GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaJ in Pandoraea thiooxydans ATSB16

Align 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized)
to candidate WP_047214215.1 PATSB16_RS11250 CoA transferase subunit B

Query= BRENDA::P0A102
         (213 letters)



>NCBI__GCF_001931675.1:WP_047214215.1
          Length = 212

 Score =  298 bits (764), Expect = 4e-86
 Identities = 148/207 (71%), Positives = 173/207 (83%), Gaps = 1/207 (0%)

Query: 6   KLSRTEMAQRVAADIQEGAYVNLGIGAPTLVANYLG-DKEVFLHSENGLLGMGPSPAPGE 64
           KLSR ++A RVA DI EGAYVNLGIG PTLVAN+L  D+E+ LHSENG+LGMGP+PAPGE
Sbjct: 3   KLSRDQIAARVAQDIPEGAYVNLGIGLPTLVANHLPKDREILLHSENGVLGMGPAPAPGE 62

Query: 65  EDDDLINAGKQHVTLLTGGAFFHHADSFSMMRGGHLDIAVLGAFQVSVKGDLANWHTGAE 124
           ED DLINAGKQ VTLL GGA+FHHADSF+MMRGGHLDI VLGAFQVS +GDLANWHTGA 
Sbjct: 63  EDGDLINAGKQPVTLLPGGAYFHHADSFAMMRGGHLDICVLGAFQVSRRGDLANWHTGAP 122

Query: 125 GSIPAVGGAMDLATGARQVFVMMDHLTKTGESKLVPECTYPLTGIACVSRIYTDLAVLEV 184
            +IPAVGGAMDLA GA+ VFVMMD LT+ G SKLV +CTYPLTGI CVSR+YTDLAV ++
Sbjct: 123 DAIPAVGGAMDLAIGAKHVFVMMDLLTREGRSKLVEQCTYPLTGIGCVSRVYTDLAVFDL 182

Query: 185 TPEGLKVVEICADIDFDELQKLSGVPL 211
            P+G+ V++  + +   EL+   G+PL
Sbjct: 183 KPDGVHVIDNFSGLAAAELEARVGLPL 209


Lambda     K      H
   0.318    0.137    0.399 

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: 225
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: 213
Length of database: 212
Length adjustment: 21
Effective length of query: 192
Effective length of database: 191
Effective search space:    36672
Effective search space used:    36672
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 24 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