GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Smeli:SMc02357 SMc02357 high-affinity
           branched-chain amino acid ABC transporter ATP-binding
           protein
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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