GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bgtA in Stutzerimonas stutzeri A1501

Align ATPase (characterized, see rationale)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA

Query= uniprot:Q31RN8
         (261 letters)



>NCBI__GCF_000013785.1:WP_011911265.1
          Length = 279

 Score =  225 bits (573), Expect = 9e-64
 Identities = 131/274 (47%), Positives = 172/274 (62%), Gaps = 16/274 (5%)

Query: 2   TPLGRQPEPVTAI--ASAP-ETMIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSG 58
           TP+    E  TA   A+AP + M+    V K YG +   L G+ L VQ GE V ++GPSG
Sbjct: 3   TPMPTTEESNTAAMAAAAPAQPMVRFASVTKRYG-ELTVLEGLDLDVQEGEKVAIIGPSG 61

Query: 59  SGKSTFLRTLNALESHQRGEIWIEGHRLSH-----------DRRDIATIRQEVGMVFQQF 107
           SGKST LR L  LE    G I ++G  L+H           + R +  +R +VGMVFQ F
Sbjct: 62  SGKSTLLRVLMTLEGIDDGLIEVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQSF 121

Query: 108 NLFPHLTVLQNLMLAPVQVRRWPVAQAEATARQLLERVRIAEQADKYPGQLSGGQQQRVA 167
           NLFPH+  LQN+M APVQV      +A   A +LL  V + ++ + +P QLSGGQQQRVA
Sbjct: 122 NLFPHMNALQNVMEAPVQVLGLSKREARERAEELLAMVGLEDKLEHFPAQLSGGQQQRVA 181

Query: 168 IARALAMQPRILLFDEPTSALDPEMVREVLDVMRDLA-SEGMTMLVATHEVGFAREVADR 226
           IARALAM+P+++LFDE TSALDPE+  EVL V+R L  +  +TML+ TH++GFARE ADR
Sbjct: 182 IARALAMRPKVMLFDEVTSALDPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFADR 241

Query: 227 VVLMADGQIVEEAPPDRFFTAPQSDRAKQFLAQI 260
           V     G+I E+  PD  F  PQ DR ++FL+ +
Sbjct: 242 VCFFHQGRIHEQGSPDALFNNPQEDRTREFLSAV 275


Lambda     K      H
   0.321    0.134    0.387 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 226
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 261
Length of database: 279
Length adjustment: 25
Effective length of query: 236
Effective length of database: 254
Effective search space:    59944
Effective search space used:    59944
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

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:

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:

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:

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