Protein WP_022669727.1 in Hippea alviniae EP5-r
Annotation: NCBI__GCF_000420385.1:WP_022669727.1
Length: 424 amino acids
Source: GCF_000420385.1 in NCBI
Candidate for 30 steps in catabolism of small carbon sources
Pathway | Step | Score | Similar to | Id. | Cov. | Bits | Other hit | Other id. | Other bits |
L-histidine catabolism | Ac3H11_2560 | lo | ABC transporter for L-Histidine, ATPase component (characterized) | 38% | 100% | 185.7 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
L-proline catabolism | opuBA | lo | BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) | 36% | 68% | 159.1 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
D-maltose catabolism | malK1 | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 39% | 59% | 158.7 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
trehalose catabolism | thuK | lo | MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) | 39% | 59% | 158.7 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
L-proline catabolism | proV | lo | glycine betaine/l-proline transport atp-binding protein prov (characterized) | 40% | 60% | 153.3 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
L-histidine catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 40% | 84% | 148.3 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
L-proline catabolism | hutV | lo | HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) | 40% | 84% | 148.3 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
D-maltose catabolism | malK_Sm | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 36% | 65% | 146.7 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
trehalose catabolism | malK | lo | MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) | 36% | 65% | 146.7 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
L-arabinose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 99% | 145.2 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
D-fructose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 99% | 145.2 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
sucrose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 99% | 145.2 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
D-xylose catabolism | araV | lo | AraV, component of Arabinose, fructose, xylose porter (characterized) | 31% | 99% | 145.2 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
D-maltose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 62% | 142.9 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
D-maltose catabolism | thuK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 62% | 142.9 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
sucrose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 62% | 142.9 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
trehalose catabolism | aglK | lo | ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) | 39% | 62% | 142.9 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
D-maltose catabolism | malK_Aa | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 32% | 71% | 140.2 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
L-arabinose catabolism | xacK | lo | Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) | 36% | 61% | 139 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
xylitol catabolism | HSERO_RS17020 | lo | ABC-type sugar transport system, ATPase component protein (characterized, see rationale) | 39% | 53% | 137.9 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
L-arabinose catabolism | xacJ | lo | Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) | 34% | 63% | 137.5 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
D-glucosamine (chitosamine) catabolism | SM_b21216 | lo | ABC transporter for D-Glucosamine, ATPase component (characterized) | 34% | 74% | 136.3 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
D-maltose catabolism | malK | lo | ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) | 33% | 71% | 135.2 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
lactose catabolism | lacK | lo | LacK, component of Lactose porter (characterized) | 40% | 57% | 134.8 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
D-maltose catabolism | musK | lo | ABC-type maltose transporter (EC 7.5.2.1) (characterized) | 36% | 61% | 134.4 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
xylitol catabolism | Dshi_0546 | lo | ABC transporter for Xylitol, ATPase component (characterized) | 33% | 85% | 133.7 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
L-asparagine catabolism | bgtA | lo | ATPase (characterized, see rationale) | 34% | 75% | 112.8 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
L-aspartate catabolism | bgtA | lo | ATPase (characterized, see rationale) | 34% | 75% | 112.8 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
glycerol catabolism | glpS | lo | ABC transporter for Glycerol, ATPase component 1 (characterized) | 35% | 54% | 110.5 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
glycerol catabolism | glpT | lo | GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) | 30% | 60% | 107.5 | Aliphatic sulfonates import ATP-binding protein SsuB; EC 7.6.2.- | 41% | 193.7 |
Sequence Analysis Tools
View WP_022669727.1 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
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Sequence
MEIIKLENINMIFPISKSESLTVLENISLSIEEGKIVSILGPSGCGKSTLLRIITGLLKP
TKGKVFYKGKVQSGVNDKMAMVFQNFALFPWKTVWDNIAIGIRNREIRNKDEMIKRVIDI
VGLEGFEDVYPKSLSGGMKQRVGIARALVSNPEILCMDEPFSALDVLTAENLREELMDLW
LSRKTSLKGIVIVTHNITEAVYMSDEIIIMASRPGRVQLVYKNKLSYPRDQNSADFLKIV
DAIRNYLTKNIIPDEPYTKIHEQLLPIPNATVGEVIGLLEVLEDNDGKIEMFELSERINR
RFTVAMIIATAAELMGFVQTPFRYIVLTNTGRKFLDADINERKEIFRTELLKLPIVKIFV
KFIKENNGSINSKEAKKFLRKKLPKEKPNSVLKPLLNFCMYAEILDYDSRDDEISINPDI
PIKI
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