GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17605 in Acidovorax caeni R-24608

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_082366659.1 BN2503_RS17290 ATP-binding cassette domain-containing protein

Query= uniprot:A0A1N7U8S3
         (276 letters)



>NCBI__GCF_001298675.1:WP_082366659.1
          Length = 393

 Score =  169 bits (428), Expect = 9e-47
 Identities = 99/219 (45%), Positives = 138/219 (63%), Gaps = 12/219 (5%)

Query: 37  GEHEVLKGVSLNARQGDVISLIGASGSGKSTMLRCINFLEQPDAGVITLDGISIEMRQGR 96
           G  + L  +SL    G +  +IG SG+GKS++LR IN LEQP +G + +DG+ I      
Sbjct: 57  GTVQALDAISLEIAPGSIFGIIGRSGAGKSSLLRTINRLEQPTSGQVLVDGVDI------ 110

Query: 97  AGTRAPHQDQLQNLRTRLAMVFQHFNLWSHMTVLENITMAPRRVLDVSAAEAEKRARMYL 156
            GT +  +  L  LR R+ M+FQHFNL S  TV EN+ + P +V  V AA+   R +  L
Sbjct: 111 -GTLS--EAGLVQLRRRIGMIFQHFNLLSAKTVAENVAL-PLKVAGVPAAQIAARVQELL 166

Query: 157 DKVGLPSRVADQYPAFLSGGQQQRVAIARALAMEPEIILFDEPTSALDPELVGEVLKVIQ 216
             VGL  + AD YP+ LSGGQ+QRV +ARALA  PEI+L DE TSALDPE    +L++++
Sbjct: 167 LLVGLQDK-ADTYPSRLSGGQKQRVGVARALATGPEILLCDEATSALDPETTHSILQLLR 225

Query: 217 TLAEE-GRTMLMVTHEMGFARQVSSQVLFLHQGRVEEHG 254
            +    G T++++THEM   R+++ QVL L QGR+ E G
Sbjct: 226 DINRTLGITVVLITHEMSVIREIADQVLVLEQGRIAELG 264


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: 262
Number of extensions: 14
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: 393
Length adjustment: 28
Effective length of query: 248
Effective length of database: 365
Effective search space:    90520
Effective search space used:    90520
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: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. 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