love these songs. Other songs seem to grow on me with repeated listens. I never like Alvin row or chocolate girl because I never got to the end parts where the songs change, but when I did make it to the end I really enjoyed them and appreciated the slow build up to the last part of the song.
I remember watching the first episode of the Wire and not enjoying it at all, and as of right now it is one of my favorite shows of all time. The problem with these things is that usually slow things or things intended for groups of people can be easily over looked. I know a lot of the things I like, even things like mustard, took time or some sort of epiphany to really appreciate. Usually it was a change in circumstances that would allow me to like something more than I usually would. Sometimes you like things because it is a phase but I can FEEL when I REALLY like something. I really like MLPFiM and I love Animal Collective. Deal with it.
sort of off topic, but i cant think of more than one song on DM that requires patience living toys is the only song that drones onnnn and onnn for me
Ahh Good Country comes to mind...
i dont get bored with songs that build i guess. thats why i love dan deacon haha
Most of the albums that I love are the ones that I didn't get into until 4-5 listens. Is there anyone else in the forum that likes mindless repetition? I feel like a lot of people get annoyed by it, like Visiting Friends on Sung Tongs. I mean, it's certainly not my favourite on the album, but I get a certain joy out of it.
Mindless repetition is wonderful
mindless repetition is good if it fits in with the rest of the album that it's in. Visiting Friends is a perfect example of when reptition is awesome
I think it's great because you can get lost in the song. All the little changes seem so much larger if the song contains a large amount of repetition. It's like a landscape in your head
music that utterly changes every 5 seconds or so! THE FUTURE!
I want an Animal Collective soundboard that switches samples that they use every 5 seconds.
G.O., that's the "music" inside your head. Back in the day of raves...she said, leaning on her cane...repetition was orgasmic. The release from repetition! heh heh heh
Yeah, now, in retrospect, I don't think it (DM) requires as much patience as I implied. I think it took me a while because of the way its recorded and I first started listening to it while driving or walking around with headphones that don't block out other noise, so I didn't hear it like I hear it now. I guess I don't hear it now like I'll hear it later, either.
The actually quality of the recording was what had been a problem for me on all of their early records (pre Sung Tongs) but eventually one can overcome that by focusing on the music, and a pair of good headphones help.
Yep--Campfire Songs comes to mind especially. Yeah--headphones'll help I bet. I have an ipod and it just doesn't do the trick like I wish it would, and the other day I went to test out some headphones with it and they didn't seem to help much. There are a hell of a lot of headphones that I haven't been able to test out, so I don't know if they'll help or not. I suspect the fact that I'm trying to get a good sound out of an ipod might be the problem. Tell me any suggestions--headphones that won't put me on the streets begging for money that might actually sound good? With an ipod? What about headphone amps? I've been wondering about those, too.
I have no idea. Sorry. Also I have a decent stereo system in which to plug in my headphones so that helps. I use my dads old ones from the 80's and they are still better than ANY headphones i've ever tried.
ooh, Deadfly had a great headphone thread. Searching on here sucks aukbutt, BUT try keywords deadfly and headphones.
i felt so bored with campfire songs for about the first 5 listens. just wait. it'll come to you. i decided to play it after not listening to it for a while and i just fell in love, it was like a completely different album. you just have to go out of your way to find the melodies. doggy is one of their, if not, best melody they've written imo
My advice is good ol' Seinnheiser headphones. In my opinion they're the best quality for the lower price range. JUST NOT DR. DRE BEATS. For the love of god, those earphones suck.
Ok Wini. Hey Ticonderoga--I like Campfire Songs quite a bit. I was referring to the quality of the recording when I mentioned it. And I like your advice about putting something down for a bit and returning to it. That often breathes new life into it. Senor Claude! Seinnheiser. Yeah, I thought as much, but they're one of ones I went into the store and tested. I even tested them with Animal Collective! I listened to "Derek," well, part of the song, with my apple buds and then tried the same part with the Seinnheiser and I didn't hear too much of a difference. I went into the store thinking I was going to buy them, too, but after what I heard, I left without them.
Really? Which did you try? I have the HD419 which cost me 90 bucks, the difference between these and apple earbuds is margarine and butter. MARGARINE AND BUTTER. ... Sorry I'm a bit passionate about headphones. I mean, really, if you want good sound, you have to pay for it, but Seinnheiser is the closest I've come to a non-bank busting headphone for the buddng audiophile.
can't STAND audiophiles! to me they are somewhere only slightly above those OTHER type of 'philes! uh! miles of smiles and? BROTHER NILES!
my friend has these. listening to down there with them was an experience http://www.google.com/products/catalog?hl=en&sugexp=cdvst&qe=c3RyZXRjaCBoZWFkcA&qesig=Eh3HGVoiFIBCywCx9BFuDQ&pkc=AFgZ2tn0jmdot-Otq7o-Hit-RULpfw_eYax8k0jrZ3QPp9ggoY6Zc5TrVc5wfQmVKoINeDNjNEq9ij3Xf4K3PJr99ryJ4F0wkQ&pq=panasonic+stretch&cp=13&gs_id=1i&xhr=t&q=stretch+headphones&safe=off&client=safari&rls=en&bav=on.2,or.r_gc.r_pw.r_qf.,cf.osb&biw=1239&bih=816&um=1&ie=UTF-8&tbm=shop&cid=8108926874808574453&sa=X&ei=_NOZT8rzOMXc6QH499CBBw&sqi=2&ved=0CJABEPMCMAE#ps-sellers
I love repetition. not all the time, but I do enjoy it. I have more than enough patience to listen to 40 minute tracks, but none for anything else like driving or waiting or anything of that kind.
Are we all audiophiles, Mr. Ghosty? Lovers of audio? I usually have to be doing something else while listening to really long tracks.
I loved listening to Pink Floyd's Echos while just sitting in the dark, but now I get freaked out by the middle of that song. I still glisten to "Impossible Soul".
we must all one day glisten! i still want to one day at some random bar play just long songs on the jukebox... imagine Alvin Row (yes they have it!), The Doors - The End, IN THE GARDEN OF EDEN (by Iron Bugger Fly!), ECHOES, etc... all in a row! you could dominate the music for like 2 hours with just a few songs! it'd be so mean!
@PeaceFish, meddle is an amazing album! echoes is a crazy, track that doesnt really require patience for me
I was at a restaurant in Boulder and I played Echoes on a jukebox. Funny. People seemed annoyed that the song lasted so long.
I loved Echoes on my first listen but really only the begining and the end of the song. Now I like the whole thang, even the ambient Floyd in the middle.
Impossible Soul is like 6 songs in one anyway, but one of my favourite ridiculously long songs! Almost every song on Joanna Newsom's Ys is really long, about 9 minutes to 12 and I love them all. I played Desire Lines in the car with my family and my mum got annoyed.
My dad is surprisenly open to a a lot of the music I play. He liked Fireworks and Peacebone along with the album Tomboy. He even liked some of MPP and Feels. It's weird when your dad likes your music more than your friends.
My dad really likes He Would Have Laughed at the end of Halcyon Digest which is cool. He also likes Turn on the Bright Lights by Interpol.
I don't play AnCo in the car cause I don't think my parents would like it, at least not my mum. She hates anything that's noisey.
Same here Clawed! She actually liked some of the ambient chill stuff from early AnCo. Like I would be cleaning with her with it on and she would comment on how soothing it was. My dad liked the more rock side of AC.
what ambient early anco do you speak of?
Probably Campflames
Visiting Friends, De soto De son, etc.
ahhh for some reason i dont think of sung tongs as early anco. even if it released like only 3 years after STGSTV. whatevs
mid period AC! aaron THE CART HER