Summary: CobW/HypB/UreG, nucleotide-binding domain
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Cobalamin biosynthesis Edit Wikipedia article
adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (cobu) from salmonella typhimurium
|CobW C terminal|
dethiobiotin synthetase complexed with 7,8-diamino-nonanoic acid, 5'-adenosyl-methylene-triphosphate, and manganese
structural genomics, 1.9a crystal structure of cobalamin biosynthesis protein (cbid) from archaeoglobus fulgidus
|CbiG N terminus|
|CbiG central region|
|CbiG C terminus|
crystal structure of hypothetical protein af0721 from archaeoglobus fulgidus
In molecular biology, cobalamin biosynthesis is the synthesis of cobalamin (vitamin B12).
Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these enzymes include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia-lyase, and diol dehydratase. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase.
Pathways of cobalamin biosynthesis
- Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway; found in Pseudomonas denitrificans and Rhodobacter capsulatus.
- Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii.
Either pathway can be divided into two parts:
- Corrin ring synthesis (differs in aerobic and anaerobic pathways)
- Adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways).
Proteins involved in cobalamin biosynthesis
There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans.
Aerobic cobalt chelatase consists of three subunits, CobT, CobN and CobS. Cobalamin (vitamin B12) can be complexed with metal via the ATP-dependent reactions (aerobic pathway) (e.g., in P. denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in Salmonella typhimurium). The corresponding cobalt chelatases are not homologous. However, aerobic cobalt chelatase subunits CobN and CobS are homologous to Mg-chelatase subunits BchH and BchI, respectively. CobT, too, has been found to be remotely related to the third subunit of Mg-chelatase, BchD (involved in bacteriochlorophyll synthesis, e.g., in Rhodobacter capsulatus).
The CobS protein is a cobalamin-5-phosphate synthase that catyalzes the reactions:
- Adenosylcobinamide-GDP + alpha-ribazole-5'-P = adenosylcobalamin-5'-phosphate + GMP
- Adenosylcobinamide-GDP + alpha-ribazole = adenosylcobalamin + GMP
The protein product from these catalyses is associated with a large complex of proteins and is induced by cobinamide. CobS is involved in part III of cobalamin biosynthesis, one of the late steps in adenosylcobalamin synthesis that, together with CobU, CobT, and CobC proteins, defines the nucleotide loop assembly pathway.
CobU proteins are bifunctional cobalbumin biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity. The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape.
CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. CobW-like proteins include P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site.
The CbiA family of proteins consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from Salmonella typhimurium., and CobQ from Rhodobacter capsulatus. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III.
CbiD is an essential protein for cobalamin biosynthesis in both Salmonella typhimurium and Bacillus megaterium. A deletion mutant of CbiD suggests that this enzyme is involved in C-1 methylation and deacylation reactions required during the ring contraction process in the anaerobic pathway to cobalamin (similar role as CobF). The CbiD protein has a putative S-AdoMet binding site. CbiD has no counterpart in the aerobic pathway.
CbiG proteins are specific for anaerobic cobalamin biosynthesis. CbiG, which shows homology with CobE of the aerobic pathway, participates in the conversion of cobalt-precorrin 5 into cobalt-precorrin 6. CbiG is responsible for the opening of the delta-lactone ring and extrusion of the C2-unit. The aerobic pathway uses molecular oxygen to trigger the events at C-20 leading to contraction and expulsion of the C2-unit as acetic acid from a metal-free intermediate, whereas the anaerobic route involves the internal delivery of oxygen from a carboxylic acid terminus to C-20 followed by extrusion of the C2-unit as acetaldehyde, using cobalt complexes as substrates.
The CbiJ family of proteins includes the CobK and CbiJ precorrin-6x reductases EC 184.108.40.206. In the aerobic pathway, CobK catalyses the reduction of the macrocycle of precorrin-6X to produce precorrin-6Y; while in the anaerobic pathway CbiJ catalyses the reduction of the macrocycle of cobalt-precorrin-6X into cobalt-precorrin-6Y.
CbiM is a transmembrane cobalamin transporter.
The cobalt transport protein CbiN is part of the active cobalt transport system involved in uptake of cobalt into the cell involved with cobalamin biosynthesis (vitamin B12). It has been suggested that CbiN may function as the periplasmic binding protein component of the active cobalt transport system.
The CbiQ family consists of various cobalt transport proteins Most of which are found in Cobalamin (Vitamin B12) biosynthesis operons. In Salmonella the cbiN cbiQ (product CbiQ in this family) and cbiO are likely to form an active cobalt transport system.
The CbiX protein functions as a cobalt-chelatase in the anaerobic biosynthesis of cobalamin. It catalyses the insertion of cobalt into sirohydrochlorin. The structure of CbiX from Archaeoglobus fulgidus consists of a central mixed beta-sheet flanked by four alpha-helices, although it is about half the size of other Class II tetrapyrrole chelatases. The CbiX proteins found in archaea appear to be shorter than those found in eubacteria.
The CbiZ family of proteins includes CbiZ, which is involved in the salvage pathway of cobinamide in archaea. Archaea convert adenosylcobinamide (AdoCbi) into adenosylcobinamide phosphate (AdoCbi-P) in two steps. First, the amidohydrolase activity of CbiZ cleaves off the aminopropanol moiety of AdoCbi yielding adenosylcobyric acid (AdoCby); second, AdoCby is converted into AdoCbi-P by the action of adenosylcobinamide-phosphate synthase (CbiB). Adenosylcobyric acid is an intermediate of the de novo coenzyme B12 biosynthetic route.
- Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS (October 2003). "Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes". J. Biol. Chem. 278 (42): 41148–59. doi:10.1074/jbc.M305837200. PMID 12869542.
- Banerjee R (April 2006). "B12 trafficking in mammals: A for coenzyme escort service". ACS Chem. Biol. 1 (3): 149–59. doi:10.1021/cb6001174. PMID 17163662.
- Roessner CA, Santander PJ, Scott AI (2001). "Multiple biosynthetic pathways for vitamin B12: variations on a central theme". Vitam. Horm. 61: 267–97. doi:10.1016/s0083-6729(01)61009-4. PMID 11153269.
- Heldt D, Lawrence AD, Lindenmeyer M, Deery E, Heathcote P, Rigby SE, Warren MJ (August 2005). "Aerobic synthesis of vitamin B12: ring contraction and cobalt chelation". Biochem. Soc. Trans. 33 (Pt 4): 815–9. doi:10.1042/BST0330815. PMID 16042605.
- Roessner CA, Huang KX, Warren MJ, Raux E, Scott AI (June 2002). "Isolation and characterization of 14 additional genes specifying the anaerobic biosynthesis of cobalamin (vitamin B12) in Propionibacterium freudenreichii (P. shermanii)". Microbiology (Reading, Engl.) 148 (Pt 6): 1845–53. PMID 12055304.
- Raux E, Schubert HL, Warren MJ (December 2000). "Biosynthesis of cobalamin (vitamin B12): a bacterial conundrum". Cell. Mol. Life Sci. 57 (13-14): 1880–93. doi:10.1007/PL00000670. PMID 11215515.
- Woodson JD, Zayas CL, Escalante-Semerena JC (December 2003). "A new pathway for salvaging the coenzyme B12 precursor cobinamide in archaea requires cobinamide-phosphate synthase (CbiB) enzyme activity". J. Bacteriol. 185 (24): 7193–201. doi:10.1128/jb.185.24.7193-7201.2003. PMC 296239. PMID 14645280.
- Roth JR, Lawrence JG, Bobik TA (1996). "Cobalamin (coenzyme B12): synthesis and biological significance". Annu. Rev. Microbiol. 50: 137–81. doi:10.1146/annurev.micro.50.1.137. PMID 8905078.
- Fodje MN, Hansson A, Hansson M, Olsen JG, Gough S, Willows RD, Al-Karadaghi S (August 2001). "Interplay between an AAA module and an integrin I domain may regulate the function of magnesium chelatase". J. Mol. Biol. 311 (1): 111–22. doi:10.1006/jmbi.2001.4834. PMID 11469861.
- Maggio-Hall LA, Escalante-Semerena JC (October 1999). "In vitro synthesis of the nucleotide loop of cobalamin by Salmonella typhimurium enzymes". Proc. Natl. Acad. Sci. U.S.A. 96 (21): 11798–803. doi:10.1073/pnas.96.21.11798. PMC 18366. PMID 10518530.
- Maggio-Hall LA, Claas KR, Escalante-Semerena JC (May 2004). "The last step in coenzyme B(12) synthesis is localized to the cell membrane in bacteria and archaea". Microbiology (Reading, Engl.) 150 (Pt 5): 1385–95. doi:10.1099/mic.0.26952-0. PMID 15133100.
- Thompson TB, Thomas MG, Escalante-Semerena JC, Rayment I (May 1998). "Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3 A resolution,". Biochemistry 37 (21): 7686–95. doi:10.1021/bi973178f. PMID 9601028.
- Hashimoto Y, Nishiyama M, Horinouchi S, Beppu T (October 1994). "Nitrile hydratase gene from Rhodococcus sp. N-774 requirement for its downstream region for efficient expression". Biosci. Biotechnol. Biochem. 58 (10): 1859–65. doi:10.1271/bbb.58.1859. PMID 7765511.
- Zambelli B, Musiani F, Savini M, Tucker P, Ciurli S (March 2007). "Biochemical studies on Mycobacterium tuberculosis UreG and comparative modeling reveal structural and functional conservation among the bacterial UreG family". Biochemistry 46 (11): 3171–82. doi:10.1021/bi6024676. PMID 17309280.
- Pollich M, Klug G (August 1995). "Identification and sequence analysis of genes involved in late steps in cobalamin (vitamin B12) synthesis in Rhodobacter capsulatus". J. Bacteriol. 177 (15): 4481–7. PMC 177200. PMID 7635831.
- Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM (June 1993). "Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium". J. Bacteriol. 175 (11): 3303–16. PMC 204727. PMID 8501034.
- Roessner CA, Williams HJ, Scott AI (April 2005). "Genetically engineered production of 1-desmethylcobyrinic acid, 1-desmethylcobyrinic acid a,c-diamide, and cobyrinic acid a,c-diamide in Escherichia coli implies a role for CbiD in C-1 methylation in the anaerobic pathway to cobalamin". J. Biol. Chem. 280 (17): 16748–53. doi:10.1074/jbc.M501805200. PMID 15741157.
- Raux E, Lanois A, Warren MJ, Rambach A, Thermes C (October 1998). "Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon". Biochem. J. 335 (1): 159–66. PMC 1219764. PMID 9742225.
- Scott AI, Roessner CA (August 2002). "Biosynthesis of cobalamin (vitamin B(12))". Biochem. Soc. Trans. 30 (4): 613–20. doi:10.1042/bst0300613. PMID 12196148.
- Kajiwara Y, Santander PJ, Roessner CA, PÃ©rez LM, Scott AI (August 2006). "Genetically engineered synthesis and structural characterization of cobalt-precorrin 5A and -5B, two new intermediates on the anaerobic pathway to vitamin B12: definition of the roles of the CbiF and CbiG enzymes". J. Am. Chem. Soc. 128 (30): 9971–8. doi:10.1021/ja062940a. PMID 16866557.
- Kim W, Major TA, Whitman WB (December 2005). "Role of the precorrin 6-X reductase gene in cobamide biosynthesis in Methanococcus maripaludis". Archaea 1 (6): 375–84. doi:10.1155/2005/903614. PMC 2685584. PMID 16243778.
- Shearer N, Hinsley AP, Van Spanning RJ, Spiro S (November 1999). "Anaerobic growth of Paracoccus denitrificans requires cobalamin: characterization of cobK and cobJ genes". J. Bacteriol. 181 (22): 6907–13. PMC 94164. PMID 10559155.
- Roth, J. R.; Lawrence, J. G.; Rubenfield, M.; Kieffer-Higgins, S.; Church, G. M. (1993). "Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium". Journal of bacteriology 175 (11): 3303–3316. PMC 204727. PMID 8501034.
- Yin J, Xu LX, Cherney MM, Raux-Deery E, Bindley AA, Savchenko A, Walker JR, Cuff ME, Warren MJ, James MN (March 2006). "Crystal structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus". J. Struct. Funct. Genomics 7 (1): 37–50. doi:10.1007/s10969-006-9008-x. PMID 16835730.
- Brindley AA, Raux E, Leech HK, Schubert HL, Warren MJ (June 2003). "A story of chelatase evolution: identification and characterization of a small 13-15-kDa "ancestral" cobaltochelatase (CbiXS) in the archaea". J. Biol. Chem. 278 (25): 22388–95. doi:10.1074/jbc.M302468200. PMID 12686546.
- Woodson JD, Escalante-Semerena JC (March 2004). "CbiZ, an amidohydrolase enzyme required for salvaging the coenzyme B12 precursor cobinamide in archaea". Proc. Natl. Acad. Sci. U.S.A. 101 (10): 3591–6. doi:10.1073/pnas.0305939101. PMC 373507. PMID 14990804.
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.
CobW/HypB/UreG, nucleotide-binding domain Provide feedback
This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif [2,3]. HypB has GTPase activity and is a guanine nucleotide binding protein . It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression . UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins . This family of domains also contains P47K (P31521), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product (P29937), which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans .
Olson JW, Fu C, Maier RJ; , Mol Microbiol 1997;24:119-128.: The HypB protein from Bradyrhizobium japonicum can store nickel and is required for the nickel-dependent transcriptional regulation of hydrogenase. PUBMED:9140970 EPMC:9140970
Moncrief MB, Hausinger RP; , J Bacteriol 1997;179:4081-4086.: Characterization of UreG, identification of a UreD-UreF-UreG complex, and evidence suggesting that a nucleotide-binding site in UreG is required for in vivo metallocenter assembly of Klebsiella aerogenes urease. PUBMED:9209019 EPMC:9209019
Maier T, Jacobi A, Sauter M, Bock A; , J Bacteriol 1993;175:630-635.: The product of the hypB gene, which is required for nickel incorporation into hydrogenases, is a novel guanine nucleotide-binding protein. PUBMED:8423137 EPMC:8423137
Lee MH, Mulrooney SB, Renner MJ, Markowicz Y, Hausinger RP; , J Bacteriol 1992;174:4324-4330.: Klebsiella aerogenes urease gene cluster: sequence of ureD and demonstration that four accessory genes (ureD, ureE, ureF, and ureG) are involved in nickel metallocenter biosynthesis. PUBMED:1624427 EPMC:1624427
Crouzet J, Levy-Schil S, Cameron B, Cauchois L, Rigault S, Rouyez MC, Blanche F, Debussche L, Thibaut D; , J Bacteriol 1991;173:6074-6087.: Nucleotide sequence and genetic analysis of a 13.1-kilobase-pair Pseudomonas denitrificans DNA fragment containing five cob genes and identification of structural genes encoding Cob(I)alamin adenosyltransferase, cobyric acid synthase, and bifunctional cob PUBMED:1655697 EPMC:1655697
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003495
Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase [PUBMED:12869542]. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase [PUBMED:17163662].
There are at least two distinct cobalamin biosynthetic pathways in bacteria [PUBMED:11153269]:
- Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway [PUBMED:16042605]; found in Pseudomonas denitrificans and Rhodobacter capsulatus.
- Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis [PUBMED:12055304]; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii.
Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) [PUBMED:11215515]. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans.
CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis [PUBMED:12869542]. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids.
This entry represents CobW-like proteins, including P47K (SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression [PUBMED:7765511], and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site [PUBMED:17309280].
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AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes .
The clan contains the following 198 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_4 AAA_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_2 Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arch_ATPase Arf ArgK ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 Bac_DnaA CbiA CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DEAD DEAD_2 DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DUF1253 DUF1611 DUF2075 DUF2478 DUF258 DUF2791 DUF2813 DUF3584 DUF463 DUF815 DUF853 DUF87 DUF927 Dynamin_N Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GTP_EFTU GTP_EFTU_D2 GTP_EFTU_D4 Gtr1_RagA Guanylate_kin GvpD HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD Herpes_Helicase Herpes_ori_bp Herpes_TK IIGP IPPT IPT IstB_IS21 KaiC KAP_NTPase Kinesin Kinesin-relat_1 Kinesin-related KTI12 LpxK MCM MEDS Mg_chelatase Mg_chelatase_2 MipZ Miro MMR_HSR1 MobB MukB MutS_V Myosin_head NACHT NB-ARC NOG1 NTPase_1 ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK Rad17 Rad51 Ras RecA ResIII RHD3 RHSP RNA12 RNA_helicase RuvB_N SbcCD_C SecA_DEAD Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2_N Spore_IV_A SRP54 SRPRB Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulphotransf T2SE 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 UPF0079 UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YhjQ Zeta_toxin Zot
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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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Seed source:||Pfam-B_428 (release 4.0) & Pfam-B_1247 (release 5.4)|
|Author:||Bateman A, Mian N, Bashton M|
|Number in seed:||62|
|Number in full:||9942|
|Average length of the domain:||177.40 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||56.79 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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a FASTA-format file
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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 cobW domain has been found. There are 7 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.
Loading structure mapping...