GapMind for catabolism of small carbon sources

 

Protein WP_010932070.1 in Chlorobaculum tepidum TLS

Annotation: NCBI__GCF_000006985.1:WP_010932070.1

Length: 651 amino acids

Source: GCF_000006985.1 in NCBI

Candidate for 15 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 40% 84% 148.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 40% 84% 148.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 41% 92% 143.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 41% 92% 143.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
L-glutamate catabolism gltL med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 41% 92% 143.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
L-arginine catabolism artP lo AotP aka PA0892, component of Arginine/ornithine (but not lysine) porter (characterized) 36% 94% 143.3 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 38% 86% 142.1 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 34% 94% 139.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
L-histidine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 35% 93% 138.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
L-lysine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 35% 93% 138.7 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 35% 91% 135.2 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 35% 85% 134.8 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
2'-deoxyinosine catabolism nupA lo Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized) 30% 62% 114.4 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 31% 91% 100.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7
L-phenylalanine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale) 31% 91% 100.9 Macrolide export ATP-binding/permease protein MacB; EC 7.6.2.- 39% 443.7

Sequence Analysis Tools

View WP_010932070.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MIEIVNVTKTYRIGESSVKALDGVSLTIGQGEFVAIMGASGSGKSTLMHILGLLDVPDTG
QYRLMGKEVSRMSDDELAGIRNNVAGFVFQQFHLLSRMSTIDNVVLPCIYSGQRGDFRKD
ALKRLEMVGLAQRSDHRPNQMSGGEQQRVAIARALIRDPMLIFADEPTGNLDTKNSHEIM
RILTDLHRQGKTIIMVTHETDIAEFADRVITMKDGVVVDDRKKQDARLNPQMPQGGMEAA
HSALFQPSRLLGFVVQAFQSIASNKIRTFLSVLGILVGVASVIAMMALGTGAKASMEEQL
KSMGSNLLSVRGGSAKIGGASQGFGTVTRFTEKDAAAIQAIPNLIDHVSGDVTGSGQLVY
LDKNWSTSVEGVDYDYGEMRAAIPTVGRWFTREEIQERAKVAILGTTVAMQLFGDADPVD
KIIKINRINFRVIGVAPAKGFAGPRDQDDVVYIPVSTAMYRVLGKLYLDGIYVEVSSAEN
IAPATQAIDALIRKRHKLAADDQDSFNIRDMTQFQQMLSATTQTMSMLLGSIAAISLVVG
GIGIMNIMLVSVTERTREIGLRKAIGARKGDIMLQFLIESVGMTLSGGIIGIVVGVGVSV
MLSAFAGWAVKTSMFSVVLATGFSVLIGLFFGLWPARKAAALKPVEALRYE

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory