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13  structures 1953  species 2  interactions 2070  sequences 2  architectures

Family: SMC_ScpB (PF04079)

Summary: Segregation and condensation complex subunit ScpB

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Condensin". More...

Condensin Edit Wikipedia article

An interphase nucleus (left) and a set of mitotic chromosomes (right) from human tissue culture cells. Bar, 10 μm.

Condensins are large protein complexes that play a central role in chromosome assembly and segregation during mitosis and meiosis.[1][2]

Subunit composition

Eukaryotic condensins

Subunit composition of condensin complexes

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.[3][4] 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[5] and a pair of HEAT-repeat subunits[6]). The nematode Caenorhabditis elegans possesses a third complex (closely related to condensin I) that participates in chromosome-wide gene regulation, i.e., dosage compensation.[7] 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.[8][9] 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.[10]

Prokaryotic condensins

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[11] and MukBEF.[12] Many eubacterial and archaeal species have SMC-ScpAB, whereas a subgroup of eubacteria (known as gamma-proteobacteria) has MukBEF.

Complex Subunit Classification B. subtilis Caulobacter E.coli
SMC-ScpAB SMC ATPase SMC/BsSMC SMC -
SMC-ScpAB ScpA kleisin ScpA ScpA -
SMC-ScpAB ScpB winged-helix ScpB ScpB -
MukBEF MukB ATPase - - MukB
MukBEF MukE  ? - - MukE
MukBEF MukF kleisin - - MukF

Molecular mechanisms

Molecular activities

Purified condensin I introduces positive superhelical tension into double-stranded DNA in an ATP-hydrolysis-dependent manner.[13] It also displays a DNA-stimulated ATPase activity in vitro. An SMC2-SMC4 dimer has an ability to reanneal complementary single-stranded DNA.[14] This activity does not require ATP.

Molecular structures

SMC dimers that act as the core subunits of condensins display a highly unique V-shape (see SMC proteins for details).[15] The holocomplex of condensin I has been visualized by electron microscopy.[16]

Mitotic functions

Distribution of condensin I (green) and condensin II (red) in human metaphase chromosomes. Bar, 1 μm.

In human tissue culture cells, the two condensin complexes are regulated differently during the cell cycle.[17][18] 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.[4] 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).[19]

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[20] as well as in clustering of the tRNA genes.[21] In Drosophila, condensin II subunits contribute to the dissolution of polytene chromosomes[22] and the formation of chromosome territories[23] 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.[24] It has been shown that, in human cells, condensin II’s contribution to resolving sister chromatids initiates as early as in S phase.[25]

Relatives

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.

See also

References

  1. ^ Hirano T (2012). "Condensins: universal organizers of chromosomes with diverse functions". Genes Dev 26 (15): 1659–1678. doi:10.1101/gad.194746.112. PMC 3418584. PMID 22855829. 
  2. ^ 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 3491780. PMID 20442714. 
  3. ^ 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. 
  4. ^ a b 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. 
  5. ^ 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. 
  6. ^ 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. PMID 11042144. 
  7. ^ 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. PMID 19119011. 
  8. ^ 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. PMID 10485849. 
  9. ^ 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. PMID 10811823. 
  10. ^ 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. PMID 23783031. 
  11. ^ 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. PMID 12065423. 
  12. ^ 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. PMID 10545099. 
  13. ^ 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. 
  14. ^ 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. 
  15. ^ 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. PMID 9744887. 
  16. ^ 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. PMID 11815634. 
  17. ^ 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. PMID 15146063. 
  18. ^ 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. 
  19. ^ 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. 
  20. ^ 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. PMID 16507999. 
  21. ^ 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. PMID 18708579. 
  22. ^ 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. 
  23. ^ 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. PMID 22956908. 
  24. ^ 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. PMID 21917552. 
  25. ^ 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. PMID 23401001. 

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This is the Wikipedia entry entitled "Domain of unknown function". More...

Domain of unknown function Edit Wikipedia article

A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. There are now over 3,000 DUF families within the Pfam database representing over 20% of known families.[1]

History

The DUF naming scheme was introduced by Chris Ponting, through the addition of DUF1 and DUF2 to the SMART database.[2] These two domains were found to be widely distributed in bacterial signaling proteins. Subsequently, the functions of these domains were identified and they have since been renamed as the GGDEF domain and EAL domain respectively.

Structure

Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The structures of over 250 DUF families have been solved.[3] This work showed that about two thirds of DUF families had a structure similar to a previously solved one and therefore likely to be divergent members of existing protein superfamilies, whereas about one third possessed a novel protein fold.

Frequency and conservation

Protein domains and DUFs in different domains of life. Left: Annotated domains. Right: domains of unknown function. Not all overlaps shown.[4]

More than 20% of all protein domains were annotated as DUFs in 2013. About 2,700 DUFs are found in bacteria compared with just over 1,500 in eukaryotes. Over 800 DUFs are shared between bacteria and eukaryotes, and about 300 of these are also present in archaea. A total of 2,786 bacterial Pfam domains even occur in animals, including 320 DUFs.[4]

Role in biology

Many DUFs are highly conserved, indicating an important role in biology. However, many such DUFs are not essential, hence their biological role often remains unknown. For instance, DUF143 is present in most bacteria and eukaryotic genomes.[5] However, when it was deleted in Escherichia coli no obvious phenotype was detected. Later it was shown that the proteins that contain DUF143, are ribosomal silencing factors that block the assembly of the two ribosomal subunits.[5] While this function is not essential, it helps the cells to adapt to low nutrient conditions by shutting down protein biosynthesis. As a result, these proteins and the DUF only become relevant when the cells starve.[5] It is thus believed that many DUFs (or proteins of unknown function, PUFs) are only required under certain conditions.

Essential DUFs (eDUFs)

Goodacre et al. identified 238 DUFs in 355 essential proteins (in 16 model bacterial species), most of which represent single-domain proteins, clearly establishing the biological essentiality of DUFs. These DUFs are called "essential DUFs" or eDUFs.[4]

External links

References

  1. ^ Bateman A, Coggill P, Finn RD (October 2010). "DUFs: families in search of function". Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 66 (Pt 10): 1148–52. doi:10.1107/S1744309110001685. PMC 2954198. PMID 20944204. 
  2. ^ Schultz J, Milpetz F, Bork P, Ponting CP (May 1998). "SMART, a simple modular architecture research tool: identification of signaling domains". Proc. Natl. Acad. Sci. U.S.A. 95 (11): 5857–64. doi:10.1073/pnas.95.11.5857. PMC 34487. PMID 9600884. 
  3. ^ Jaroszewski L, Li Z, Krishna SS, et al. (September 2009). "Exploration of uncharted regions of the protein universe". PLoS Biol. 7 (9): e1000205. doi:10.1371/journal.pbio.1000205. PMC 2744874. PMID 19787035. 
  4. ^ a b c Goodacre, N. F.; Gerloff, D. L.; Uetz, P. (2013). "Protein Domains of Unknown Function Are Essential in Bacteria". MBio 5 (1): e00744–e00713. doi:10.1128/mBio.00744-13. PMID 24381303. 
  5. ^ a b c Häuser, R.; Pech, M.; Kijek, J.; Yamamoto, H.; Titz, B. R.; Naeve, F.; Tovchigrechko, A.; Yamamoto, K.; Szaflarski, W.; Takeuchi, N.; Stellberger, T.; Diefenbacher, M. E.; Nierhaus, K. H.; Uetz, P. (2012). Hughes, Diarmaid, ed. "RsfA (YbeB) Proteins Are Conserved Ribosomal Silencing Factors". PLoS Genetics 8 (7): e1002815. doi:10.1371/journal.pgen.1002815. PMC 3400551. PMID 22829778. 

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.

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].

Literature references

  1. 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

  2. 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

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].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan HTH (CL0123), which has the following description:

This family contains a diverse range of mostly DNA-binding domains that contain a helix-turn-helix motif.

The clan contains the following 254 members:

AbiEi_3_N AbiEi_4 ANAPC2 AphA_like Arg_repressor ARID B-block_TFIIIC Bac_DnaA_C BetR Bot1p BrkDBD 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 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

Alignments

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...

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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.

  Seed
(110)
Full
(2070)
Representative proteomes UniProt
(7893)
NCBI
(10537)
Meta
(2162)
RP15
(616)
RP35
(1774)
RP55
(2943)
RP75
(4434)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(110)
Full
(2070)
Representative proteomes UniProt
(7893)
NCBI
(10537)
Meta
(2162)
RP15
(616)
RP35
(1774)
RP55
(2943)
RP75
(4434)
Alignment:
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Order:
Sequence:
Gaps:
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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.

  Seed
(110)
Full
(2070)
Representative proteomes UniProt
(7893)
NCBI
(10537)
Meta
(2162)
RP15
(616)
RP35
(1774)
RP55
(2943)
RP75
(4434)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

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...

Trees

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.

Curation View help on the curation process

Seed source: TIGRFAMs (release 2.0);
Previous IDs: DUF387;
Type: Family
Author: TIGRFAMs, Finn RD
Number in seed: 110
Number in full: 2070
Average length of the domain: 157.70 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 73.37 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.4 27.4
Trusted cut-off 27.5 27.4
Noise cut-off 27.1 27.1
Model length: 160
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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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...

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The tree shows the occurrence of this domain across different species. More...

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Interactions

There are 2 interactions for this family. More...

SMC_ScpA SMC_ScpB

Structures

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 seqence.

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