GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaI in Pseudomonas simiae WCS417

Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate GFF2064 PS417_10525 succinyl-CoA:3-ketoacid-CoA transferase

Query= CharProtDB::CH_021928
         (231 letters)



>FitnessBrowser__WCS417:GFF2064
          Length = 232

 Score =  196 bits (497), Expect = 4e-55
 Identities = 96/215 (44%), Positives = 140/215 (65%), Gaps = 2/215 (0%)

Query: 3   NKTYESIASAVEGITDGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEIGL 62
           +K   S   A+ G+ DG T++ GGFG  G+P  LI  +   G RDLT++SNN G    GL
Sbjct: 5   DKRVASYEEALAGLEDGMTVLSGGFGLCGIPENLIAEIKRKGTRDLTVVSNNCGVDGFGL 64

Query: 63  AALLMAGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAFFS 122
             LL    + KV+ S+    ++ +F++   +G+IE+ + PQG LAE++ A G+GI AFF+
Sbjct: 65  GVLLEEKQISKVIASYV--GENALFEKQLLSGEIEVVLTPQGTLAEKMRAGGAGIPAFFT 122

Query: 123 PTGYGTLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPIMA 182
            TG GT +AEGKETRE +GR Y++E  +  DFA++K  K D +GN+ YR  A+NF P+ A
Sbjct: 123 ATGVGTPVAEGKETREFNGRPYLMEESITGDFAIVKGWKADHFGNVIYRHTAQNFNPLAA 182

Query: 183 MAAKTAIAQVDQVVELGELDPEHIITPGIFVQRVV 217
            A K  + +V+++VE GELDP  I TPGI+V R++
Sbjct: 183 TAGKITVVEVEEIVEPGELDPAQIHTPGIYVDRII 217


Lambda     K      H
   0.318    0.135    0.381 

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: 147
Number of extensions: 5
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: 231
Length of database: 232
Length adjustment: 23
Effective length of query: 208
Effective length of database: 209
Effective search space:    43472
Effective search space used:    43472
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