Protein WP_057507534.1 in Stenotrophomonas chelatiphaga DSM 21508
Annotation: NCBI__GCF_001431535.1:WP_057507534.1
Length: 229 amino acids
Source: GCF_001431535.1 in NCBI
Candidate for 40 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| D-glucosamine (chitosamine) catabolism | AO353_21725 | med | ABC transporter for D-Glucosamine, putative ATPase component (characterized) | 40% | 86% | 145.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 35% | 80% | 139.4 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 60% | 135.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 60% | 135.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 60% | 135.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 60% | 135.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 60% | 135.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 33% | 60% | 135.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-maltose catabolism | malK | lo | Maltose-transporting ATPase (EC 3.6.3.19) (characterized) | 37% | 58% | 134.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-sorbitol (glucitol) catabolism | mtlK | lo | ABC transporter for D-Sorbitol, ATPase component (characterized) | 36% | 65% | 134 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-mannitol catabolism | mtlK | lo | SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) | 36% | 65% | 133.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 36% | 53% | 131.7 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| trehalose catabolism | thuK | lo | Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) | 38% | 50% | 131.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-mannose catabolism | TM1750 | lo | TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) | 32% | 66% | 127.5 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 34% | 60% | 126.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 36% | 60% | 125.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 36% | 60% | 125.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 36% | 60% | 125.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 36% | 60% | 125.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 36% | 59% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 36% | 59% | 123.6 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-cellobiose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 119.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-glucose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 119.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| lactose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 119.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-maltose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 119.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| sucrose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 119.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| sucrose catabolism | thuK | lo | ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) | 35% | 57% | 119.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| trehalose catabolism | aglK' | lo | Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) | 35% | 58% | 119.8 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 33% | 57% | 113.2 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| L-alanine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 34% | 83% | 109 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| L-histidine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 34% | 83% | 109 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| L-leucine catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 34% | 83% | 109 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| L-proline catabolism | natE | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 34% | 83% | 109 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| L-serine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 34% | 83% | 109 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| L-threonine catabolism | braG | lo | NatE aka LivF aka SLR1881, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) | 34% | 83% | 109 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-cellobiose catabolism | TM0027 | lo | TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) | 31% | 88% | 106.3 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| L-isoleucine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 81% | 105.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| L-valine catabolism | natE | lo | NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) | 31% | 81% | 105.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| D-alanine catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 32% | 80% | 95.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
| L-proline catabolism | AZOBR_RS08250 | lo | Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) | 32% | 80% | 95.9 | Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- | 48% | 216.1 |
Sequence Analysis Tools
View WP_057507534.1 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
MSTLVSLRSITKTYQRGPEQVKVLHGIDLDIETGDFVALMGPSGSGKTTLLNLIGGLDSP
SGGEITIEGERIDQMGGGQLSTWRSHHVGFVFQFYNLMPMLTAQKNVELPLLLTHLGAAQ
RRRNAEIALTLVGLADRRSHRPNELSGGQQQRVAIARAIVSDPTFLICDEPTGDLDRQSA
EEILQLLQQLNREHGKTIIMVTHDPKAAEYATHTVHLDKGELADAPLAH
This GapMind analysis is from Sep 24 2021. 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