Summary: Sigma-70, region 4
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Sigma factor Edit Wikipedia article
A sigma factor (Ïƒ factor or specificity factor) is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is homologous to archaeal transcription factor B and to eukaryotic factor TFIIB. The specific sigma factor used to initiate transcription of a given gene will vary, depending on the gene and on the environmental signals needed to initiate transcription of that gene. Selection of promoters by RNA polymerase is dependent on the sigma factor that associates with it. They are also found in plant chloroplasts as a part of the bacteria-like plastid-encoded polymerase (PEP).
The sigma factor, together with RNA polymerase, is known as the RNA polymerase holoenzyme. Every molecule of RNA polymerase holoenzyme contains exactly one sigma factor subunit, which in the model bacterium Escherichia coli is one of those listed below. The number of sigma factors varies between bacterial species. E. coli has seven sigma factors. Sigma factors are distinguished by their characteristic molecular weights. For example, Ïƒ70 is the sigma factor with a molecular weight of 70 kDa.
The sigma factor in the RNA polymerase holoenzyme complex is required for the initiation of transcription, although once that stage is finished, it is dissociated from the complex and the RNAP continues elongation on its own.
Specialized sigma factors
Different sigma factors are utilized under different environmental conditions. These specialized sigma factors bind the promoters of genes appropriate to the environmental conditions, increasing the transcription of those genes.
Sigma factors in E. coli:
- Ïƒ70(RpoD) â€“ ÏƒA â€“ the "housekeeping" sigma factor or also called as primary sigma factor (Group 1), transcribes most genes in growing cells. Every cell has a "housekeeping" sigma factor that keeps essential genes and pathways operating. In the case of E. coli and other gram-negative rod-shaped bacteria, the "housekeeping" sigma factor is Ïƒ70. Genes recognized by Ïƒ70 all contain similar promoter consensus sequences consisting of two parts. Relative to the DNA base corresponding to the start of the RNA transcript, the consensus promoter sequences are characteristically centered at 10 and 35 nucleotides before the start of transcription (âˆ’10 and âˆ’35).
- Ïƒ19 (FecI) â€“ the ferric citrate sigma factor, regulates the fec gene for iron transport and metabolism
- Ïƒ24 (RpoE) â€“ extreme heat stress response and the extracellular proteins sigma factor
- Ïƒ28 (RpoF/FliA) â€“ the flagellar synthesis and chemotaxis sigma factor
- Ïƒ32 (RpoH) â€“ the heat shock sigma factor, it is turned on when the bacteria are exposed to heat. Due to the higher expression, the factor will bind with a high probability to the polymerase-core-enzyme. Doing so, other heatshock proteins are expressed, which enable the cell to survive higher temperatures. Some of the enzymes that are expressed upon activation of Ïƒ32 are chaperones, proteases and DNA-repair enzymes.
- Ïƒ38 (RpoS) â€“ the starvation/stationary phase sigma factor
- Ïƒ54 (RpoN) â€“ the nitrogen-limitation sigma factor
There are also anti-sigma factors that inhibit the function of sigma factors and anti-anti-sigma factors that restore sigma factor function.
N-terminus --------------------- C-terminus 1.1 2 3 4
The regions are further subdivided. For example, region 2 includes 1.2 and 2.1 through 2.4.
Domain 1.1 is found only in "primary sigma factors" (RpoD, RpoS in E.coli; "Group 1"). It is involved in ensuring the sigma factor will only bind the promoter when it is complexed with the RNA polymerase. Domains 2-4 each interact with specific promoter elements and with RNAP. Region 2.4 recognizes and binds to the promoter âˆ’10 element (called the "Pribnow box"). Region 4.2 recognizes and binds to the promoter âˆ’35 element.
Not every sigma factor of the Ïƒ70 family contains all the domains. Group 2, which includes RpoS, is very similar to Group 1 but lacks domain 1. Group 3 also lacks domain 1, and includes Ïƒ28. Group 4, also known as the Extracytoplasmic Function (ECF) group, lack both Ïƒ1.1 and Ïƒ3. RpoE is a member.
Retention during transcription elongation
The core RNA polymerase (consisting of 2 alpha (Î±), 1 beta (Î²), 1 beta-prime (Î²'), and 1 omega (Ï‰) subunits) binds a sigma factor to form a complex called the RNA polymerase holoenzyme. It was previously believed that the RNA polymerase holoenzyme initiates transcription, while the core RNA polymerase alone synthesizes RNA. Thus, the accepted view was that sigma factor must dissociate upon transition from transcription initiation to transcription elongation (this transition is called "promoter escape"). This view was based on analysis of purified complexes of RNA polymerase stalled at initiation and at elongation. Finally, structural models of RNA polymerase complexes predicted that, as the growing RNA product becomes longer than ~15 nucleotides, sigma must be "pushed out" of the holoenzyme, since there is a steric clash between RNA and a sigma domain. However, Ïƒ70 can remain attached in complex with the core RNA polymerase in early elongation and sometimes throughout elongation. Indeed, the phenomenon of promoter-proximal pausing indicates that sigma plays roles during early elongation. All studies are consistent with the assumption that promoter escape reduces the lifetime of the sigma-core interaction from very long at initiation (too long to be measured in a typical biochemical experiment) to a shorter, measurable lifetime upon transition to elongation.
It had long been thought that the sigma factor obligatorily leaves the core enzyme once it has initiated transcription, allowing it to link to another core enzyme and initiate transcription at another site. Thus, the sigma factor would cycle from one core to another. However, fluorescence resonance energy transfer was used to show that the sigma factor does not obligatorily leave the core. Instead, it changes its binding with the core during initiation and elongation. Therefore, the sigma factor cycles between a strongly bound state during initiation and a weakly bound state during elongation.
- Gruber TM, Gross CA (2003). "Multiple sigma subunits and the partitioning of bacterial transcription space". Annual Review of Microbiology. 57: 441â€“66. doi:10.1146/annurev.micro.57.030502.090913. PMIDÂ 14527287.
- Kang JG, Hahn MY, Ishihama A, Roe JH (July 1997). "Identification of sigma factors for growth phase-related promoter selectivity of RNA polymerases from Streptomyces coelicolor A3(2)". Nucleic Acids Research. 25 (13): 2566â€“73. doi:10.1093/nar/25.13.2566. PMCÂ 146787. PMIDÂ 9185565.
- Burton SP, Burton ZF (6 November 2014). "The Ïƒ enigma: bacterial Ïƒ factors, archaeal TFB and eukaryotic TFIIB are homologs". Transcription. 5 (4): e967599. doi:10.4161/21541264.2014.967599. PMCÂ 4581349. PMIDÂ 25483602.
- Ho TD, Ellermeier CD (April 2012). "Extra cytoplasmic function Ïƒ factor activation". Current Opinion in Microbiology. 15 (2): 182â€“8. doi:10.1016/j.mib.2012.01.001. PMCÂ 3320685. PMIDÂ 22381678.
- Schweer J, TÃ¼rkeri H, Kolpack A, Link G (December 2010). "Role and regulation of plastid sigma factors and their functional interactors during chloroplast transcription - recent lessons from Arabidopsis thaliana". European Journal of Cell Biology. 89 (12): 940â€“6. doi:10.1016/j.ejcb.2010.06.016. PMIDÂ 20701995.
- Sharma UK, Chatterji D (September 2010). "Transcriptional switching in Escherichia coli during stress and starvation by modulation of sigma activity". FEMS Microbiology Reviews. 34 (5): 646â€“57. doi:10.1111/j.1574-6976.2010.00223.x. PMIDÂ 20491934.
- Paget MS (June 2015). "Bacterial Sigma Factors and Anti-Sigma Factors: Structure, Function and Distribution". Biomolecules. 5 (3): 1245â€“65. doi:10.3390/biom5031245. PMCÂ 4598750. PMIDÂ 26131973.
- Merrick MJ (December 1993). "In a class of its own--the RNA polymerase sigma factor sigma 54 (sigma N)". Molecular Microbiology. 10 (5): 903â€“9. doi:10.1111/j.1365-2958.1993.tb00961.x. PMIDÂ 7934866. S2CIDÂ 84789281.
- Kapanidis AN, Margeat E, Laurence TA, Doose S, Ho SO, Mukhopadhyay J, Kortkhonjia E, Mekler V, Ebright RH, Weiss S (November 2005). "Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis". Molecular Cell. 20 (3): 347â€“56. doi:10.1016/j.molcel.2005.10.012. PMIDÂ 16285917.
- Harden TT, Wells CD, Friedman LJ, Landick R, Hochschild A, Kondev J, Gelles J (January 2016). "Bacterial RNA polymerase can retain Ïƒ70 throughout transcription". Proc Natl Acad Sci U S A. 113 (3): 602â€“7. Bibcode:2016PNAS..113..602H. doi:10.1073/pnas.1513899113. PMCÂ 4725480. PMIDÂ 26733675.
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.
Sigma-70, region 4 Provide feedback
Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif .
Campbell EA, Muzzin O, Chlenov M, Sun JL, Olson CA, Weinman O, Trester-Zedlitz ML, Darst SA; , Mol Cell 2002;9:527-539.: Structure of the bacterial RNA polymerase promoter specificity sigma subunit. PUBMED:11931761 EPMC:11931761
Internal database links
|SCOOP:||CENP-B_N Crp DUF134 DUF1492 DUF2089 DUF6362 DUF6456 DUF742 Fe_dep_repress GcrA GerE GntR HTH_1 HTH_10 HTH_11 HTH_17 HTH_19 HTH_20 HTH_22 HTH_23 HTH_24 HTH_26 HTH_27 HTH_28 HTH_3 HTH_30 HTH_31 HTH_32 HTH_34 HTH_36 HTH_37 HTH_40 HTH_5 HTH_50 HTH_7 HTH_8 HTH_Crp_2 HTH_DeoR HTH_IclR HTH_Mga HTH_psq HTH_Tnp_1 HTH_Tnp_1_2 HTH_Tnp_4 HTH_Tnp_IS630 HTH_Tnp_ISL3 HTH_WhiA KORA LacI LexA_DNA_bind LZ_Tnp_IS481 MarR MarR_2 MerR MerR_1 Mga Phage_antitermQ Phage_CI_repr Phage_terminase Rrf2 SatD Sigma70_ECF Sigma70_r4 Terminase_5 TnsD TrmB Trp_repressor UPF0122 UPF0175 Xre-like-HTH YdaS_antitoxin|
|Similarity to PfamA using HHSearch:||GerE MerR HTH_5 MarR DUF134 HTH_7 CENP-B_N UPF0122 Sigma70_r4 HTH_10 Terminase_5 Phage_antitermQ DUF1492 Sigma70_ECF GcrA HTH_11 DUF1804 DUF2089 Phage_terminase HTH_17 HTH_20 HTH_Tnp_1_2 HTH_23 HTH_AsnC-type HTH_24 HTH_28 HTH_Tnp_ISL3 HTH_29 HTH_30 HTH_Tnp_4 HTH_38 HTH_40 TnsD DUF6362|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR013249
The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme [ PUBMED:3052291 ]. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.
With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [ PUBMED:3092189 , PUBMED:1597408 ].
The plastids of higher plants originating from an ancestral cyanobacterial endosymbiont also contain sigma factors that are encoded by a small family of nuclear genes. All plastid sigma factors belong to the superfamily of sigmaA/sigma70 and have sequences homologous to the conserved regions 1.2, 2, 3, and 4 of bacterial sigma factors [ PUBMED:25596450 ].
Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [ PUBMED:11931761 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||DNA binding (GO:0003677)|
|sigma factor activity (GO:0016987)|
|DNA-binding transcription factor activity (GO:0003700)|
|Biological process||regulation of transcription, DNA-templated (GO:0006355)|
|DNA-templated transcription, initiation (GO:0006352)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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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 381 members:AbiEi_3_N AbiEi_4 ANAPC2 AphA_like AraR_C Arg_repressor ARID ArsR B-block_TFIIIC B5 Bac_DnaA_C Baculo_PEP_N BetR BHD_3 BLACT_WH Bot1p BrkDBD BrxA BsuBI_PstI_RE_N C_LFY_FLO CaiF_GrlA CarD_CdnL_TRCF CDC27 Cdc6_C Cdh1_DBD_1 CDT1 CDT1_C CENP-B_N Costars CPSase_L_D3 Cro Crp CSN4_RPN5_eIF3a CSN8_PSD8_EIF3K CtsR Cullin_Nedd8 CUT CUTL CvfB_WH DBD_HTH DDRGK DEP Dimerisation Dimerisation2 DNA_binding_1 DNA_meth_N DpnI_C DprA_WH DsrC DsrD DUF1016_N DUF1133 DUF1153 DUF1323 DUF134 DUF1376 DUF1441 DUF1492 DUF1495 DUF1670 DUF1804 DUF1836 DUF1870 DUF2089 DUF2250 DUF2316 DUF2513 DUF2551 DUF2582 DUF3116 DUF3161 DUF3253 DUF3489 DUF3853 DUF3860 DUF3895 DUF3908 DUF433 DUF434 DUF4364 DUF4373 DUF4423 DUF4447 DUF4777 DUF480 DUF4817 DUF5635 DUF573 DUF5805 DUF6088 DUF6262 DUF6362 DUF6432 DUF6462 DUF6471 DUF722 DUF739 DUF742 DUF937 DUF977 E2F_TDP EAP30 eIF-5_eIF-2B ELL ESCRT-II Ets EutK_C Exc F-112 FaeA Fe_dep_repr_C Fe_dep_repress FeoC FokI_D1 FokI_dom_2 Forkhead FtsK_gamma FUR GcrA GerE GntR GP3_package HARE-HTH HemN_C HNF-1_N Homeobox_KN Homeodomain Homez HPD HrcA_DNA-bdg HSF_DNA-bind HTH_1 HTH_10 HTH_11 HTH_12 HTH_13 HTH_15 HTH_16 HTH_17 HTH_18 HTH_19 HTH_20 HTH_21 HTH_22 HTH_23 HTH_24 HTH_25 HTH_26 HTH_27 HTH_28 HTH_29 HTH_3 HTH_30 HTH_31 HTH_32 HTH_33 HTH_34 HTH_35 HTH_36 HTH_37 HTH_38 HTH_39 HTH_40 HTH_41 HTH_42 HTH_43 HTH_45 HTH_46 HTH_47 HTH_48 HTH_49 HTH_5 HTH_50 HTH_51 HTH_52 HTH_53 HTH_54 HTH_55 HTH_56 HTH_57 HTH_58 HTH_59 HTH_6 HTH_60 HTH_61 HTH_7 HTH_8 HTH_9 HTH_ABP1_N HTH_AraC HTH_AsnC-type HTH_CodY HTH_Crp_2 HTH_DeoR HTH_IclR HTH_Mga HTH_micro HTH_OrfB_IS605 HTH_PafC HTH_ParB HTH_psq HTH_SUN2 HTH_Tnp_1 HTH_Tnp_1_2 HTH_Tnp_2 HTH_Tnp_4 HTH_Tnp_IS1 HTH_Tnp_IS630 HTH_Tnp_ISL3 HTH_Tnp_Mu_1 HTH_Tnp_Mu_2 HTH_Tnp_Tc3_1 HTH_Tnp_Tc3_2 HTH_Tnp_Tc5 HTH_WhiA HxlR IBD IF2_N IRF KicB KilA-N Kin17_mid KORA KorB La LacI LexA_DNA_bind Linker_histone LZ_Tnp_IS481 MADF_DNA_bdg MAGE MARF1_LOTUS MarR MarR_2 MC6 MC7 MC8 MerR MerR-DNA-bind MerR_1 MerR_2 Mga Mnd1 MogR_DNAbind Mor MotA_activ MqsA_antitoxin MRP-L20 Mrr_N MukE Myb_DNA-bind_2 Myb_DNA-bind_3 Myb_DNA-bind_4 Myb_DNA-bind_5 Myb_DNA-bind_6 Myb_DNA-bind_7 Myb_DNA-binding Neugrin NFRKB_winged NOD2_WH NUMOD1 ORC_WH_C OST-HTH P22_Cro PaaX PadR PapB PAX PCI Penicillinase_R Phage_AlpA Phage_antitermQ Phage_CI_repr Phage_CII Phage_NinH Phage_Nu1 Phage_rep_O Phage_rep_org_N Phage_terminase PheRS_DBD1 PheRS_DBD2 PheRS_DBD3 PhetRS_B1 Pou Pox_D5 PqqD PRC2_HTH_1 PUFD PuR_N Put_DNA-bind_N pXO2-72 Raf1_HTH Rap1-DNA-bind Rep_3 RepA_C RepA_N RepB RepC RepL Replic_Relax RFX_DNA_binding Ribosomal_S18 Ribosomal_S19e Ribosomal_S25 Rio2_N RNA_pol_Rpc34 RNA_pol_Rpc82 RNase_H2-Ydr279 ROQ_II ROXA-like_wH RP-C RPA RPA_C RPN6_C_helix RQC Rrf2 RTP RuvB_C S10_plectin SAC3_GANP SANT_DAMP1_like SatD SelB-wing_1 SelB-wing_2 SelB-wing_3 SgrR_N Sigma54_CBD Sigma54_DBD Sigma70_ECF Sigma70_ner Sigma70_r2 Sigma70_r3 Sigma70_r4 Sigma70_r4_2 SinI SKA1 Ski_Sno SLIDE Slx4 SMC_Nse1 SMC_ScpB SoPB_HTH SpoIIID SRP19 SRP_SPB STN1_2 Stn1_C Stork_head Sulfolobus_pRN Suv3_N Swi6_N SWIRM Tau95 TBPIP TEA Terminase_5 TetR_N TFA2_Winged_2 TFIIE_alpha TFIIE_beta TFIIF_alpha TFIIF_beta Tn7_Tnp_TnsA_C Tn916-Xis TraI_2_C Trans_reg_C TrfA TrmB tRNA_bind_2 tRNA_bind_3 Trp_repressor UPF0122 UPF0175 Vir_act_alpha_C XPA_C Xre-like-HTH YdaS_antitoxin YidB 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 and the UniProtKB sequence database. More...
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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_125 (Release 17.0)|
|Number in seed:||141|
|Number in full:||91401|
|Average length of the domain:||53.40 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||24.26 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||15|
|Download:||download the raw HMM for this family|
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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.
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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.
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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.
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 Sigma70_r4_2 domain has been found. There are 42 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...
AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
|Protein||Predicted structure||External Information|
|A0QTP2||View 3D Structure||Click here|
|A0R2D4||View 3D Structure||Click here|
|G8QM61||View 3D Structure||Click here|
|L0TCG5||View 3D Structure||Click here|
|O05404||View 3D Structure||Click here|
|O05409||View 3D Structure||Click here|
|O07582||View 3D Structure||Click here|
|O07627||View 3D Structure||Click here|
|O53590||View 3D Structure||Click here|
|P0A2F0||View 3D Structure||Click here|
|P0AGB6||View 3D Structure||Click here|
|P0AGB8||View 3D Structure||Click here|
|P0AGB9||View 3D Structure||Click here|
|P17869||View 3D Structure||Click here|
|P23484||View 3D Structure||Click here|
|P35165||View 3D Structure||Click here|
|P37978||View 3D Structure||Click here|
|P38133||View 3D Structure||Click here|
|P39784||View 3D Structure||Click here|
|P44790||View 3D Structure||Click here|
|P45215||View 3D Structure||Click here|
|P46358||View 3D Structure||Click here|
|P55379||View 3D Structure||Click here|
|P9WGG5||View 3D Structure||Click here|
|P9WGG7||View 3D Structure||Click here|
|P9WGG9||View 3D Structure||Click here|
|P9WGH1||View 3D Structure||Click here|
|P9WGH3||View 3D Structure||Click here|
|P9WGH9||View 3D Structure||Click here|
|Q06198||View 3D Structure||Click here|
|Q45585||View 3D Structure||Click here|
|Q52997||View 3D Structure||Click here|
|Q7AKG9||View 3D Structure||Click here|
|Q82EA9||View 3D Structure||Click here|