text:
Stopping the Settlements: Can a Veto Mean Victory?
Sometimes a Security Council vote can mean a victory for human rights no matter which side wins. The recent vote on a resolution mildly condemning Israeli settlement activity is one example. If the U.S. had voted for the resolution, or even abstained and allowed others to pass it, it would have strengthened the international opposition to the Israeli occupation, and perhaps helped set the stage for greater UN and international engagement in ending the Israeli occupation and challenging Israel's apartheid policies and other violations of human rights. It would have been a great victory.
But instead, the U.S. vetoed the resolution—the vote was 14 to 1, with no abstentions. On this issue once again, the U.S. stood absolutely isolated. And ironically, that was a victory too, because of the unity of other countries. Britain, Russia, Brazil and others spoke after the vote, expressing stronger than usual support for the anti-settlement resolution, and referencing (Britain most strongly) their recognition of a Palestinian state that may be declared in September.
That recognition by itself is unlikely to achieve an end to the Israeli occupation; the PLO's 1988 declaration of an independent state quickly won close recognition from close to 100 governments and the occupation intensified. But the recent moves toward greater recognition—especially from a number of Latin American countries who had not previously recognized Palestine—may foreshadow greater UN involvement in holding Israel accountable for its violations.
The U.S. had been threatening the veto for weeks. But in the last few days there had been rumors of a possible shift. A bribe was offered: if the Palestinians would withdraw the resolution, the U.S. would accept a "presidential statement" from the Council, a diplomatic step-down from the power and enforceability of a resolution. The Palestinian diplomats, backed by global support for the resolution and facing massive popular discontent at home because of concessions offered to Israel during peace negotiations, stood firm. Then there was another rumor, that maybe the U.S. would abstain, allowing the resolution to pass.
In the end, the Obama administration's early threats proved accurate. The U.S. stood alone. Ambassador Susan Rice's statement was astonishingly defensive—she went to great lengths to claim that the U.S. actually agrees with
the resolution, that no one has done more than the U.S. to support a
two-state solution, that the U.S. thinks settlement activity (not, we
should note, the continuing existence of longstanding settlements now
home to 500,000 Jewish settlers in the West Bank and occupied
East Jerusalem, only new settlement activity) violates Israel's
international commitments and more. She tried to convince the world
that "opposition to the resolution should not be misunderstood" to mean
that the U.S. supports settlement activity—only that the Obama
administration "thinks it unwise" for the United Nations to try to stop
that settlement activity. She defined settlements as one of the "core
issues that divide Israelis and Palestinians," not as a violation of
international law and a host of specific UN resolutions—therefore,
she claimed, the issue was just one of the UN being the wrong venue for this debate.
Waging Peace from Afar: Divestment and Israeli Occupation
A growing grassroots movement
is using the techniques of the anti-apartheid movement to challenge U.S. support for Israel's occupation of Palestinian territories.
We're really against settlements, she pleaded, we just want to end them our way. On our terms. In our peace talks. And we all know how well that's gone so far.
In fact, the U.S. veto in the Security Council was consistent with a long and sordid history. As of 2009, fully half of the vetoes ever cast were to protect Israel from being held accountable in the UN for violations of international law and human rights. Another third were to protect racist regimes in southern Africa—South Africa and pre-independence South-West Africa—from the same accountability. Taken together, fully five out of six, or more than 80 percent, of U.S. vetoes have been cast to protect Washington's allies accused of apartheid practices.
The Middle East is in the throes of a new wave of democratic revolutionary motion, and it is high time Palestinians were able to be part of that wave. While the U.S.'s use of the veto remains part of a sordid history, this time the veto may be different. It may actually help set the stage for much greater international engagement in the United Nations that, if combined with the mobilization for boycotts, divestment, and sanctions as well as growing opposition to U.S. military aid, could move once and for all to end the Israeli occupation and apartheid.
Here's how both sides could gain by building on their common interest for peace and fairness.
14 women find their voice in this collection of essays.


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For automated purification of total RNA from cells and tissues on the QIAcube
The RNeasy Mini QIAcube Kit is a highly convenient format of the RNeasy Mini Kit, dedicated for use on the QIAcube. The RNeasy Mini QIAcube Kit enables purification of consistent yields of high-quality RNA from cells and tissues.
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subset: commoncrawl


text:
Digital Youth with Disabilities: An Interview with Meryl Alper (Part Two)/
You hint here that our perceptions of what kinds of media are appropriate for youth with disabilities tends to prioritize educational and assistive technologies over the use of new media for recreational and social purposes. What are some of the implications of these biases?
I get frustrated when talk of children with disabilities and technology drifts into a common trope in which disability is imagined as a problem that needs solving, and technology (in school and therapeutic settings) provides the solution. One implication is that it perpetuates the idea of children with disabilities as "poster children" (Longmore, 2013), defined primarily by their medical needs and deserving of charity. Often—as one of my dissertation committee members, Beth Haller, has written—technology or technologists (usually able-bodied) are emphasized in the popular press for the good they do for people with disabilities. There is far less emphasis on the ways in which individuals with disabilities appropriate and adapt technology, and are active consumers, creators, and circulators of media. For example, Bess Williamson has pointed out ways in which individuals with disabilities were pioneers of maker culture in the post-WWII era.
Another is that digital media researchers are missing opportunities to study and learn from youth with disabilities. For example, there is exciting work being done by a fellow Ph.D. student, Kate Ringland at UC Irvine, on parent and youth participation in a Minecraft server called Autcraft, which is a dedicated space for individuals on the autism spectrum. There is a lot to be learned in Autcraft not just about autism, but also with respect to the methods of digital ethnography and the study of social norms and reciprocity.
Lastly, it is also important to understand the ways in which youth with disabilities figure into what we already know about how kids are "hanging out, messing around, and geeking out" (or the ways in which they are being excluded) so that they too are able to reap the benefits of a more participatory culture. Most high-tech educational and assistive devices are beyond the financial means of many families without additional financial support from school districts or health insurance. Parents express feeling like the professionals that work with their children lack an understanding of their family media habits (Nally, Houlton, & Ralph, 2000). Without understanding the media ecologies of youth with disabilities more fully, and their use of everyday tools like YouTube or Snapchat, the well-intentioned introduction of these technologies across the settings where children learn may not be as effective.
You spend a large chunk of the book dissecting and critiquing the concept of "screen time." Why has this been such a problematic way to formulate policies shaping media use within family life? Why is this concept especially inappropriate for thinking about media consumption/participation by youth with disabilities?
For those unfamiliar, over past 15 years, the phrase "screen time" has come to signify how much time children spend with the growing array of screen-based media and technology. It entered the popular vernacular in 2001, as part of a policy statement issued by American Academy of Pediatrics (AAP), the leading professional group for pediatricians in the U.S. While child development experts (especially psychologists) have weighed in on children's media use since days of radio, in the 1970s, pediatricians and the AAP began a more concerted effort to make public statements on children and media. In its current incarnation, the AAP's policy statement on children and media specifically targets "entertainment screen media" (which is still a pretty sweeping category).
The AAP statements make the relationship between media and children seem far more clear and simple than the research actually indicates. In the book chapter, I detail a few ways in which screen time is generally a flawed concept: its oversimplification of the notion of family "time"; its negative characterization of "entertainment screen media" content as something to be avoided; its unproved hypothesis that screen time directly displaces other activities children might otherwise be doing (like homework or playing outside); and its lumping together of all screen-based communication technologies even though they have very different capabilities. I also discuss each of these critiques in relation to children with disabilities.
There also seemed to be an aspect of screen time that was potentially harmful to children with disabilities and their families. I detail in the chapter how screen time presumes a child whose diet and exercise, sleep, and attention would be "normal" were it not for screen media. This standard is implicitly projected as the ideal media-using child and essentially "others" children with disabilities. Thus, screen time is inherently "ableist," a worldview in which disability is understood as aberrant—something for statisticians to "control for" in their data—and not a natural human difference.
I have an example from my dissertation fieldwork of how screen time can perpetuate ableism in everyday life. I conducted an interview with a mom, Perri, whose preschool-age son, Cory (both pseudonyms), has a developmental disability that impairs his ability to produce embodied oral speech. Cory primarily "talks" using an iPad with an app called Proloquo2Go. The system provides him with text-to-speech features and tools for selecting words, symbols, and images to communicate his thoughts. Perri told me that she was "of course" worried about the negative impact of "screen time," but "as a special needs parent, you have to block out the rest of the world." Perri felt guilty for sometimes falling on the wrong side of screen time guidelines; for example, the only thing that helped Cory sit still during difficult 45-minute daily medical treatments was watching a DVD.
She detailed a social situation that required her to shut out dominant cultural messages about screen time. When her and Cory go to the playground, she said, she feels that other parents are judging her. They must be thinking, Perri told me, "'Look at that parent, giving that child an iPad.'" She assumed that other parents associated letting a child use an iPad on a playground as a poor parenting move. To be fair, from the vantage point of the other parents, they might not know what else Cory could possibly be using the iPad for besides recreation. He does not visibly appear to have a disability from the opposite end of the playground—he is not in a wheelchair, he can walk, and he has a lot of energy. However, the situation for Perri and Cory would be much improved by greater societal awareness about how screen media serves different purposes in the lives of diverse families. Perri should not have to "block out the rest of the world"—those on the opposite ends of the playground should be less quick to judge her and her son. A serious dialogue about screen time and disability is but one starting point to create a more enabling and supportive environment for Perri and her son.
Meryl Alper is a Ph.D. Candidate in Communication at the Annenberg School for Communication and Journalism at the University of Southern California. She studies the social and cultural implications of networked communication technologies, with a particular focus on disability and digital media, children and families' technology use, and mobile communication. Prior to USC, she worked in the children's media industry as a researcher and strategist with Sesame Workshop, Nickelodeon, and Disney. She can be found on Twitter @merylalper and online at merylalper.com


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When I was growing up, one of my dad's favorite sayings was "Don't let anybody ever tell you you're a dumb Mexican."
Our mom definitely taught us that there are times when we must stand up for our convictions and not back down.
Loretta Sanchez became my hero when she defeated the disgusting right wing extremist Bob Dornan in an upset victory in Orange County, California. Several years later, her sister Linda Sanchez was elected to a nearby district and they became the first ever sisters to serve in Congress.
As the children of Mexican immigrants, their story is obviously one of overcoming great odds and prejudice. But they have overcome those odds with grace, intelligence and great skill.
In 2008 Loretta and Linda (along with Richard Buskin) published their story, a book called Dream in Color.
I love the title as much as I love the Sanchez sisters. And I always meant to buy the book. But I tend to read either ancient history or pure escapist science fiction or fantasy. The stupid turn to the discredited and failed right wing Republican agenda in the 2010 midterm election was what made me finally buy the book, because I knew it would be an inspiring story, and I needed an inspiring story. And I was not wrong in my expectation.
Many people work hard to conceal their background, conforming or projecting themselves in ways that are deemed socially acceptable, politically correct, physically desirable, or otherwise in vogue. And women and minorities are often more prone to this, partly because they're taught to aspire to some mythical ideal. Not us.
Growing up in a traditional Mexican family, we learned about the rich cultural values of our heritage, and as Latinas in Congress we draw daily strength from the lessons that our parents instilled in us. One of the strongest examples of such a lesson is the way Mom stood her ground when told by one of our grade school teachers that we should speak only English at home. She knew that being bilingual was an asset, and we have both repeatedly reaped the benefits of her foresight...
In most of the world being bi-, tri- or multi-lingual is not just an asset, it is a requirement. In Europe most people speak three or more languages. In Japan and India at least two. These are the countries America COMPETES with and our failure to recognize the need to speak multiple languages is one of several reasons (all fueled by right wing stupidity) that America is slowly, but surely, losing its competitive edge.
As for hiding one's ethnic identity, currently living in NYC where almost every ethic group has its own parade it amazes me that America would EVER want to abandon or deny its rich, amazing ethnic and immigrant past and present. America is an immigrant nation and has been from day one. And that has been one of our greatest strengths. Yet Republican America wants to DENY that strong, amazing, idealistic immigrant past. I am descended from German refugees from economic and political problems in the wake of the 1848 Revolutions. And I am descended from Jewish refugees from pogroms. I am interested in, shaped by and proud of those roots. Why would I expect Mexican-Americans to be any less interested in, shaped by or proud of THEIR roots?
Dream in Color is the story of these daughters of Mexican immigrants (that word, "immigrant" that is supposed to be so horrible, but in reality describes all of our ancestries unless you happen to be pure Native American) who rose from tough, though not poverty, circumstances to become Congresswomen. What most right wingers could never, NEVER admit, is that in many ways this book is the ultimate story of the American Dream. The American Dream was, is and always will be the story of the immigrant family that came to America with nothing but dreamed big, worked hard, and achieved great things. THAT is the American dream and the Honorable Sanchez sisters are a perfect example of that dream.
I grew up in California and always found it somewhat amusing and disturbing that people saw my state as so liberal. I lived in Los Angeles where the stereotype largely held, but neighboring Orange County was one of the most conservative districts in the nation and was represented by right wing crazies like Bob Dornan, who wound up so batshit crazy even Newt Gingrich hesitated to openly support him for awhile.
So when, in 1996, a young woman named Loretta Sanchez had the huevos to run against Bob Dornan, I eagerly donated to her campaign, though I had little hope she could pull it off. But that donation was one of my most enthusiastic donations.
Loretta's reason for running, which I didn't know until reading Dream in Color, was basically because when she was pushing hard for improved education in her district, her Congressman Bob Dornan blew her off.
I next tried to make an appointment to see my Congress member, Bob Dornan, but he refused to meet with me. If I had wanted to meet with him about a defense project, he would have been all over it, but as far as I could tell, education held no interest for him. So, at that point, I went home and said, "I'm going to run for Congress..."
The first person I called was mu mom. When I told her what I wanted to do, she said, "Okay, we can do that..."
The fight was hard and Bob Dornan, a truely miserable human being in my opinion, was as nasty as could be, demonstrating just what true Republican "values" are these days.
When I won the pirmary...no one even knew who I was...I'd appeared out of nowhere to beat the candidates and now I was the opponent to Bob Dornan. Well, when he found out who I was he described me as a dream candidate to run against. "She can't beat me," he told the Orange County newspaper, the OC Weekly. "Bob Dornan [I guess like Bob Dole Dornan refers to himself in the third person] is a father of five, grandfather of ten, military man, been married forty-one years. She has no kids, no military, no track record. I win."
Dismissing me resulted in his defeat. And when we had a rematch two years later, Dornan turned extremely nasty.
To my utter astonishment, moderate Democrat (former moderate Republican) Loretta Sanchez beat right wing extremist Bob Dornan. Bob Dornan, who would make today's Teabaggers (remember, THEY came up with that term!) like Carl Paladino seem reasonable, was ousted by an upstart Latina. Dornan spent the next year showing up to Congress anyway, claiming Loretta hadn't really won. He demanded a rematch two years later and was soundly defeated by the now incumbent Loretta Sanchez. I vaguely remember getting drunk in celebration of Loretta's second, absolutely definitive, win. I was immensely proud to have donated to Loretta's first two runs for Congress. The only reason I have not donated since is because she doesn't need my money and other great candidates do.
Within her first year in Congress, Loretta Sanchez proved her worth, despite being resented by many Republicans and despite being a freshman, in the passage of changes to the Uniform Code of Military Justice (that book that features so prominently in the movie "A Few Good Men) to address the problem of rape of women in military service. In many ways the Uniform Code of Military Justice had failed to keep up with changes in civilian law regarding rape and so wound up protecting rapists and victimizing rape victims. Loretta Sanchez saw this problem for women in the military and sought to change it. She was, of course, solidly opposed by the good-old-boys network of the military and initially by the good-old-boys network of Congress. But she refused to let what was clearly an important issue get pushed aside, and to give credit where credit is due, she was helped by a Republican, John McHugh. Now I never really liked McHugh, but in this case he did the right thing, even to the point, according to Loretta Sanchez, of standing up to fellow Republican Duncan Hunter who wanted to let Loretta's bill die. John McHugh decided Loretta's bill was worth supporting and he went the extra mile for it. Together Sanchez and McHugh, against the inertia of the military, revised the military law codes to better handle rape cases. This all happened, from start to finish, within Loretta's first two years in Congress while Bob Dornan was still showing up and claiming he still represented the district.
I think this experience shaped Loretta Sachez's entire approach towards Congress. Loretta Sanchez is a Blue Dog Dem, which usually means bad things in my book, but Loretta represents a relatively conservative district and, though a Blue Dog, votes well and stands up on fights few other Dems stand up on. So I have always liked her. And her unconventional image, drawn from her Hispanic, hard working, immigrant background, has always endeared her to me.
As a Blue Dog, Loretta tends to be one of those compromisers in Congress that many progressives hate. But in judging Loretta one has to take into account her district (which is conservative) and her experience with Republican John McHugh, where through patience and determination she was able to find common ground and compromise and so pass a much needed bill. She learned the lesson then and there that compromise was possible and could accomplish important things. I think she has stuck to that view, though she has also never been one of the more conservative members of the Blue Dogs. I feel she remains true to progressive ideals though she also maintains a cooperative stance with conservatives. If all Blue Dogs were like Loretta Sanchez, we'd be much better off both as a party and as a country.
Loretta also, like Arianna Huffington, left the Republican party because of the realization that the Republicans did NOT represent her true values...didn't even represent the values they claimed to represent. Loretta Sanchez grew up in a family where one parent was a Democrat and one a Republican, so the choice between the two seemed a reasonable one...at first:
Whereas Mom was a compassionate Democrat, Dad ended up running his own business and reading the libertarian Orange County Register, so he was very antitax and pro-Republican. Neither of them voted back then...they didn't become US citizens until [1996]. By then, like me, Dad had converted from Republican to Democrat...
I remained registered as a Republican and never really thought about it much. That was, until one night when I was flicking through the TV channels at home and just happened to catch Pat Buchanan making an inflammatory speech, calling for an end to immigrants coming to America. I was so angry that a high-profile Republican was allowed to spew that kind of hatred on national television, the very next day I registered as a Democrat.
When Loretta's younger sister, Linda, ran for Congress in 2003, I considered it a given I would donate. If she was HALF as kick ass as Loretta, it was worth supporting her. And she won, making Loretta and Linda Sanchez not only rare in Congress as Latinas (I personally know and like Nydia Velasquez, one of the other rare Latinas in Congress), but literally unique as being the first and so far ONLY sisters to serve in Congress.
Linda Sanchez, partly because she represents a solidly Democratic district and partly because of her own personality, is a more liberal Democrat than her sister. Linda, in fact, is a member of the Congressional Progressive Caucus while Loretta is a member of the Blue Dog Caucus. Loretta grew up with more to prove, as an older sibling, and I think it is reflected in her more conservative attitude, shaped by a greater need for financial security than social activism. They both make clear that the older siblings had a rougher time and were raised with a more traditional philosophy, but by the time Linda was growing up this was somewhat relaxed and Linda, from an early age, recognized that there were inequities in the world and that becoming a lawyer was a path towards solving those inequities. She was encouraged to become a lawyer by her older sister, but Loretta had imagined Linda using her law degree more practically, getting a higher paying job. Instead, Linda went into labor law and became a union organizer. And she was kick ass in pushing for labor reforms. When a new Congressional district was created in Southern California, Linda decided to run for it...and won. She started as the longshot, as a young Latina, but when she proved so effective that she rapidly became the frontrunner, she became the target for attacks by all the other campaigns in the primary. I get the feeling from her description in the book that this may have been one of the toughest things she had faced: a concerted attack from several other fellow Democrats.
And yet she won. I think this shows the strength of the Sanchez family, that they could turn not just one, but TWO long-shot runs for office into wins.
Like Loretta, Linda Sanchez also proved her worth within the first year, though in a more locally focused way.
One of the smaller cities I represent desperately needed funding to renovate and repave its major street, which was old and falling into disrepair. For ten years the city had been begging its former congressman to try to help get federal funds for the roadwork, but he never secured any real funding for the project. Well, when the time came, and [Congressman] Obey asked for projects, that was one of the projects I submitted. It made it into the omnibus bill, and the omnibus bill passed. That meant that after being in Congress for only six weeks I had gotten it the funding! And wheras before the city had been skeptical, I now had a victory to show them, and it was grateful.
And then, of course, Linda had to face the same obstacles that Loretta had to face as a rare Latina in Congress as well as a freshman. She relates how she frequently felt like asking people (I assume she never actually did!):
Excuse me, but did you just blow me off because I'm a woman, because I'm Hispanic, or because I'm young? Could you let me know?
Linda Sanchez has some of the best lines in the book, the lines that make me think, "YES! That is how I always wanted to say it!" For example:
Sometimes I've encountered Republicans who seem to believe that people are poor because they choose to be poor, and that this wouldn't be the case if they just worked harder. Well, that isn't true. A lot of people start with advantages that they don't even consider to be advantages and I always point this out when I get into fights...
I believe there are two kinds of people in this life. There are those who succeed and attribute all the success to themselves--"I've got mine, you guys have to get yours." And then there are those who succeed and not only credit the teachers who cared, the mentors who helped them, the bosses who took them under their wing, and the parents who pushed them to do well, but also the resolve to help the next group of people who are struggling. For the life of me, I don't understand those who fall into the former category, because the belief that they did it all on their own is just nonsense.
And right there a major FALSE Republican talking point falls by the wayside.
Dream in Color is interesting on several levels. It may not be high literature in style, but it is a very readable, straightforward description of what life is like for Latinas in America and what people can accomplish if they work REALLY hard and take calculated risks. It also provides very interesting perspectives on how Congress works...and doesn't always work. It also provides a much needed counterpoint to the hostile and nasty Republican anti-immigrant rhetoric we hear all too much, instilling a respect for hard working immigrants of ALL ethnicities.
Overall Dream in Color is a quick read, and, though perhaps not immensely profound, is very inspiring, particularly now when Democrats seem a tad demoralized.
Return to Mole's Book Page.
Return to I Had a Thought


text:
Summary: Septin
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Septin Edit Wikipedia article
|Cell division/GTP binding protein
|Pfam clan
Septins are a group of GTP-binding proteins found primarily in eukaryotic cells of fungi and animals, but also in some green algae.[1][2] Different septins form protein complexes with each other. These complexes can further assemble into filaments, rings and gauzes. Assembled as such, septins function in cells by localizing other proteins, either by providing a scaffold to which proteins can attach, or by preventing diffusion of molecules from one compartment of the cell to another.[1][2][3][4]
Septins have been implicated in the localization of cellular processes at the site of cell division, at the plasma membrane, at sites where specialized structures like cilia or flagella are attached to the cell body.[3] In yeast cells, they compartmentalize parts of the cell and build scaffolding to provide structural support during cell division at the septum, from which they derive their name.[2] Recent research in human cells suggests that septins build cages around bacterial pathogens, immobilizing the harmful microbes and preventing them from invading other cells.[5]
As filament forming proteins, septins can be considered part of the cytoskeleton.[3] Apart from forming non-polar filaments, septins associate with cell membranes, actin filaments and microtubules.[3] Although present in most eukaryotes, septins have not been observed in green plants,[4] but they have been reported in red algae.[6]
- 1 Structure
- 2 Occurrence
- 3 In Saccharomyces cerevisiae
- 4 In Filamentous fungi
- 5 In metazoa
- 6 In mitochondria
- 7 History
- 8 References
- 9 Further reading
Septins are P-Loop-NTPase proteins that range in weight from 30-65 kDa. Septins are highly conserved between different eukaryotic species. They are composed of a variable-length proline rich N-terminus with a basic phosphoinositide binding motif important for membrane association, a GTP-binding domain, a highly conserved Septin Unique Element domain, and a C-terminal extension including a coiled coil domain of varying length.[3]
Septins interact either via their respective GTP-binding domains, or via both their N- and C-termini. Different organisms express a different number of septins, and from those symmetric oligomeres are formed. For example, in humans Sept7-Sept6-Sept2-Sept2-Sept6-Sept7 form one complex, and in yeast Cdc11-Cdc12-Cdc3-Cdc10-Cdc10-Cdc3-Cdc12-Cdc11 form another one. These complexes then associate to form non-polar filaments, filament bundles, cages or ring structures in cells.[3]
Septins are found in fungi, animals, some green algae, and some red algae, but not in higher plants.
|Group (phylogenetic)
|Septin genes
|Saccharomyces cerevisiae
|Cdc11, Shs1, Spr28
|Cdc12, Spr3
|Schizosaccharomyces pombe
|Spn3, Spn5, Spn7
|Spn4, Spn6
|Candida albicans
|Cdc11, Sep7, Spr28
|Cdc12, Spr3
|Aspergillus nidulans
|Sept1, Spet2, Sept4, Sept5
|Sept3, Sept9, Sept12
|Sept6, Sept8, Sept10, Sept11, Sept14
|Sept7 (Sept13 as a pseudogene)[3]
|Caenorhabditis elegans
In Saccharomyces cerevisiae
There are seven different septins in Saccharomyces cerevisiae. Five of those are involved in mitosis, while two (Spr3 and Spr28) are specific to sporulation.[1][2] Mitotic septins (Cdc3, Cdc10, Cdc11, Cdc12, Shs1) form a ring structure at the bud neck during cell division.[1][3] They are involved in the selection of the bud-site, the positioning of the mitotic spindle, polarized growth, and cytokinesis. The sporulating septins (Spr3, Spr28) localize together with Cdc3 and Cdc11 to the edges of prospore membranes.[1]
The septin cortex undergoes several changes throughout the cell cycle: The first visible septin structure is a distinct ring which appears ~15 min before bud emergence. After bud emergence, the ring broadens to assume the shape of an hourglass around the mother-bud neck. During cytokinesis, the septin cortex splits into a double ring which eventually disappears. How can the septin cortex undergo such dramatic changes, although some of its functions may require it to be a stable structure? FRAP analysis has revealed that the turnover of septins at the neck undergoes multiple changes during the cell cycle. The predominant, functional conformation is characterized by a low turnover rate (frozen state), during which the septins are phosphorylated. Structural changes require a destabilization of the septin cortex (fluid state) induced by dephosphorylation prior to bud emergence, ring splitting and cell separation.[2]
The composition of the septin cortex does not only vary throughout the cell cycle but also along the mother-bud axis. This polarity of the septin network allows concentration of some proteins primarily to the mother side of the neck, some to the center and others to the bud site.
The septins act as a scaffold, recruiting many proteins. These protein complexes are involved in cytokinesis, chitin deposition, cell polarity, spore formation, in the morphogenesis checkpoint, spindle alignment checkpoint and bud site selection.
Budding yeast cytokinesis is driven through two septin dependent, redundant processes: recruitment and contraction of the actomyosin ring and formation of the septum by vesicle fusion with the plasma membrane. In contrast to septin mutants, disruption of one single pathway only leads to a delay in cytokinesis, not complete failure of cell division. Hence, the septins are predicted to act at the most upstream level of cytokinesis.
Cell polarity
After the isotropic-apical switch in budding yeast, cortical components, supposedly of the exocyst and polarisome, are delocalized from the apical pole to the entire plasma membrane of the bud, but not the mother cell. The septin ring at the neck serves as a cortical barrier that prevents membrane diffusion of these factors between the two compartments. This asymmetric distribution is abolished in septin mutants.
Some conditional septin mutants do not form buds at their normal axial location. Moreover, the typical localization of some bud-site-selection factors in a double ring at the neck is lost or disturbed in these mutants. This indicates that the septins may serve as anchoring site for such factors in axially budding cells.
In Filamentous fungi
Since their discovery in S. cerevisiae, septin homologues have been found in other eukaryotic species, including filamentous fungi. Septins in filamentous fungi display a variety of different shapes within single cells, where they control aspects of filamentous morphology.[7]
Candida albicans
The genome of C. albicans encodes homologues to all S. cerevisiae septins. Without Cdc3 and Cdc12 genes Candida albicans cannot proliferate, other septins affect morphology and chitin deposition, but are not essential. Candida albicans can display different morphologies of vegetative growth, which determines the appearance of septin structures. Newly forming hyphae form a septin ring at the base, Double rings form at sites of hyphal septation, and a septin cap forms at hyphal tips. Elongated septin-filaments encircle the spherical chlamydospores. Double rings of septins at the septation site also bear growth polarity, with the growing tip ring disassembling, while the basal ring remaining intact.[7]
Aspergillus nidulans
Five septins are found in A. nidulans (AnAspAp, AnAspBp, AnAspCp, AnAspDp, AnAspEp). AnAspBp forms single rings at septation sites that eventually split into double rings. Additionally, AnAspBp forms a ring at sites of branch emergence which broadens into a band as the branch grows. Like in C. albicans, double rings reflect polarity of the hypha. In the case of Aspergillus nidulans polarity is conveyed by disassembly of the more basal ring (the ring further away from the hyphal growth tip), leaving the apical ring intact, potentially as a growth guidance cue.[1][7]
Ashbya gossypii
The ascomycete A. gossypii possesses homologues to all S. cerevisiae septins, with one being duplicated (AgCDC3, AgCDC10, AgCDC11A, AgCDC11B, AgCDC12, AgSEP7). In vivo studies of AgSep7p-GFP have revealed that septins assemble into discontinuous hyphal rings close to growing tips and sites of branch formation,[1] and into asymmetric structures at the base of branching points. Rings are made of filaments which are long and diffuse close to growing tips and short and compact further away from the tip. During septum formation, the septin ring splits into two to form a double ring. Agcdc3Δ, Agcdc10Δ and Agcdc12Δ deletion mutants display aberrant morphology and are defective for actin-ring formation, chitin-ring formation, and sporulation. Due to the lack of septa, septin deletion mutants are highly sensitive, and damage of a single hypha can result in complete lysis of a young mycelium.
In metazoa
In contrast to septins in yeast, and in contrast to other cytoskeletal components of metazoa, septins do not form a continuous network in metazoan cells, but several dispersed ones in the cortical cytoplasm. These are integrated with actin bundles and microtubules. For example, the actin bundling protein anillin is required for correct spatial control of septin organization.[4] In the sperm cells of mammals, septins form a stable ring called annulus in the tail. In mice (and potentially in humans, too), defective annulus formation leads to male infertility.[3][4]
In humans, septins are involved in cytokinesis, cilium formation and neurogenesis through the capability to recruit other proteins or serve as a diffusion barrier. There are 13 different human genes coding for septins. The septin proteins produced by these genes are grouped into four subfamilies each named after its founding member: (i) SEPT2 (SEPT1, SEPT4, SEPT5), (ii) SEPT3 (SEPT9, SEPT12), (iii) SEPT6 (SEPT8, SEPT10, SEPT11, SEPT14), and (iv) SEPT7. Septin protein complexes are assembled to form either hetero-hexamers (incorporating monomers selected from three different groups and the monomer from each group is present in two copies; 3 x 2 = 6) or hetero-octamers (monomers from four different groups, each monomer present in two copies; 4 x 2 = 8). These hetero-oligomers in turn form higher-order structures such as filaments and rings.[3][4]
Septins form cage-like structures around bacterial pathogens, immobilizing harmful microbes and preventing them from invading healthy cells. This cellular defence system could potentially be exploited to create therapies for dysentery and other illnesses. For example, Shigella is a bacterium that causes lethal diarrhoea in humans. To propagate from cell to cell, Shigella bacteria develop actin-polymer 'tails', which propel the microbes and allow them to gain entry into neighbouring host cells. As part of the immune response, human cells produce a cell-signalling protein called TNF-α which trigger thick bundles of septin filaments to encircle the microbes within the infected host cell.[8] Microbes that become trapped in these septin cages are broken down by autophagy.[9] Disruptions in septins and mutations in the genes that code for them could be involved in causing leukaemia, colon cancer and neurodegenerative conditions such as Parkinson's disease and Alzheimer's disease. Potential therapies for these, as well as for bacterial conditions such as dysentery caused by Shigella, might bolster the body's immune system with drugs that mimic the behaviour of TNF-α and allow the septin cages to proliferate.[5]
Caenorhabditis elegans
In the nematode worm Caenorhabditis elegans there are two genes coding for septins, and septin complexes contain the two different septins in a tetrameric UNC59-UNC61-UNC61-UNC59 complex. Septins in C.elegans concentrate at the cleavage furrow and the spindle midbody during cell division. Septins are also involved in cell migration and axon guidance in C.elegans.[1]
In mitochondria
The septin localized in the mitochondria is called mitochondrial septin (M-septin). It was identified as a CRMP/CRAM-interacting protein in developing mouse brain.[10]
The septins were discovered in 1970 by Leland H. Hartwell and colleagues in a screen for temperature-sensitive mutants affecting cell division (cdc mutants) in yeast (Saccharomyces cerevisiae). The screen revealed four mutants which prevented cytokinesis at restrictive temperature. The corresponding genes represent the four original septins, ScCDC3, ScCDC10, ScCDC11, and ScCDC12.[2][3] Despite disrupted cytokinesis, the cells continued budding, DNA synthesis, and nuclear division, which resulted in large multinucleate cells with multiple, elongated buds. In 1976, analysis of electron micrographs revealed ~20 evenly spaced striations of 10-nm filaments around the mother-bud neck in wild-type but not in septin-mutant cells.[2][3][7] Immunofluorescence studies revealed that the septin proteins colocalize into a septin ring at the neck.[3][7] The localization of all four septins is disrupted in conditional Sccdc3 and Sccdc12 mutants, indicating interdependence of the septin proteins. Strong support for this finding was provided by biochemical studies: The four original septins co-purified on affinity columns, together with a fifth septin protein, encoded by ScSEP7 or ScSHS1. Purified septins from budding yeast, Drosophila, Xenopus, and mammalian cells are able to self associate in vitro to form filaments.[7] How the septins interact in vitro to form heteropentamers that assemble into filaments was studied in detail in S. cerevisiae.
Micrographs of purified filaments raised the possibility that the septins are organized in parallel to the mother-bud axis. The 10-nm striations seen on electron micrographs may be the result of lateral interaction between the filaments. Mutant strains lacking factors important for septin organization support this view. Instead of continuous rings, the septins form bars oriented along the mother-bud axis in deletion mutants of ScGIN4, ScNAP1 and ScCLA4.
- ^ a b c d e f g h i Weirich CS, Erzberger JP, Barral Y (2008). "The septin family of GTPases: architecture and dynamics". Nat. Rev. Mol. Cell Biol. 9 (6): 478–89. doi:10.1038/nrm2407. PMID 18478031.
- ^ a b c d e f g Douglas LM, Alvarez FJ, McCreary C, Konopka JB (2005). "Septin function in yeast model systems and pathogenic fungi". Eukaryotic Cell. 4 (9): 1503–12. doi:10.1128/EC.4.9.1503-1512.2005. PMC 1214204 . PMID 16151244.
- ^ a b c d e f g h i j k l m Mostowy S, Cossart P (2012). "Septins: the fourth component of the cytoskeleton". Nat. Rev. Mol. Cell Biol. 13 (3): 183–94. doi:10.1038/nrm3284. PMID 22314400.
- ^ a b c d e Kinoshita M (2006). "Diversity of septin scaffolds". Curr. Opin. Cell Biol. 18 (1): 54–60. doi:10.1016/j.ceb.2005.12.005. PMID 16356703.
- ^ a b Mascarelli A (December 2011). "Septin proteins take bacterial prisoners: A cellular defence against microbial pathogens holds therapeutic potential". Nature. doi:10.1038/nature.2011.9540.
- ^ Brawley, Blouin; et al. (2017). "Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta)". PNAS: E6361–E6370. PMID 28716924.
- ^ a b c d e f Gladfelter AS (2006). "Control of filamentous fungal cell shape by septins and formins". Nat. Rev. Microbiol. 4 (3): 223–9. doi:10.1038/nrmicro1345. PMID 16429163.
- ^ Mostowy S, Bonazzi M, Hamon MA, Tham TN, Mallet A, Lelek M, Gouin E, Demangel C, Brosch R, Zimmer C, Sartori A, Kinoshita M, Lecuit M, Cossart P (2010). "Entrapment of intracytosolic bacteria by septin cage-like structures". Cell Host Microbe. 8 (5): 433–44. doi:10.1016/j.chom.2010.10.009. PMID 21075354.
- ^ Mostowy S, Sancho-Shimizu V, Hamon MA, Simeone R, Brosch R, Johansen T, Cossart P (2011). "p62 and NDP52 proteins target intracytosolic Shigella and Listeria to different autophagy pathways". J. Biol. Chem. 286 (30): 26987–95. doi:10.1074/jbc.M111.223610. PMC 3143657 . PMID 21646350.
- ^ Takahashi S, Inatome R, Yamamura H, Yanagi S (February 2003). "Isolation and expression of a novel mitochondrial septin that interacts with CRMP/CRAM in the developing neurones". Genes Cells. 8 (2): 81–93. doi:10.1046/j.1365-2443.2003.00617.x. PMID 12581152.
Further reading
- Longtine MS, DeMarini DJ, Valencik ML, Al-Awar OS, Fares H, De Virgilio C, Pringle JR (February 1996). "The septins: roles in cytokinesis and other processes". Curr. Opin. Cell Biol. 8 (1): 106–19. doi:10.1016/S0955-0674(96)80054-8. PMID 8791410.
- Gladfelter AS, Pringle JR, Lew DJ (December 2001). "The septin cortex at the yeast mother-bud neck". Curr. Opin. Microbiol. 4 (6): 681–9. doi:10.1016/S1369-5274(01)00269-7. PMID 11731320.
- Faty M, Fink M, Barral Y (June 2002). "Septins: a ring to part mother and daughter". Curr. Genet. 41 (3): 123–31. doi:10.1007/s00294-002-0304-0. PMID 12111093.
- Versele M, Gullbrand B, Shulewitz MJ, Cid VJ, Bahmanyar S, Chen RE, Barth P, Alber T, Thorner J (October 2004). "Protein-protein interactions governing septin heteropentamer assembly and septin filament organization in Saccharomyces cerevisiae". Mol. Biol. Cell. 15 (10): 4568–83. doi:10.1091/mbc.E04-04-0330. PMC 519150 . PMID 15282341.
- Douglas LM, Alvarez FJ, McCreary C, Konopka JB (September 2005). "Septin function in yeast model systems and pathogenic fungi". Eukaryotic Cell. 4 (9): 1503–12. doi:10.1128/EC.4.9.1503-1512.2005. PMC 1214204 . PMID 16151244.
- Gladfelter AS (March 2006). "Control of filamentous fungal cell shape by septins and formins". Nat. Rev. Microbiol. 4 (3): 223–9. doi:10.1038/nrmicro1345. PMID 16429163.
- Hall PA; Russell SEH; Pringle JR (2008). The septins. Oxford: John Wiley-Blackwell. p. 370. ISBN 0-470-51969-X.
- Gonzalez-Novo A; Vázquez de Aldana CR; Jimenez J (2009). "Fungal septins: one ring to rule it all?". Cent. Eur. J. Biol. 4 (3): 274–289. doi:10.2478/s11535-009-0032-2.
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.
Septin Provide feedback
Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerise to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis [2].
Literature references
Casamayor A, Snyder M; , Mol Cell Biol 2003;23:2762-2777.: Molecular dissection of a yeast septin: distinct domains are required for septin interaction, localization, and function. PUBMED:12665577 EPMC:12665577
Kinoshita M; , Genome Biol 2003;4:236.: The septins. PUBMED:14611653 EPMC:14611653
Internal database links
|AAA_15 AAA_16 AAA_22 AAA_23 AAA_29 AAA_33 ABC_tran AIG1 Arf Dynamin_N FeoB_N FtsK_SpoIIIE GTP_EFTU Gtr1_RagA IIGP MMR_HSR1 NB-ARC PduV-EutP Ras Roc RsgA_GTPase SMC_N SRPRB T2SSE
|Similarity to PfamA using HHSearch:
|ABC_tran GTP_EFTU Dynamin_N MMR_HSR1 FeoB_N RsgA_GTPase AIG1 Gtr1_RagA Roc PduV-EutP MnmE_helical AAA_22 AAA_29 AAA_33
This tab holds annotation information from the InterPro database.
InterPro entry IPR030379
The P-loop guanosine triphosphatases (GTPases) control a multitude of biological processes, ranging from cell division, cell cycling, and signal transduction, to ribosome assembly and protein synthesis. GTPases exert their control by interchanging between an inactive GDP-bound state and an active GTP-bound state, thereby acting as molecular switches. The common denominator of GTPases is the highly conserved guanine nucleotide-binding (G) domain that is responsible for binding and hydrolysis of guanine nucleotides.
Septins are a family of eukaryotic cytoskeletal proteins conserved from yeasts to humans. The septin family belongs to the guanosine-triphosphate (GTP)ase superclass of P-loop nucleoside triphosphate (NTP)ases. Septins participate in diverse cellular functions including cytokinesis, vesicle trafficking, vesicle fusion, axonal guidance and migration, diffusion barrier, scaffolds, pathogenesis and others. Septin monomers form homo- and hetero-oligomeric complexes that assemble into filaments. Structurally all septins have a GTP-binding domain flanked by N- and C-terminal regions of variable length. The GTP-binding domain is the most highly conserved and is characterised by the presence of three of the five classical GTP-binding motifs. The G1 motif (or Walker A box, GxxxxGKS/T) forms the P-loop, which interacts directly with the nucleotide, whereas the G3 (DxxG) and G4 (xKxD) motifs are respectively essential for Mg(2+) binding and for conferring GTP binding specificity over other nucleotides. The basic structure of the septin-type G domain closely resembles the canonical G domain exemplified by Ras, with six beta-strands and five alpha-helices. A unique feature of the septin-type G domain is the presence of four additional elements compared to Ras. These are the helix alpha5' between alpha4 and beta6, the two antiparallel strands beta7 and beta8, and the alpha6 C-terminal helix that points away from the G domain at a 90deg angle relative to the axis of interaction between subunits [PUBMED:11916378, PUBMED:16009555, PUBMED:17637674, PUBMED:23163726, PUBMED:24367716].
This entry represents the septin-type G domain.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function
|GTP binding (GO:0005525)
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:
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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
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Pfam Clan
This family is a member of clan P-loop_NTPase (CL0023), which has the following description:
AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].
The clan contains the following 229 members:6PF2K AAA AAA-ATPase_like AAA_10 AAA_11 AAA_12 AAA_13 AAA_14 AAA_15 AAA_16 AAA_17 AAA_18 AAA_19 AAA_2 AAA_21 AAA_22 AAA_23 AAA_24 AAA_25 AAA_26 AAA_27 AAA_28 AAA_29 AAA_3 AAA_30 AAA_31 AAA_32 AAA_33 AAA_34 AAA_35 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DBINO DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DUF1611 DUF1726 DUF2075 DUF2326 DUF2478 DUF257 DUF2791 DUF2813 DUF3584 DUF463 DUF815 DUF853 DUF87 DUF927 Dynamin_N Dynein_heavy Elong_Iki1 ELP6 ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GTP_EFTU Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK HSA HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1C Lon_2 LpxK MCM MeaB MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB MutS_V Myosin_head NACHT NB-ARC NOG1 NTPase_1 NTPase_P4 ORC3_N ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Ploopntkinase1 Ploopntkinase2 Ploopntkinase3 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2_N Spore_IV_A SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf Terminase_1 Terminase_3 Terminase_6 Terminase_GpA Thymidylate_kin TIP49 TK TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE Zeta_toxin Zot
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:
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- alignment generated by searching the UniProtKB sequence database using the family HMM
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- alignment generated by searching the metagenomics sequence database using the family HMM
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You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
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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.
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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
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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...
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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.
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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:
|Pfam-B_440 (release 2.1)
|Previous IDs:
|Sequence Ontology:
|Bateman A
|Number in seed:
|Number in full:
|Average length of the domain:
|230.40 aa
|Average identity of full alignment:
|35 %
|Average coverage of the sequence by the domain:
|60.83 %
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:
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Species distribution
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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:
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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.
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There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
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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.
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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.
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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.
There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 Septin domain has been found. There are 35 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...