GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Magnetospirillum magneticum AMB-1

Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate WP_011382581.1 AMB_RS00675 KR domain-containing protein

Query= metacyc::MONOMER-11802
         (255 letters)



>NCBI__GCF_000009985.1:WP_011382581.1
          Length = 238

 Score = 87.0 bits (214), Expect = 3e-22
 Identities = 83/254 (32%), Positives = 114/254 (44%), Gaps = 32/254 (12%)

Query: 3   IANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLN--AQAVEAKARELGDNARFAVADI 60
           +A K  +V+G   G+GAA A  L+  GAKVM+       +          D A  A    
Sbjct: 4   LAGKLALVTGGTRGIGAAIAARLLADGAKVMVTGTRPGGEGPAGSGYLAVDFADAAATTA 63

Query: 61  SDEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLGKQGPHGL---ASFAKVINVNLIG 117
             EQAA   VD           LVN AGI        K  P      A FA++  VN+  
Sbjct: 64  FAEQAAGLGVDI----------LVNNAGI-------NKVSPFAEIDPADFARIQQVNVTA 106

Query: 118 SFNLLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAAR 177
            F L R     M   A       G I+  +SI     + G+ AY+ASK A+  LT   A 
Sbjct: 107 PFLLARAVVPGMQAKAW------GRIVTVSSIWGRISRAGRGAYSASKFAVDGLTAALAA 160

Query: 178 ELARFGIRVMTIAPGIFETPMMAG-MSDEVRASLAAGVPFPPRLGRPQEYAALARHII-- 234
           E+A+FGI    +APG  +T +    + ++    L A VP   RLGRP+E AA    +   
Sbjct: 161 EVAQFGILANCVAPGFIDTELTRQVLGEDGIKELTAQVP-ARRLGRPEEIAAFVAWLAGP 219

Query: 235 ENSMLNGEVIRLDG 248
           ENS ++G+ + +DG
Sbjct: 220 ENSYISGQNLVIDG 233


Lambda     K      H
   0.318    0.131    0.358 

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: 119
Number of extensions: 9
Number of successful extensions: 2
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: 255
Length of database: 238
Length adjustment: 24
Effective length of query: 231
Effective length of database: 214
Effective search space:    49434
Effective search space used:    49434
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: 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