GapMind for catabolism of small carbon sources

 

Alignments for a candidate for atoD in Acidovorax sp. GW101-3H11

Align acetyl-CoA:acetoacetate CoA transferase, B subunit (EC 2.8.3.8) (characterized)
to candidate Ac3H11_3921 3-oxoadipate CoA-transferase subunit B (EC 2.8.3.6)

Query= reanno::psRCH2:GFF1044
         (209 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3921
          Length = 201

 Score =  207 bits (526), Expect = 1e-58
 Identities = 109/198 (55%), Positives = 137/198 (69%), Gaps = 3/198 (1%)

Query: 13  AQELQDGFYVNLGIGLPTLVANYIPEGMDVWLQSENGLLGIGPFPTEEEIDPDLINAGKQ 72
           AQ++ DG YVNLGIG PTLVAN+IPEG +V LQSENG+LG+GP P     D DLINAGKQ
Sbjct: 2   AQDIHDGAYVNLGIGQPTLVANHIPEGREVILQSENGILGMGPAPAAGLEDYDLINAGKQ 61

Query: 73  TVTALPGSSFFDNAQSFAMIRGGHINLAILGAMQVSEKGDLANWMI--PGKMVKGMGGAM 130
            VT LPG ++F +A SFAM+RGGH+++ +LGA QVS  GDLANW    PG  +  +GGAM
Sbjct: 62  PVTLLPGGAYFHHADSFAMMRGGHLDICVLGAYQVSATGDLANWSTGEPG-AIPAVGGAM 120

Query: 131 DLVAGVKRVVVLMEHTAKGGAHKILPACDLPLTGLGVVDRIITDLGVLDVTEQGLKLVEL 190
           DL  G K+  V+M+   K GA KI+  C  PLTG+  V RI TDL  L  T  GL+L++ 
Sbjct: 121 DLAIGAKQTWVMMDLLTKQGASKIVTQCTYPLTGVACVKRIYTDLCTLACTPTGLQLIDT 180

Query: 191 AEGVSFDELQEATGSPIQ 208
             G+S  EL++  G PI+
Sbjct: 181 VPGLSQTELEQLVGLPIR 198


Lambda     K      H
   0.318    0.138    0.404 

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: 188
Number of extensions: 6
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: 209
Length of database: 201
Length adjustment: 21
Effective length of query: 188
Effective length of database: 180
Effective search space:    33840
Effective search space used:    33840
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: 45 (21.9 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