GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1695 in Azospirillum thiophilum BV-S

Align ABC transporter permease (characterized, see rationale)
to candidate WP_045584757.1 AL072_RS30680 branched-chain amino acid ABC transporter permease

Query= uniprot:A0A165KC95
         (309 letters)



>NCBI__GCF_001305595.1:WP_045584757.1
          Length = 290

 Score =  180 bits (456), Expect = 4e-50
 Identities = 110/309 (35%), Positives = 176/309 (56%), Gaps = 19/309 (6%)

Query: 1   MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60
           MD+ LQ + NGLV+G  YAL ALG T+++G+++++NFAHGE  M+G +  W     +   
Sbjct: 1   MDLFLQFLANGLVVGVFYALSALGLTLIFGLMRVVNFAHGEFYMLGGVVGWFVTTHL--G 58

Query: 61  MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120
           +    G V++ L  +I     A   F+IE+V     R       ++  IG+SI L  + +
Sbjct: 59  LDFFSGLVVVAL--VIGGFGWAVDRFLIERV-----RGQGEEPGILLTIGLSIFLVNITL 111

Query: 121 IIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180
           +   P        +   P  +G   IT  ++L + +    + +   +++ T LG AMRAT
Sbjct: 112 LAVGPAPMKVVRAITEGPIFLGPVTITKMRLLAMVIGVALIFAAHAIIHRTRLGSAMRAT 171

Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240
            ++P  ASL G++   V +ATF +G  L+A++G++ AS Y +AQ ++G L  LK+F   +
Sbjct: 172 FQDPMAASLAGIRTGQVYAATFALGCTLSALSGMLLASIY-SAQASVGGLVSLKSFVVVI 230

Query: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300
            GG+G+  GA+ GG+LLG+ EA+  GY+ T   G++     DI  FI++I+IL LRP GL
Sbjct: 231 LGGMGSFPGAIAGGLLLGVAEALWGGYVAT---GMV-----DIIGFILVILILVLRPQGL 282

Query: 301 LGERVADRA 309
              R A+RA
Sbjct: 283 FSIR-AERA 290


Lambda     K      H
   0.327    0.142    0.419 

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: 217
Number of extensions: 8
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: 309
Length of database: 290
Length adjustment: 27
Effective length of query: 282
Effective length of database: 263
Effective search space:    74166
Effective search space used:    74166
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: 48 (23.1 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