GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08245 in Mesorhizobium ciceri biovar biserrulae WSM1271

Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_013525179.1 MESCI_RS31065 ABC transporter ATP-binding protein

Query= uniprot:G8ALJ0
         (294 letters)



>NCBI__GCF_000185905.1:WP_013525179.1
          Length = 254

 Score =  228 bits (582), Expect = 8e-65
 Identities = 128/261 (49%), Positives = 169/261 (64%), Gaps = 9/261 (3%)

Query: 11  LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70
           LL V  L + FGGL  ++D+SFS   G I ++IGPNGAGKT+LFNC+TGFY P  G ++L
Sbjct: 3   LLEVRDLRLSFGGLKVLHDISFSVEKGAINSLIGPNGAGKTSLFNCLTGFYKPKGGSISL 62

Query: 71  RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130
               G+   +  +P +RI+    +ARTFQNIRLF  MSVLEN +  QH    R+    ++
Sbjct: 63  ---SGRP--ITGLPPHRITA-LGLARTFQNIRLFKEMSVLENAMSGQH---CRSRHGIVS 113

Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190
            +L LP+  R E     +   WL  V + + A   AG L YG QRRLE+ARA+ + P ++
Sbjct: 114 AILHLPAQRREEEAIRAIGMRWLGFVGIEQHAHRRAGGLSYGDQRRLELARALASAPELI 173

Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250
            LDEPAAGLN RE  +L  L+  IRDE  + VLLIEHDM +VM +S+ +VV DYG+KI+D
Sbjct: 174 LLDEPAAGLNEREKLDLIHLIRRIRDETGVTVLLIEHDMGLVMQVSEKIVVFDYGQKIAD 233

Query: 251 GDPAFVKNDPAVIRAYLGEEE 271
           G P  V+ DP VI AYLG E+
Sbjct: 234 GAPEAVRADPRVIEAYLGTED 254


Lambda     K      H
   0.319    0.137    0.397 

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: 210
Number of extensions: 6
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: 294
Length of database: 254
Length adjustment: 25
Effective length of query: 269
Effective length of database: 229
Effective search space:    61601
Effective search space used:    61601
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