Protein GFF4127 in Marinobacter adhaerens HP15
Annotation: FitnessBrowser__Marino:GFF4127
Length: 362 amino acids
Source: Marino in FitnessBrowser
Candidate for 30 steps in catabolism of small carbon sources
| Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
|---|
| putrescine catabolism | potA | med | PotG aka B0855, component of Putrescine porter (characterized) | 40% | 93% | 238.4 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-maltose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 45% | 81% | 236.9 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| trehalose catabolism | thuK | med | Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) | 45% | 81% | 236.9 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| sucrose catabolism | thuK | med | ABC transporter (characterized, see rationale) | 43% | 85% | 231.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-maltose catabolism | malK | med | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 42% | 80% | 219.9 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| lactose catabolism | lacK | med | ABC transporter for Lactose, ATPase component (characterized) | 42% | 81% | 219.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| trehalose catabolism | treV | med | TreV, component of Trehalose porter (characterized) | 44% | 75% | 214.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-mannitol catabolism | mtlK | med | ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) | 42% | 80% | 210.3 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-sorbitol (glucitol) catabolism | mtlK | med | ABC transporter for D-Sorbitol, ATPase component (characterized) | 45% | 71% | 207.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-maltose catabolism | musK | med | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 41% | 74% | 203 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 51% | 60% | 231.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-cellobiose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 98% | 228 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| L-fucose catabolism | SM_b21106 | lo | ABC transporter for L-Fucose, ATPase component (characterized) | 39% | 78% | 228 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-glucose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 98% | 228 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| lactose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 98% | 228 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-maltose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 98% | 228 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| sucrose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 98% | 228 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| trehalose catabolism | gtsD | lo | Sugar ABC transporter ATP-binding protein (characterized, see rationale) | 39% | 98% | 228 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 38% | 91% | 226.5 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-mannose catabolism | TT_C0211 | lo | Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) | 40% | 88% | 224.6 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 38% | 86% | 223.4 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-cellobiose catabolism | SMc04256 | lo | ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) | 38% | 97% | 221.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 38% | 100% | 220.7 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-maltose catabolism | malK_Bb | lo | ABC-type maltose transport, ATP binding protein (characterized, see rationale) | 40% | 80% | 217.2 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 91% | 208 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 91% | 208 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 38% | 91% | 208 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| N-acetyl-D-glucosamine catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 45% | 64% | 204.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| D-glucosamine (chitosamine) catabolism | SMc02869 | lo | N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) | 45% | 64% | 204.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
| L-tryptophan catabolism | ecfA1 | lo | Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) | 37% | 79% | 137.1 | Uncharacterized ABC transporter ATP-binding protein YdcT | 49% | 249.2 |
Sequence Analysis Tools
View GFF4127 at FitnessBrowser
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
MDSDLFCEGLVRRFGSNAAVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGD
IHIRGERMNDVPPNRRPVNMVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLE
QVGLPDLEHRNPQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHL
QKQFGTTFVYITHDQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVGDNNR
LSGELVSVRDSLAELRLDDGVLVQGRVASDNLQAGHRAELYIRPESLVLSGDALSPGFSS
MQAKVRTTLFDGANSRVEAETCGQPVYARLPQDGSAPRLSVDSSIRLAWNPSLARVFGAE
SL
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