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62  structures 4514  species 1  interaction 20629  sequences 135  architectures

Family: CbiA (PF01656)

Summary: CobQ/CobB/MinD/ParA nucleotide binding domain

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 "Cobalamin biosynthesis". More...

Cobalamin biosynthesis Edit Wikipedia article

CobD_Cbib
Identifiers
Symbol CobD_Cbib
Pfam PF03186
InterPro IPR004485
CobS
Identifiers
Symbol CobS
Pfam PF02654
InterPro IPR003805
CobT
Identifiers
Symbol CobT
Pfam PF06213
InterPro IPR006538
CobU
PDB 1cbu EBI.jpg
adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (cobu) from salmonella typhimurium
Identifiers
Symbol CobU
Pfam PF02283
Pfam clan CL0023
InterPro IPR003203
SCOP 1cbu
SUPERFAMILY 1cbu
cobW
PDB 1nij EBI.jpg
yjia protein
Identifiers
Symbol cobW
Pfam PF02492
Pfam clan CL0023
InterPro IPR003495
SCOP 1nij
SUPERFAMILY 1nij
CobW C terminal
PDB 1nij EBI.jpg
yjia protein
Identifiers
Symbol CobW_C
Pfam PF07683
InterPro IPR011629
SCOP 1nij
SUPERFAMILY 1nij
CbiA
PDB 1dah EBI.jpg
dethiobiotin synthetase complexed with 7,8-diamino-nonanoic acid, 5'-adenosyl-methylene-triphosphate, and manganese
Identifiers
Symbol CbiA
Pfam PF01656
Pfam clan CL0023
InterPro IPR002586
SCOP 1dts
SUPERFAMILY 1dts
CbiD
PDB 1sr8 EBI.jpg
structural genomics, 1.9a crystal structure of cobalamin biosynthesis protein (cbid) from archaeoglobus fulgidus
Identifiers
Symbol CbiD
Pfam PF01888
InterPro IPR002748
CbiG N terminus
Identifiers
Symbol CbiG_N
Pfam PF11760
InterPro IPR021744
CbiG central region
Identifiers
Symbol CbiG_mid
Pfam PF11761
InterPro IPR021745
CbiG C terminus
Identifiers
Symbol CbiG_C
Pfam PF01890
InterPro IPR002750
CbiJ
Identifiers
Symbol CbiJ
Pfam PF02571
InterPro IPR003723
CbiM
Identifiers
Symbol CbiM
Pfam PF01891
Pfam clan CL0315
InterPro IPR002751
TCDB 3.A.1.23
OPM superfamily 347
OPM protein 4m58
CbiN
Identifiers
Symbol CbiN
Pfam PF02553
InterPro IPR003705
TCDB 3.A.1
CbiQ
Identifiers
Symbol CbiQ
Pfam PF02361
InterPro IPR003339
TCDB 3.A.1
CbiX
PDB 1tjn EBI.jpg
crystal structure of hypothetical protein af0721 from archaeoglobus fulgidus
Identifiers
Symbol CbiX
Pfam PF01903
Pfam clan CL0043
InterPro IPR002762
CbiZ
Identifiers
Symbol CbiZ
Pfam PF01955
InterPro IPR002808

In molecular biology, cobalamin biosynthesis is the synthesis of cobalamin (vitamin B12).

Cobalamin

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.[1] In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase.[2]

Pathways of cobalamin biosynthesis

There are at least two distinct cobalamin biosynthetic pathways in bacteria:[3]

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).[6]

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.

CbiB/CobD

The CbiB or CobD protein converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group. It is part of the cob operon.[7]

CobT/CobN/CobS

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).[8][9] 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.[9] 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).[9]

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.[10][11]

CobU

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.[12]

CobW

CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis.[1] 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,[13] and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site.[14]

CbiA

The CbiA family of proteins consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from Salmonella typhimurium.,[15] and CobQ from Rhodobacter capsulatus.[16] 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.[15]

CbiD

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).[17] The CbiD protein has a putative S-AdoMet binding site.[18] CbiD has no counterpart in the aerobic pathway.

CbiG

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.[19] CbiG is responsible for the opening of the delta-lactone ring and extrusion of the C2-unit.[20] 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.[20]

CbiJ

The CbiJ family of proteins includes the CobK and CbiJ precorrin-6x reductases EC 1.3.1.54. 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.[21][22]

CbiM

CbiM is a transmembrane cobalamin transporter.

CbiN

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.[16]

CbiQ

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.[23]

CbiX

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.[24] The CbiX proteins found in archaea appear to be shorter than those found in eubacteria.[25]

CbiZ

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.[26]

References

  1. ^ a b 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. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ 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. 
  5. ^ 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. 
  6. ^ 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. 
  7. ^ 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. 
  8. ^ 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. 
  9. ^ a b c 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. 
  10. ^ 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. 
  11. ^ 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. 
  12. ^ 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. 
  13. ^ 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. 
  14. ^ 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. 
  15. ^ a b 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. 
  16. ^ a b 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. 
  17. ^ 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. 
  18. ^ 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. 
  19. ^ 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. 
  20. ^ a b Kajiwara Y, Santander PJ, Roessner CA, Pérez 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. 
  21. ^ 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. 
  22. ^ 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. 
  23. ^ 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.  edit
  24. ^ 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. 
  25. ^ 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. 
  26. ^ 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 article incorporates text from the public domain Pfam and InterPro IPR004485

This article incorporates text from the public domain Pfam and InterPro IPR003805

This article incorporates text from the public domain Pfam and InterPro IPR006538

This article incorporates text from the public domain Pfam and InterPro IPR003203

This article incorporates text from the public domain Pfam and InterPro IPR003495

This article incorporates text from the public domain Pfam and InterPro IPR011629

This article incorporates text from the public domain Pfam and InterPro IPR002586

This article incorporates text from the public domain Pfam and InterPro IPR002748

This article incorporates text from the public domain Pfam and InterPro IPR002750

This article incorporates text from the public domain Pfam and InterPro IPR003723

This article incorporates text from the public domain Pfam and InterPro IPR002751

This article incorporates text from the public domain Pfam and InterPro IPR003705

This article incorporates text from the public domain Pfam and InterPro IPR003339

This article incorporates text from the public domain Pfam and InterPro IPR002762

This article incorporates text from the public domain Pfam and InterPro IPR002808

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.

CobQ/CobB/MinD/ParA nucleotide binding domain Provide feedback

This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA P29946 and CbiP Q05597 from S.typhimurium [4] and CobQ Q52686 from R. capsulatus [3]. 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. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [4]. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family [6].

Literature references

  1. Raux E, Lanois A, Warren MJ, Rambach A, Thermes C; , Biochem J 1998;335:159-166.: Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon. PUBMED:9742225 EPMC:9742225

  2. Raux E, Lanois A, Rambach A, Warren MJ, Thermes C; , Biochem J 1998;335:167-173.: Cobalamin (vitamin B12) biosynthesis: functional characterization of the Bacillus megaterium cbi genes required to convert uroporphyrinogen III into cobyrinic acid a,c-diamide. PUBMED:9742226 EPMC:9742226

  3. Pollich M, Klug G; , J Bacteriol 1995;177:4481-4487.: Identification and sequence analysis of genes involved in late steps in cobalamin (vitamin B12) synthesis in Rhodobacter capsulatus. PUBMED:7635831 EPMC:7635831

  4. Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM; , J Bacteriol 1993;175:3303-3316.: Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium. PUBMED:8501034 EPMC:8501034

  5. Galperin MY, Grishin NV; , Proteins 2000;41:238-247.: The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase. PUBMED:10966576 EPMC:10966576

  6. Motallebi-Veshareh M, Rouch DA, Thomas CM; , Mol Microbiol 1990;4:1455-1463.: A family of ATPases involved in active partitioning of diverse bacterial plasmids. PUBMED:2149583 EPMC:2149583


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002586

This domain is found in various cobyrinic acid a,c-diamide synthases. These include CbiA (SWISSPROT) and CbiP (SWISSPROT) from S. typhimurium [PUBMED:8501034], and CobQ (SWISSPROT) from R. capsulatus [PUBMED:7635831]. 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. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria [PUBMED:8501034].

The domain is also found in dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family [PUBMED:2149583].

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 P-loop_NTPase (CL0023), which has the following description:

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes [2].

The clan contains the following 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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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

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 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: Pfam-B_782 (release 4.1)
Previous IDs: CBIA;
Type: Domain
Author: Bashton M, Bateman A, Griffiths-Jones SR
Number in seed: 79
Number in full: 20629
Average length of the domain: 208.60 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 65.21 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.7 21.7
Trusted cut-off 21.7 21.7
Noise cut-off 21.6 21.6
Model length: 195
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

Sunburst controls

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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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Tree controls

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

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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.

Interactions

There is 1 interaction for this family. More...

CbiA

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 CbiA domain has been found. There are 62 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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