GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Herbaspirillum autotrophicum IAM 14942

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_050462656.1 AKL27_RS09910 high-affinity branched-chain amino acid ABC transporter permease LivM

Query= uniprot:A0A165KER0
         (358 letters)



>NCBI__GCF_001189915.1:WP_050462656.1
          Length = 408

 Score =  261 bits (667), Expect = 2e-74
 Identities = 158/357 (44%), Positives = 215/357 (60%), Gaps = 46/357 (12%)

Query: 13  VALLVLPLILQSFGNAW-VRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71
           + LL + L+   FG+   V +  LAL+YV+L LGLNIVVG+AGLLDLGYV FYAVG Y +
Sbjct: 85  MVLLAVALVWPFFGSRGNVDVVTLALIYVVLGLGLNIVVGFAGLLDLGYVGFYAVGGYTY 144

Query: 72  ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131
           AL+                  GL  S W  +P+AA ++A FG +LG P L+LRGDYLAIV
Sbjct: 145 ALLNQYF--------------GL--SFWECLPLAAGMSALFGFLLGFPVLRLRGDYLAIV 188

Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDI-------- 183
           TLGFGEIIR+ LNNL    +LT GP G+  I    VFG+++ +   V G           
Sbjct: 189 TLGFGEIIRLLLNNL---TSLTGGPDGVSGIPKPTVFGIEMARTASVEGGTTFHDMLGLT 245

Query: 184 ----NSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLL 239
               + V   Y+L L+LV+ +  +  RL    +GRAW A+R+DEIA +++GIN   +KL 
Sbjct: 246 YQGGHMVIFLYFLGLLLVLFTYFVTSRLIRMPMGRAWEALRDDEIACRSLGINPTKIKLS 305

Query: 240 AFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSA 299
           AF +GA+F G++G+ F A QG V+PESF+ +ES +I+A+VVLGG+G   GVIL A+LL+ 
Sbjct: 306 AFTLGAAFAGLAGSFFAARQGLVNPESFTFIESALILAIVVLGGMGSQLGVILAAILLTI 365

Query: 300 LPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPSPEHGKSLTQ 356
           LPEV R                A  R L+  L M+++M+ RP+GL P+      L Q
Sbjct: 366 LPEVAR--------------SFAEYRMLIFGLVMVLMMIWRPQGLLPATRPHVELPQ 408


Lambda     K      H
   0.328    0.144    0.430 

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: 374
Number of extensions: 16
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 408
Length adjustment: 30
Effective length of query: 328
Effective length of database: 378
Effective search space:   123984
Effective search space used:   123984
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 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