GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaI in Shewanella loihica PV-4

Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate 5210131 Shew_2575 3-oxoacid CoA-transferase, A subunit (RefSeq)

Query= CharProtDB::CH_021928
         (231 letters)



>FitnessBrowser__PV4:5210131
          Length = 233

 Score =  217 bits (552), Expect = 2e-61
 Identities = 108/216 (50%), Positives = 148/216 (68%), Gaps = 2/216 (0%)

Query: 2   INKTYESIASAVEGITDGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGEIG 61
           +NK   S   A+EG+TD  T+MVGGFG  G+P  LI  ++ +GA+ LT ISNNAG  + G
Sbjct: 4   LNKLVTSYEEALEGLTDNMTVMVGGFGLCGIPEGLIAQMVKSGAKGLTAISNNAGVDDFG 63

Query: 62  LAALLMAGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGAFF 121
           L  LL +  +  ++ S+    ++  F++   +G++ + + PQG LAE+I A G+GI AFF
Sbjct: 64  LGLLLKSRQISTMIASYV--GENATFEQQMLSGELNVILTPQGTLAEKIRAGGAGIPAFF 121

Query: 122 SPTGYGTLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGPIM 181
           + TGYGT +AEGKETREIDGR YVLE  L ADFAL++A K D  GNL +RK A NF P+M
Sbjct: 122 TATGYGTPVAEGKETREIDGRHYVLEPALTADFALVRAWKADTMGNLVFRKTAANFNPMM 181

Query: 182 AMAAKTAIAQVDQVVELGELDPEHIITPGIFVQRVV 217
           A A K  + + + +VE GELDP+HI TPGI+V R++
Sbjct: 182 ATAGKITVVEAEHIVEPGELDPDHIHTPGIYVDRLI 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: 154
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: 231
Length of database: 233
Length adjustment: 23
Effective length of query: 208
Effective length of database: 210
Effective search space:    43680
Effective search space used:    43680
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