Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
6  structures 3916  species 0  interactions 4935  sequences 25  architectures

Family: CobU (PF02283)

Summary: Cobinamide kinase / cobinamide phosphate guanyltransferase

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
SymbolCobD_Cbib
PfamPF03186
InterProIPR004485
CobS
Identifiers
SymbolCobS
PfamPF02654
InterProIPR003805
CobT
Identifiers
SymbolCobT
PfamPF06213
InterProIPR006538
CobU
PDB 1cbu EBI.jpg
adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase (cobu) from salmonella typhimurium
Identifiers
SymbolCobU
PfamPF02283
Pfam clanCL0023
InterProIPR003203
SCOP21cbu / SCOPe / SUPFAM
cobW
PDB 1nij EBI.jpg
yjia protein
Identifiers
SymbolcobW
PfamPF02492
Pfam clanCL0023
InterProIPR003495
SCOP21nij / SCOPe / SUPFAM
CobW C terminal
PDB 1nij EBI.jpg
yjia protein
Identifiers
SymbolCobW_C
PfamPF07683
InterProIPR011629
SCOP21nij / SCOPe / SUPFAM
CbiA
PDB 1dah EBI.jpg
dethiobiotin synthetase complexed with 7,8-diamino-nonanoic acid, 5'-adenosyl-methylene-triphosphate, and manganese
Identifiers
SymbolCbiA
PfamPF01656
Pfam clanCL0023
InterProIPR002586
SCOP21dts / SCOPe / SUPFAM
CbiD
PDB 1sr8 EBI.jpg
structural genomics, 1.9a crystal structure of cobalamin biosynthesis protein (cbid) from archaeoglobus fulgidus
Identifiers
SymbolCbiD
PfamPF01888
InterProIPR002748
CbiG N terminus
Identifiers
SymbolCbiG_N
PfamPF11760
InterProIPR021744
CbiG central region
Identifiers
SymbolCbiG_mid
PfamPF11761
InterProIPR021745
CbiG C terminus
Identifiers
SymbolCbiG_C
PfamPF01890
InterProIPR002750
CbiJ
Identifiers
SymbolCbiJ
PfamPF02571
InterProIPR003723
CbiM
Identifiers
SymbolCbiM
PfamPF01891
Pfam clanCL0315
InterProIPR002751
CbiN
Identifiers
SymbolCbiN
PfamPF02553
InterProIPR003705
TCDB3.A.1
CbiQ
Identifiers
SymbolCbiQ
PfamPF02361
InterProIPR003339
TCDB3.A.1

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 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]

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]

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.

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]

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 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 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]

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 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 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]

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 is an intergral membrane protein which is involved in cobalamin synthesis, its exact function in unknown.

The cobalt transport protein CbiN is part of the active cobalt transport system involved in uptake of cobalt in to 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]

References

  1. ^ a b Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ Banerjee R (2006). "B12 trafficking in mammals: A for coenzyme escort service". ACS Chem. Biol. 1 (3): 149–59. doi:10.1021/cb6001174. PMID 17163662. {{cite journal}}: Unknown parameter |month= ignored (help)
  3. ^ Roessner CA, Santander PJ, Scott AI (2001). "Multiple biosynthetic pathways for vitamin B12: variations on a central theme". Vitam. Horm. 61: 267–97. PMID 11153269.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ Heldt D, Lawrence AD, Lindenmeyer M, Deery E, Heathcote P, Rigby SE, Warren MJ (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  5. ^ Roessner CA, Huang KX, Warren MJ, Raux E, Scott AI (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  6. ^ Raux E, Schubert HL, Warren MJ (2000). "Biosynthesis of cobalamin (vitamin B12): a bacterial conundrum". Cell. Mol. Life Sci. 57 (13–14): 1880–93. PMID 11215515. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  7. ^ Woodson JD, Zayas CL, Escalante-Semerena JC (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. PMC 296239. PMID 14645280. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  9. ^ a b c Fodje MN, Hansson A, Hansson M, Olsen JG, Gough S, Willows RD, Al-Karadaghi S (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  10. ^ Maggio-Hall LA, Escalante-Semerena JC (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. PMC 18366. PMID 10518530. {{cite journal}}: Unknown parameter |month= ignored (help)
  11. ^ Maggio-Hall LA, Claas KR, Escalante-Semerena JC (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. PMID 15133100. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  12. ^ Thompson TB, Thomas MG, Escalante-Semerena JC, Rayment I (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  13. ^ Hashimoto Y, Nishiyama M, Horinouchi S, Beppu T (1994). "Nitrile hydratase gene from Rhodococcus sp. N-774 requirement for its downstream region for efficient expression". Biosci. Biotechnol. Biochem. 58 (10): 1859–65. PMID 7765511. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  14. ^ Zambelli B, Musiani F, Savini M, Tucker P, Ciurli S (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  15. ^ a b Pollich M, Klug G (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. {{cite journal}}: Unknown parameter |month= ignored (help)
  16. ^ a b Roth JR, Lawrence JG, Rubenfield M, Kieffer-Higgins S, Church GM (1993). "Characterization of the cobalamin (vitamin B12) biosynthetic genes of Salmonella typhimurium". J. Bacteriol. 175 (11): 3303–16. PMC 204727. PMID 8501034. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  17. ^ Roessner CA, Williams HJ, Scott AI (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  18. ^ Raux E, Lanois A, Warren MJ, Rambach A, Thermes C (1998). "Cobalamin (vitamin B12) biosynthesis: identification and characterization of a Bacillus megaterium cobI operon". Biochem. J. 335 ( Pt 1): 159–66. PMC 1219764. PMID 9742225. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  19. ^ Scott AI, Roessner CA (2002). "Biosynthesis of cobalamin (vitamin B(12))". Biochem. Soc. Trans. 30 (4): 613–20. doi:10.1042/. PMID 12196148. {{cite journal}}: Check |doi= value (help); Unknown parameter |month= ignored (help)
  20. ^ a b Kajiwara Y, Santander PJ, Roessner CA, Pérez LM, Scott AI (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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  21. ^ Kim W, Major TA, Whitman WB (2005). "Role of the precorrin 6-X reductase gene in cobamide biosynthesis in Methanococcus maripaludis". Archaea. 1 (6): 375–84. PMC 2685584. PMID 16243778. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  22. ^ Shearer N, Hinsley AP, Van Spanning RJ, Spiro S (1999). "Anaerobic growth of Paracoccus denitrificans requires cobalamin: characterization of cobK and cobJ genes". J. Bacteriol. 181 (22): 6907–13. PMC 94164. PMID 10559155. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
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 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.

Cobinamide kinase / cobinamide phosphate guanyltransferase Provide feedback

This family is composed of a group of bifunctional cobalamin 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 [1].

Literature references

  1. Thompson TB, Thomas MG, Escalante-Semerena JC, Rayment I; , Biochemistry 1998;37:7686-7695.: Three-dimensional structure of adenosylcobinamide kinase/adenosylcobinamide phosphate guanylyltransferase from Salmonella typhimurium determined to 2.3 A resolution,. PUBMED:9601028 EPMC:9601028


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003203

This family is composed of a group of bifunctional cobalamin 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 [ PUBMED:9601028 ].

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...

Loading domain graphics...

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 245 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_5 AAA_6 AAA_7 AAA_8 AAA_9 AAA_PrkA ABC_ATPase ABC_tran ABC_tran_Xtn Adeno_IVa2 Adenylsucc_synt ADK AFG1_ATPase AIG1 APS_kinase Arf ArsA_ATPase ATP-synt_ab ATP_bind_1 ATP_bind_2 ATPase ATPase_2 Bac_DnaA BCA_ABC_TP_C Beta-Casp bpMoxR BrxC_BrxD BrxL_ATPase Cas_Csn2 Cas_St_Csn2 CbiA CBP_BcsQ CDC73_C CENP-M CFTR_R CLP1_P CMS1 CoaE CobA_CobO_BtuR CobU cobW CPT CSM2 CTP_synth_N Cytidylate_kin Cytidylate_kin2 DAP3 DEAD DEAD_2 divDNAB DLIC DNA_pack_C DNA_pack_N DNA_pol3_delta DNA_pol3_delta2 DnaB_C dNK DO-GTPase1 DO-GTPase2 DUF1611 DUF2075 DUF2326 DUF2478 DUF257 DUF2813 DUF3584 DUF463 DUF4914 DUF5906 DUF6079 DUF815 DUF835 DUF87 DUF927 Dynamin_N Dynein_heavy Elong_Iki1 ELP6 ERCC3_RAD25_C Exonuc_V_gamma FeoB_N Fer4_NifH Flavi_DEAD FTHFS FtsK_SpoIIIE G-alpha Gal-3-0_sulfotr GBP GBP_C GpA_ATPase GpA_nuclease GTP_EFTU Gtr1_RagA Guanylate_kin GvpD_P-loop HDA2-3 Helicase_C Helicase_C_2 Helicase_C_4 Helicase_RecD HerA_C Herpes_Helicase Herpes_ori_bp Herpes_TK HydF_dimer HydF_tetramer Hydin_ADK IIGP IPPT IPT iSTAND IstB_IS21 KAP_NTPase KdpD Kinase-PPPase Kinesin KTI12 LAP1_C LpxK MCM MeaB MEDS Mg_chelatase Microtub_bd MipZ MMR_HSR1 MMR_HSR1_C MobB MukB Mur_ligase_M MutS_V Myosin_head NACHT NAT_N NB-ARC NOG1 NTPase_1 NTPase_P4 ORC3_N P-loop_TraG ParA Parvo_NS1 PAXNEB PduV-EutP PhoH PIF1 Ploopntkinase1 Ploopntkinase2 Ploopntkinase3 Podovirus_Gp16 Polyoma_lg_T_C Pox_A32 PPK2 PPV_E1_C PRK PSY3 Rad17 Rad51 Ras RecA ResIII RHD3_GTPase RhoGAP_pG1_pG2 RHSP RNA12 RNA_helicase Roc RsgA_GTPase RuvB_N SbcC_Walker_B SecA_DEAD Senescence Septin Sigma54_activ_2 Sigma54_activat SKI SMC_N SNF2-rel_dom SpoIVA_ATPase Spore_III_AA SRP54 SRPRB SulA Sulfotransfer_1 Sulfotransfer_2 Sulfotransfer_3 Sulfotransfer_4 Sulfotransfer_5 Sulphotransf SWI2_SNF2 T2SSE T4SS-DNA_transf TerL_ATPase Terminase_3 Terminase_6N Thymidylate_kin TIP49 TK TmcA_N TniB Torsin TraG-D_C tRNA_lig_kinase TrwB_AAD_bind TsaE UvrB UvrD-helicase UvrD_C UvrD_C_2 Viral_helicase1 VirC1 VirE YqeC Zeta_toxin Zot

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 and the UniProtKB sequence database. More...

View options

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
(112)
Full
(4935)
Representative proteomes UniProt
(22262)
RP15
(571)
RP35
(2461)
RP55
(5157)
RP75
(9073)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(112)
Full
(4935)
Representative proteomes UniProt
(22262)
RP15
(571)
RP35
(2461)
RP55
(5157)
RP75
(9073)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(112)
Full
(4935)
Representative proteomes UniProt
(22262)
RP15
(571)
RP35
(2461)
RP55
(5157)
RP75
(9073)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Pfam-B_7022 (release 5.2)
Previous IDs: COBU;
Type: Domain
Sequence Ontology: SO:0000417
Author: Mian N , Bateman A
Number in seed: 112
Number in full: 4935
Average length of the domain: 162.2 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 80.03 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.2
Noise cut-off 26.9 26.9
Model length: 170
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

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

Loading...

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.

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 CobU domain has been found. There are 6 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...