Summary: Segregation and condensation complex subunit ScpB
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Condensin Edit Wikipedia article
Many eukaryotic cells possess two different types of condensin complexes, known as condensin I and condensin II, each of which is composed of five subunits. Condensins I and II share the same pair of core subunits, SMC2 and SMC4, both belonging to a large family of chromosomal ATPases, known as SMC proteins (SMC stands for Structural Maintenance of Chromosomes). Each of the complexes contains a distinct set of non-SMC regulatory subunits (a kleisin subunit and a pair of HEAT-repeat subunits). The nematode Caenorhabditis elegans possesses a third complex (closely related to condensin I) that participates in chromosome-wide gene regulation, i.e., dosage compensation. In this complex, known as condensin IDC, the authentic SMC4 subunit is replaced with its variant, DPY-27.
|Complex||Subunit||Classification||S. cerevisiae||S. pombe||C. elegans||D. melanogaster||Vertebrates (human genes)|
|condensin I & II||SMC2||ATPase||Smc2||Cut14||MIX-1||DmSmc2||CAP-E (SMC2)|
|condensin I & II||SMC4||ATPase||Smc4||Cut3||SMC-4||DmSmc4||CAP-C (SMC4)|
|condensin I||CAP-D2||HEAT||Ycs4||Cnd1||DPY-28||CG1911||CAP-D2 (NCAPD2)|
|condensin I||CAP-G||HEAT||Ycg1||Cnd3||CAP-G1||cap-g||CAP-G (NCAPG)|
|condensin I||CAP-H||kleisin||Brn1||Cnd2||DPY-26||barren||CAP-H (NCAPH)|
|condensin II||CAP-D3||HEAT||-||-||HCP-6||CG31989||CAP-D3 (NCAPD3)|
|condensin II||CAP-G2||HEAT||-||-||CAP-G2||-?||CAP-G2 (NCAPG2)|
|condensin II||CAP-H2||kleisin||-||-||KLE-2||CG14685||CAP-H2 (NCAPH2)|
|condensin IDC||SMC4 variant||ATPase||-||-||DPY-27||-||-|
The structure and function of condensin I are conserved from yeast to humans, but yeast has no condensin II. There is no apparent relationship between the occurrence of condensin II and the size of eukaryotic genomes. In fact, the primitive red alga Cyanidioschyzon merolae has both condensins I and II although its genome size is small and comparable to that of yeast.
Prokaryotic species also have condensin-like complexes that play an important role in chromosome organization and segregation. The prokaryotic condensins can be classified into two types: SMC-ScpAB and MukBEF. Many eubacterial and archaeal species have SMC-ScpAB, whereas a subgroup of eubacteria (known as gamma-proteobacteria) has MukBEF. ScpA and MukF belong to a family of proteins called "kleisins", whereas ScpB and MukF have recently been classified into a new family of proteins named "kite".
Purified condensin I introduces positive superhelical tension into double-stranded DNA in an ATP-hydrolysis-dependent manner. It also displays a DNA-stimulated ATPase activity in vitro. An SMC2-SMC4 dimer has an ability to reanneal complementary single-stranded DNA. This activity does not require ATP.
In preparation for the mitosis, it was hypothesized that condensin plays a key role in compaction and segregation of the sister chromatids. The same was demonstrated by the polymer physics simulations. However, the direct evidence for the DNA loop extrusion activity provided by single-molecule experiments . In that experiments, the activity of individual condensin complexes on DAN was visualized by real-time fluorescence imaging revealing that condensin indeed is a fast loop-extruding motor and single condensin complex can extrude 1500 bp of DNA per second in a strictly ATP dependent manner. Furthermore, these results showed that condensin anchors DNA between kleisin-Ycg1 subunits and pulls DNA asymmetrically to form large loops.
SMC dimers that act as the core subunits of condensins display a highly unique V-shape (see SMC proteins for details). The holocomplex of condensin I has been visualized by electron microscopy.
In human tissue culture cells, the two condensin complexes are regulated differently during the cell cycle. Condensin II is present within the cell nucleus during interphase and is involved in an early stage of chromosome condensation within the prophase nucleus. On the other hand, condensin I is present in the cytoplasm during interphase, and gains access to chromosomes only after the nuclear envelope breaks down at the end of prophase. During prometaphase and metaphase, both condensin I and condensin II contribute to the assembly of condensed chromosomes, in which two sister chromatids are fully resolved. The two complexes apparently stay associated with chromosomes after the sister chromatids separate from each other in anaphase. At least one of the subunits of condensin I is known to be a direct target of a cyclin-dependent kinase (Cdk).
Chromosomal functions outside of mitosis
Recent studies have shown that condensins participate in a wide variety of chromosome functions outside of mitosis or meiosis. In budding yeast, for instance, condensin I (the sole condensin in this organism) is involved in copy number regulation of the rDNA repeat as well as in clustering of the tRNA genes. In Drosophila, condensin II subunits contribute to the dissolution of polytene chromosomes and the formation of chromosome territories in ovarian nurse cells. Evidence is also available that they negatively regulate transvection in diploid cells. In A. thaliana, condensin II is essential for tolerance of excess boron stress, possibly by alleviating DNA damage. It has been shown that, in human cells, condensin II’s contribution to resolving sister chromatids initiates as early as in S phase.
Eukaryotic cells have two additional classes of SMC protein complexes. Cohesin contains SMC1 and SMC3 and is involved in sister chromatid cohesion. The SMC5/6 complex contains SMC5 and SMC6 and is implicated in recombinational repair.
- Hirano T (2016). "Condensin-based chromosome organization from bacteria to vertebrates". Cell. 164 (5): 847–857. doi:10.1016/j.cell.2016.01.033. PMID 26919425.
- Wood AJ, Severson AF, Meyer BJ (2010). "Condensin and cohesin complexity: the expanding repertoire of functions". Nat Rev Genet. 11 (6): 391–404. doi:10.1038/nrg2794. PMC . PMID 20442714.
- Hirano T, Kobayashi R, Hirano M (1997). "Condensins, chromosome condensation complex containing XCAP-C, XCAP-E and a Xenopus homolog of the Drosophila Barren protein". Cell. 89 (4): 511–21. doi:10.1016/S0092-8674(00)80233-0. PMID 9160743.
- Ono T, Losada A, Hirano M, Myers MP, Neuwald AF, Hirano T (2003). "Differential contributions of condensin I and condensin II to mitotic chromosome architecture in vertebrate cells". Cell. 115 (1): 109–21. doi:10.1016/S0092-8674(03)00724-4. PMID 14532007.
- Jeppsson K, Kanno T, Shirahige K, Sjögren C (2014). "The maintenance of chromosome structure: positioning and functioning of SMC complexes". Nat. Rev. Mol. Cell Biol. 15: 601–614. doi:10.1038/nrm3857. PMID 25145851.
- Uhlmann F (2016). "SMC complexes: from DNA to chromosomes". Nat. Rev. Mol. Cell Biol. 17: 399–412. doi:10.1038/nrm.2016.30. PMID 27075410.
- Schleiffer A, Kaitna S, Maurer-Stroh S, Glotzer M, Nasmyth K, Eisenhaber F (2003). "Kleisins: a superfamily of bacterial and eukaryotic SMC protein partners". Mol. Cell. 11 (3): 571–5. doi:10.1016/S1097-2765(03)00108-4. PMID 12667442.
- Neuwald AF, Hirano T (2000). "HEAT repeats associated with condensins, cohesins, and other complexes involved in chromosome-related functions". Genome Res. 10 (10): 1445–52. doi:10.1101/gr.147400. PMC . PMID 11042144.
- Yoshimura SH, Hirano T (2016). "HEAT repeats - versatile arrays of amphiphilic helices working in crowded environments?". J. Cell Sci. 129 (21): 3963–3970. doi:10.1242/jcs.185710. PMID 27802131.
- Csankovszki G, Collette K, Spahl K, Carey J, Snyder M, Petty E, Patel U, Tabuchi T, Liu H, McLeod I, Thompson J, Sarkeshik A, Yates J, Meyer BJ, Hagstrom K (2009). "Three distinct condensin complexes control C. elegans chromosome dynamics". Curr. Biol. 19 (1): 9–19. doi:10.1016/j.cub.2008.12.006. PMC . PMID 19119011.
- Sutani T, Yuasa T, Tomonaga T, Dohmae N, Takio K, Yanagida M (1999). "Fission yeast condensin complex: essential roles of non-SMC subunits for condensation and Cdc2 phosphorylation of Cut3/SMC4". Genes Dev. 13 (17): 2271–83. doi:10.1101/gad.13.17.2271. PMC . PMID 10485849.
- Freeman L, Aragon-Alcaide L, Strunnikov A (2000). "The condensin complex governs chromosome condensation and mitotic transmission of rDNA". J. Cell Biol. 149 (4): 811–824. doi:10.1083/jcb.149.4.811. PMC . PMID 10811823.
- Fujiwara T, Tanaka K, Kuroiwa T, Hirano T (2013). "Spatiotemporal dynamics of condensins I and II: evolutionary insights from the primitive red alga Cyanidioschyzon merolae". Mol. Biol. Cell. 24 (16): 2515–27. doi:10.1091/mbc.E13-04-0208. PMC . PMID 23783031.
- Mascarenhas J, Soppa J, Strunnikov AV, Graumann PL (2002). "Cell cycle-dependent localization of two novel prokaryotic chromosome segregation and condensation proteins in Bacillus subtilis that interact with SMC protein". EMBO J. 21 (12): 3108–18. doi:10.1093/emboj/cdf314. PMC . PMID 12065423.
- Yamazoe M, Onogi T, Sunako Y, Niki H, Yamanaka K, Ichimura T, Hiraga S (1999). "Complex formation of MukB, MukE and MukF proteins involved in chromosome partitioning in Escherichia coli". EMBO J. 18 (21): 5873–84. doi:10.1093/emboj/18.21.5873. PMC . PMID 10545099.
- Palecek JJ, Gruber S (2015). "Kite proteins: a superfamily of SMC/kleisin partners conserved across Bacteria, Archaea, and Eukaryotes". Structure. 23 (12): 2183–2190. doi:10.1016/j.str.2015.10.004. PMID 26585514.
- Kimura K, Hirano T (1997). "ATP-dependent positive supercoiling of DNA by 13S condensin: a biochemical implication for chromosome condensation". Cell. 90 (4): 625–634. doi:10.1016/s0092-8674(00)80524-3. PMID 9288743.
- Sutani T, Yanagida M (1997). "DNA renaturation activity of the SMC complex implicated in chromosome condensation". Nature. 388 (6644): 798–801. doi:10.1038/42062. PMID 9285594.
- Goloborodko, Anton; Imakaev, Maxim V; Marko, John F; Mirny, Leonid (2016-05-18). "Compaction and segregation of sister chromatids via active loop extrusion". eLife. 5. doi:10.7554/eLife.14864. ISSN 2050-084X.
- Ganji, Mahipal; Shaltiel, Indra A.; Bisht, Shveta; Kim, Eugene; Kalichava, Ana; Haering, Christian H.; Dekker, Cees (2018-04-06). "Real-time imaging of DNA loop extrusion by condensin". Science. 360 (6384): 102–105. doi:10.1126/science.aar7831. ISSN 0036-8075. PMID 29472443.
- Ganji, Mahipal; Shaltiel, Indra A.; Bisht, Shveta; Kim, Eugene; Kalichava, Ana; Haering, Christian H.; Dekker, Cees (2018-04-06). "Real-time imaging of DNA loop extrusion by condensin". Science. 360 (6384): 102–105. doi:10.1126/science.aar7831. ISSN 0036-8075. PMID 29472443.
- Melby TE, Ciampaglio CN, Briscoe G, Erickson HP (1998). "The symmetrical structure of structural maintenance of chromosomes (SMC) and MukB proteins: long, antiparallel coiled coils, folded at a flexible hinge". J. Cell Biol. 142 (6): 1595–1604. doi:10.1083/jcb.142.6.1595. PMC . PMID 9744887.
- Anderson DE, Losada A, Erickson HP, Hirano T (2002). "Condensin and cohesin display different arm conformations with characteristic hinge angles". J. Cell Biol. 156 (6): 419–424. doi:10.1083/jcb.200111002. PMC . PMID 11815634.
- Ono T, Fang Y, Spector DL, Hirano T (2004). "Spatial and temporal regulation of Condensins I and II in mitotic chromosome assembly in human cells". Mol. Biol. Cell. 15 (7): 3296–308. doi:10.1091/mbc.E04-03-0242. PMC . PMID 15146063.
- Hirota T, Gerlich D, Koch B, Ellenberg J, Peters JM (2004). "Distinct functions of condensin I and II in mitotic chromosome assembly". J. Cell Sci. 117 (Pt 26): 6435–45. doi:10.1242/jcs.01604. PMID 15572404.
- Kimura K, Hirano M, Kobayashi R, Hirano T (1998). "Phosphorylation and activation of 13S condensin by Cdc2 in vitro". Science. 282 (5388): 487–490. doi:10.1126/science.282.5388.487. PMID 9774278.
- Hirano T (2012). "Condensins: universal organizers of chromosomes with diverse functions". Genes Dev. 26 (15): 1659–1678. doi:10.1101/gad.194746.112. PMC . PMID 22855829.
- Johzuka K, Terasawa M, Ogawa H, Ogawa T, Horiuchi T (2006). "Condensin loaded onto the replication fork barrier site in the rRNA gene repeats during S phase in a FOB1-dependent fashion to prevent contraction of a long repetitive array in Saccharomyces cerevisiae". Mol Cell Biol. 26 (6): 2226–2236. doi:10.1128/MCB.26.6.2226-2236.2006. PMC . PMID 16507999.
- Haeusler RA, Pratt-Hyatt M, Good PD, Gipson TA, Engelke DR (2008). "Clustering of yeast tRNA genes is mediated by specific association of condensin with tRNA gene transcription complexes". Genes Dev. 22 (16): 2204–2214. doi:10.1101/gad.1675908. PMC . PMID 18708579.
- Hartl TA, Smith HF, Bosco G (2008). "Chromosome alignment and transvection are antagonized by condensin II". Science. 322 (5906): 1384–1387. doi:10.1126/science.1164216. PMID 19039137.
- Bauer CR, Hartl TA, Bosco G (2012). "Condensin II promotes the formation of chromosome territories by inducing axial compaction of polyploid interphase chromosomes". PLoS Genet. 8 (8): e1002873. doi:10.1371/journal.pgen.1002873. PMC . PMID 22956908.
- Sakamoto T, Inui YT, Uraguchi S, Yoshizumi T, Matsunaga S, Mastui M, Umeda M, Fukui K, Fujiwara T (2011). "Condensin II alleviates DNA damage and is essential for tolerance of boron overload stress in Arabidopsis". Plant Cell. 23 (9): 3533–3546. doi:10.1105/tpc.111.086314. PMC . PMID 21917552.
- Ono T, Yamashita D, Hirano T (2013). "Condensin II initiates sister chromatid resolution during S phase". J. Cell Biol. 200 (4): 429–441. doi:10.1083/jcb.201208008. PMC . PMID 23401001.
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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.
Segregation and condensation complex subunit ScpB Provide feedback
This is a family of prokaryotic proteins that form one of the subunits, ScpB, of the segregation and condensation complex, condensin, that plays a key role in the maintenance of the chromosome. In prokaryotes the complex consists of three proteins, SMC, ScpA (kleisin) and ScpB. ScpB dimerises and binds to ScpA. As originally predicted, ScpB is structurally a winged-helix at both its N- and C-terminal halves. IN Bacillus subtilis,one Smc dimer is bridged by a single ScpAB to generate asymmetric tripartite rings analogous to eukaryotic SMC complex ring-shaped assemblies [1,2].
Burmann F, Shin HC, Basquin J, Soh YM, Gimenez-Oya V, Kim YG, Oh BH, Gruber S;, Nat Struct Mol Biol. 2013;20:371-379.: An asymmetric SMC-kleisin bridge in prokaryotic condensin. PUBMED:23353789 EPMC:23353789
Kamada K, Miyata M, Hirano T;, Structure. 2013;21:581-594.: Molecular basis of SMC ATPase activation: role of internal structural changes of the regulatory subcomplex ScpAB. PUBMED:23541893 EPMC:23541893
Internal database links
|SCOOP:||B-block_TFIIIC Fe_dep_repress HTH_11 HTH_15 HTH_20 HTH_24 HTH_27 HTH_34 HTH_5 HTH_Crp_2 HTH_IclR MarR MarR_2 Penicillinase_R TrmB|
This tab holds annotation information from the InterPro database.
InterPro entry IPR005234
This family represents ScpB, which along with ScpA (INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [PUBMED:12065423, PUBMED:12897137]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [PUBMED:10545099], where MukB (INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (INTERPRO) or MukF (INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions.
In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes [PUBMED:12100548].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||chromosome separation (GO:0051304)|
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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This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif.
The clan contains the following 256 members:AbiEi_3_N AbiEi_4 ANAPC2 AphA_like Arg_repressor ARID B-block_TFIIIC Bac_DnaA_C BetR Bot1p BrkDBD C_LFY_FLO Cdc6_C CENP-B_N Cro Crp CSN8_PSD8_EIF3K Cullin_Nedd8 CUT DDRGK DEP Dimerisation Dimerisation2 DsrD DUF1133 DUF1153 DUF1323 DUF134 DUF1441 DUF1492 DUF1495 DUF1670 DUF1804 DUF1836 DUF1870 DUF2089 DUF2250 DUF2316 DUF2582 DUF3116 DUF3253 DUF3853 DUF3860 DUF3908 DUF433 DUF4364 DUF4447 DUF480 DUF722 DUF739 DUF742 DUF977 E2F_TDP EAP30 ELL ESCRT-II Ets Exc F-112 FaeA Fe_dep_repr_C Fe_dep_repress FeoC FokI_C FokI_N Forkhead Ftsk_gamma FUR GcrA GerE GntR HARE-HTH HemN_C HNF-1_N Homeobox Homeobox_KN 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_5 HTH_6 HTH_7 HTH_8 HTH_9 HTH_AraC HTH_AsnC-type HTH_CodY HTH_Crp_2 HTH_DeoR HTH_IclR HTH_Mga HTH_micro HTH_OrfB_IS605 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 KORA KorB La LacI LexA_DNA_bind Linker_histone LZ_Tnp_IS481 MADF_DNA_bdg MarR MarR_2 MerR MerR-DNA-bind MerR_1 MerR_2 Mga Mnd1 Mor MotA_activ MqsA_antitoxin MRP-L20 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 NUMOD1 OST-HTH P22_Cro PaaX PadR PAX PCI Penicillinase_R Phage_AlpA Phage_antitermQ Phage_CI_repr Phage_CII Phage_rep_org_N Phage_terminase Pou Pox_D5 PuR_N Put_DNA-bind_N Rap1-DNA-bind Rep_3 RepA_C RepA_N RepC RepL Replic_Relax RFX_DNA_binding Ribosomal_S19e Ribosomal_S25 Rio2_N RNA_pol_Rpc34 RP-C RPA RPA_C RQC Rrf2 RTP RuvB_C 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 SLIDE SMC_ScpB SpoIIID STN1_2 Sulfolobus_pRN SWIRM TBPIP Terminase_5 TetR_N TFIIE_alpha TFIIE_beta TFIIF_alpha TFIIF_beta Tn7_Tnp_TnsA_C Tn916-Xis TraI_2_C Trans_reg_C TrfA TrmB Trp_repressor UPF0122 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.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- 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:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
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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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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.
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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
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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.
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:||TIGRFAMs (release 2.0);|
|Author:||TIGRFAMs, Finn RD|
|Number in seed:||109|
|Number in full:||3451|
|Average length of the domain:||158.00 aa|
|Average identity of full alignment:||34 %|
|Average coverage of the sequence by the domain:||73.22 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
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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 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:
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.
The tree shows the occurrence of this domain across different species. More...
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.
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 are 2 interactions 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 SMC_ScpB domain has been found. There are 13 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...