GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Sinorhizobium meliloti 1021

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate SMc02357 SMc02357 high-affinity branched-chain amino acid ABC transporter ATP-binding protein

Query= TCDB::Q55164
         (267 letters)



>FitnessBrowser__Smeli:SMc02357
          Length = 244

 Score =  168 bits (426), Expect = 9e-47
 Identities = 93/251 (37%), Positives = 146/251 (58%), Gaps = 22/251 (8%)

Query: 19  LLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFN 78
           L    +S  F GLRA+DH  + V  G + GLIGPNG+GKTTL N ++  ++   G +   
Sbjct: 6   LAVNDVSVEFTGLRALDHVSLSVAAGEVVGLIGPNGSGKTTLINAITGQVKLATGTIAAG 65

Query: 79  GDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQK 138
             ++  L+P +IAL G  R+FQ+ ++ + +TV+EN+  A   +   +             
Sbjct: 66  DTTLSGLSPREIALAGVSRSFQIVRIFNSMTVMENVEAAALAKGASR------------- 112

Query: 139 EERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGVN 198
               + E+A  +L  +GL AKA +   +LS G ++ +E+ARAL + P+ +LLDEPAAG+N
Sbjct: 113 --TVSAERAKGLLAELGLTAKADELGESLSYGDKRRVEIARALAAEPRFLLLDEPAAGMN 170

Query: 199 ----PTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQ 254
                TL+  + E      ++G+  L+I+H+M +IM LCH + VLA GR +A+G    ++
Sbjct: 171 DAETETLLHTLAELP---EKRGLGLLIIDHDMGLIMRLCHRLHVLASGRTIAEGDAAHVR 227

Query: 255 SDPRVLEAYLG 265
           S P V+EAYLG
Sbjct: 228 SHPAVIEAYLG 238


Lambda     K      H
   0.319    0.136    0.389 

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: 177
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: 267
Length of database: 244
Length adjustment: 24
Effective length of query: 243
Effective length of database: 220
Effective search space:    53460
Effective search space used:    53460
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: 47 (22.7 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