GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaJ in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized)
to candidate Echvi_3271 Echvi_3271 3-oxoacid CoA-transferase, B subunit

Query= BRENDA::P0A102
         (213 letters)



>FitnessBrowser__Cola:Echvi_3271
          Length = 218

 Score =  206 bits (524), Expect = 3e-58
 Identities = 102/200 (51%), Positives = 141/200 (70%), Gaps = 3/200 (1%)

Query: 7   LSRTEMAQRVAADIQEGAYVNLGIGAPTLVANYLGDK-EVFLHSENGLLGMGPSPAPGEE 65
           L++ ++AQR+A +I+ G Y+NLGIG PTLVANY+ +  EV L SENGLLG+GP P   + 
Sbjct: 2   LNKEQIAQRIAKEIKNGQYINLGIGIPTLVANYIPEGLEVVLQSENGLLGIGPFPTEDQV 61

Query: 66  DDDLINAGKQHVTLLTGGAFFHHADSFSMMRGGHLDIAVLGAFQVSVKGDLANWHTGAEG 125
           D DLINAGKQ ++++ G A F+ ADSF+M+RGGH+D+ +LGA +VS  GD+ANW    + 
Sbjct: 62  DADLINAGKQTISMVKGSALFNSADSFTMIRGGHVDLTILGAMEVSENGDIANWKIPGK- 120

Query: 126 SIPAVGGAMDLATGARQVFVMMDHLTKTGESKLVPECTYPLTGIACVSRIYTDLAVLEVT 185
            +  +GGAMDL   A  + V M H +K G+SKL+  CT PLTGI CV +I TDLA L+V 
Sbjct: 121 MVKGMGGAMDLVASAENIIVAMQHCSKDGKSKLLKRCTLPLTGIQCVKKIVTDLAYLKVL 180

Query: 186 PE-GLKVVEICADIDFDELQ 204
           PE G K++E    +  +E++
Sbjct: 181 PEGGFKLIERAPGVSVEEIR 200


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: 187
Number of extensions: 9
Number of successful extensions: 3
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: 218
Length adjustment: 22
Effective length of query: 191
Effective length of database: 196
Effective search space:    37436
Effective search space used:    37436
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