Protein WP_013835621.1 in Thiomicrospira cyclica ALM1
Annotation: NCBI__GCF_000214825.1:WP_013835621.1
Length: 234 amino acids
Source: GCF_000214825.1 in NCBI
Candidate for 38 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-asparagine catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 38% | 84% | 141.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-aspartate catabolism | peb1C | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 38% | 84% | 141.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-glutamate catabolism | gltL | lo | PEB1C, component of Uptake system for glutamate and aspartate (characterized) | 38% | 84% | 141.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-asparagine catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 35% | 87% | 139.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-aspartate catabolism | bztD | lo | BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) | 35% | 87% | 139.4 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-histidine catabolism | BPHYT_RS24015 | lo | ABC transporter related (characterized, see rationale) | 38% | 90% | 139 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
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) | 37% | 85% | 137.5 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-asparagine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 81% | 136.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-aspartate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 81% | 136.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-glutamate catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 81% | 136.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-histidine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 81% | 136.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-leucine catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 81% | 136.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-proline catabolism | aapP | lo | AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) | 38% | 81% | 136.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 36% | 86% | 136.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 36% | 86% | 136.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-histidine catabolism | PA5503 | lo | Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) | 34% | 59% | 136.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-arginine catabolism | artP | lo | Arginine transport ATP-binding protein ArtM (characterized) | 35% | 91% | 131.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-histidine catabolism | bgtA | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 36% | 87% | 130.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-lysine catabolism | hisP | lo | BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) | 36% | 87% | 130.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
D-alanine catabolism | Pf6N2E2_5405 | lo | ABC transporter for D-Alanine, ATPase component (characterized) | 35% | 86% | 129 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
D-maltose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 31% | 56% | 128.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
trehalose catabolism | thuK | lo | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 31% | 56% | 128.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 60% | 128.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-asparagine catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 37% | 86% | 128.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-aspartate catabolism | aatP | lo | Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) | 37% | 86% | 128.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 37% | 60% | 128.3 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 52% | 124 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 34% | 56% | 121.7 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 34% | 53% | 119 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-tryptophan catabolism | ecfA2 | lo | Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) | 35% | 77% | 118.6 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
D-glucosamine (chitosamine) catabolism | AO353_21725 | lo | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 34% | 87% | 118.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-isoleucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 108.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-leucine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 108.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-phenylalanine catabolism | livG | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 108.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-proline catabolism | HSERO_RS00895 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 108.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-serine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 108.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
L-tyrosine catabolism | Ac3H11_1693 | lo | ABC transporter ATP-binding protein (characterized, see rationale) | 31% | 93% | 108.2 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
D-mannose catabolism | TM1749 | lo | TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 31% | 69% | 99.8 | lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- | 54% | 245.7 |
Sequence Analysis Tools
View WP_013835621.1 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
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Sequence
MSKSDSVILQAQGLSQVFQEGLLATPVLHDINFSLHAGERLAIVGASGSGKSTLLHLLAG
LAQPSEGEVFLQGQAFASLSEAQRSQLRNQHLGFVYQFHYLLAELTALENVMLPLRIARV
PAKQAQHKAQELLAAVGLAARADHKPSELSGGERQRVAIARALITEPACILADEPTGNLD
SKSAEQVLALMLNLNEQFNTALLVVTHDLQLAKQLGNKIELVDGQIQRDNDANA
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:
- ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
- HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.
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:
- ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
- ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
- HMMer finds a hit (regardless of coverage or other bits).
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:
- our ignorance of proteins' functions,
- omissions in the gene models,
- frame-shift errors in the genome sequence, or
- the organism lacks the pathway.
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