GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etfA in Sinorhizobium meliloti 1021

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 2/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate SMa0819 SMa0819 FixB electron transfer flavoprotein alpha chain

Query= BRENDA::D2RIQ3
         (340 letters)



>lcl|FitnessBrowser__Smeli:SMa0819 SMa0819 FixB electron transfer
           flavoprotein alpha chain
          Length = 353

 Score =  229 bits (583), Expect = 1e-64
 Identities = 129/324 (39%), Positives = 185/324 (57%), Gaps = 5/324 (1%)

Query: 13  KDLWVYVEHYKGEPVHVVYELLGECRKLADKCNQKLAAVLITDDAKDVPSKLIAR----G 68
           +++WV++E   G+   V  ELLGE RKLADK    LA V+I        +  IA     G
Sbjct: 13  RNVWVFIELEHGQVHPVSIELLGEGRKLADKLGVHLAGVVIGPPGGQGTANAIADAFAYG 72

Query: 69  ADLVYVCQDPAFKYYSTDEYTNAFCEMIDEYQPSSVFIGATNDGRDLGPRIAARVNTGLC 128
           ADL Y+ + P   +Y  + +T A  +++   +P  + +GAT  GRDL   +A  + TGL 
Sbjct: 73  ADLSYLVESPLLAHYRNEPFTKALTDLVLANKPEILLLGATTLGRDLAGSVATTLKTGLT 132

Query: 129 ADCTILDAEEDGLIEWTRPAAGGNIMATILCKEHRPQMGTVRPKTFKAMEPDASRTGEVI 188
           ADCT L+ + DG +  TRP  GG+++ TI   + RPQM TVRP      +     TG +I
Sbjct: 133 ADCTELNVDSDGSLAATRPTFGGSLLCTIYTLKCRPQMATVRPSVMATPQRVNRPTGSII 192

Query: 189 NYTLKNHVDDRVTCIRREEVVSEGEMA-IDDAPFVCSGGRGMKAKENFSLLYDLAHALGG 247
            + LK   ++  T +       +  +A +  A  V +GG G+ A +N  LL DLA  LGG
Sbjct: 193 RHDLKMLEEEIATKVLAFFSDCDSTIANLAYADVVVAGGLGLGAVQNLQLLKDLARTLGG 252

Query: 248 AVGGSRAAVDEGFIEHPRQVGQSGKTVTPKIYFACGISGSVQHKAGMSKSDTIVCINKDP 307
             G SR  V +G++   RQ+GQ+G T+ PK+Y A GISG+VQH+ G+  SD IV IN DP
Sbjct: 253 DFGCSRPLVQKGWMPFDRQIGQTGNTIRPKLYIAAGISGAVQHRVGVEGSDLIVAINTDP 312

Query: 308 DAPMFEISKYGIVGDALKILPLLT 331
           +AP+F+ +  G+V DA+  LP LT
Sbjct: 313 NAPIFDFAHLGVVADAISFLPALT 336


Lambda     K      H
   0.318    0.136    0.406 

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: 307
Number of extensions: 18
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: 340
Length of database: 353
Length adjustment: 29
Effective length of query: 311
Effective length of database: 324
Effective search space:   100764
Effective search space used:   100764
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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 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