GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaI in Caulobacter crescentus NA1000

Align 3-oxoadipate CoA-transferase subunit A; EC 2.8.3.6 (characterized)
to candidate CCNA_00206 CCNA_00206 succinyl-CoA:3-ketoacid-coenzyme A transferase subunit A

Query= CharProtDB::CH_021928
         (231 letters)



>FitnessBrowser__Caulo:CCNA_00206
          Length = 236

 Score =  215 bits (547), Expect = 7e-61
 Identities = 110/218 (50%), Positives = 149/218 (68%), Gaps = 3/218 (1%)

Query: 1   MINKTYESIASAVEGIT-DGSTIMVGGFGTAGMPSELIDGLIATGARDLTIISNNAGNGE 59
           M++K  +    A+ G+  DG TIM GGFG  G+P  LI  +   G +DLT+ISNN G   
Sbjct: 1   MVDKVKKDAVEALAGLLFDGMTIMAGGFGLCGIPENLIAAIREAGTKDLTVISNNCGVDG 60

Query: 60  IGLAALLMAGSVRKVVCSFPRQSDSYVFDELYRAGKIELEVVPQGNLAERIAAAGSGIGA 119
            GL  LL    ++K+V S+    ++ +F++LY +G++ELE  PQG LAERI A G+GI A
Sbjct: 61  FGLGILLENRQIKKMVSSYV--GENKLFEQLYLSGELELEFNPQGTLAERIRAGGAGIPA 118

Query: 120 FFSPTGYGTLLAEGKETREIDGRMYVLEMPLHADFALIKAHKGDRWGNLTYRKAARNFGP 179
           FF+ TGYGTL+AEGKETRE DG MYV+E  L AD +++KA K D  GNL YRK ARNF P
Sbjct: 119 FFTRTGYGTLVAEGKETREFDGEMYVMERGLTADLSIVKAWKADAEGNLIYRKTARNFNP 178

Query: 180 IMAMAAKTAIAQVDQVVELGELDPEHIITPGIFVQRVV 217
           +MA A K  + +V+++V +GELD + I TPGI+V R++
Sbjct: 179 MMATAGKKTVVEVEELVAIGELDKDAIHTPGIYVDRLI 216


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: 160
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: 236
Length adjustment: 23
Effective length of query: 208
Effective length of database: 213
Effective search space:    44304
Effective search space used:    44304
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