GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Sinorhizobium meliloti 1021

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate SMc02357 SMc02357 high-affinity branched-chain amino acid ABC transporter ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__Smeli:SMc02357
          Length = 244

 Score =  178 bits (451), Expect = 1e-49
 Identities = 108/254 (42%), Positives = 146/254 (57%), Gaps = 16/254 (6%)

Query: 6   NEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGT 65
           +E  L V  +S  F GL+AL  V +++  G+V GLIGPNG+GKTT  N ITG      GT
Sbjct: 2   SETRLAVNDVSVEFTGLRALDHVSLSVAAGEVVGLIGPNGSGKTTLINAITGQVKLATGT 61

Query: 66  FELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTK 125
                      +  E+A AG++R+FQ +R+F  MT +ENV              A    K
Sbjct: 62  IAAGDTTLSGLSPREIALAGVSRSFQIVRIFNSMTVMENV-------------EAAALAK 108

Query: 126 GFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPA 185
           G  A     A+RA+ LL  +G+   AD    +LSYGD+RR+EIARALA +P+ + LDEPA
Sbjct: 109 G--ASRTVSAERAKGLLAELGLTAKADELGESLSYGDKRRVEIARALAAEPRFLLLDEPA 166

Query: 186 AGMNATE-KVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEV 244
           AGMN  E +  L  L +        +L+I+HD+ L+M LC R+ VL  G+ IAEG+ A V
Sbjct: 167 AGMNDAETETLLHTLAELPEKRGLGLLIIDHDMGLIMRLCHRLHVLASGRTIAEGDAAHV 226

Query: 245 QKNEKVIEAYLGTG 258
           + +  VIEAYLG G
Sbjct: 227 RSHPAVIEAYLGKG 240


Lambda     K      H
   0.319    0.137    0.384 

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: 189
Number of extensions: 10
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: 260
Length of database: 244
Length adjustment: 24
Effective length of query: 236
Effective length of database: 220
Effective search space:    51920
Effective search space used:    51920
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 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 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