GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17605 in Stutzerimonas stutzeri A1501

Align ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale)
to candidate WP_011911265.1 PST_RS00075 ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA

Query= uniprot:A0A1N7U8S3
         (276 letters)



>NCBI__GCF_000013785.1:WP_011911265.1
          Length = 279

 Score =  219 bits (558), Expect = 5e-62
 Identities = 129/274 (47%), Positives = 177/274 (64%), Gaps = 15/274 (5%)

Query: 2   NQSAQALAAYPVDEPVAQPVTAAIKLQVEGIHKRYGEHEVLKGVSLNARQGDVISLIGAS 61
           N +A A AA       AQP+     ++   + KRYGE  VL+G+ L+ ++G+ +++IG S
Sbjct: 12  NTAAMAAAA------PAQPM-----VRFASVTKRYGELTVLEGLDLDVQEGEKVAIIGPS 60

Query: 62  GSGKSTMLRCINFLEQPDAGVITLDGISI-EMRQGRAGTRAPHQDQLQNLRTRLAMVFQH 120
           GSGKST+LR +  LE  D G+I +DG  +  M  G       +   L+ +R ++ MVFQ 
Sbjct: 61  GSGKSTLLRVLMTLEGIDDGLIEVDGEPLTHMPDGHGRLVPANARHLRRVRGKVGMVFQS 120

Query: 121 FNLWSHMTVLENITMAPRRVLDVSAAEAEKRARMYLDKVGLPSRVADQYPAFLSGGQQQR 180
           FNL+ HM  L+N+  AP +VL +S  EA +RA   L  VGL  ++ + +PA LSGGQQQR
Sbjct: 121 FNLFPHMNALQNVMEAPVQVLGLSKREARERAEELLAMVGLEDKL-EHFPAQLSGGQQQR 179

Query: 181 VAIARALAMEPEIILFDEPTSALDPELVGEVLKVIQTLAE-EGRTMLMVTHEMGFARQVS 239
           VAIARALAM P+++LFDE TSALDPEL GEVL VI+ L E    TMLMVTH+MGFAR+ +
Sbjct: 180 VAIARALAMRPKVMLFDEVTSALDPELCGEVLSVIRRLGEAHNLTMLMVTHQMGFAREFA 239

Query: 240 SQVLFLHQGRVEEHGDA-RILDQPNSERLQQFLS 272
            +V F HQGR+ E G    + + P  +R ++FLS
Sbjct: 240 DRVCFFHQGRIHEQGSPDALFNNPQEDRTREFLS 273


Lambda     K      H
   0.319    0.133    0.372 

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: 218
Number of extensions: 11
Number of successful extensions: 4
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: 276
Length of database: 279
Length adjustment: 25
Effective length of query: 251
Effective length of database: 254
Effective search space:    63754
Effective search space used:    63754
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 (21.8 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