Protein GFF4127 in Marinobacter adhaerens HP15
Annotation: FitnessBrowser__Marino:GFF4127
Length: 362 amino acids
Source: Marino in FitnessBrowser
Candidate for 31 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 |
| myo-inositol catabolism | PGA1_c07320 | lo | Inositol transport system ATP-binding protein (characterized) | 31% | 90% | 107.8 | 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
Fitness BLAST: loading...
Sequence
MDSDLFCEGLVRRFGSNAAVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGD
IHIRGERMNDVPPNRRPVNMVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLE
QVGLPDLEHRNPQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHL
QKQFGTTFVYITHDQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVGDNNR
LSGELVSVRDSLAELRLDDGVLVQGRVASDNLQAGHRAELYIRPESLVLSGDALSPGFSS
MQAKVRTTLFDGANSRVEAETCGQPVYARLPQDGSAPRLSVDSSIRLAWNPSLARVFGAE
SL
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Links
Downloads
Related tools
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