GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaJ in Caulobacter crescentus NA1000

Align 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized)
to candidate CCNA_00207 CCNA_00207 succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B

Query= BRENDA::P0A102
         (213 letters)



>FitnessBrowser__Caulo:CCNA_00207
          Length = 213

 Score =  191 bits (484), Expect = 1e-53
 Identities = 99/202 (49%), Positives = 137/202 (67%), Gaps = 8/202 (3%)

Query: 8   SRTEMAQRVAADIQEGAYVNLGIGAPTLVANYLGD-KEVFLHSENGLLGMGPSPAPGEED 66
           +R E+A R A ++Q+G YVNLGIG PTLVAN++ +   V L SENG+LGMGP P  GEED
Sbjct: 4   TRDEVAARAAKELQDGFYVNLGIGIPTLVANHIPEGMHVTLQSENGMLGMGPFPYEGEED 63

Query: 67  DDLINAGKQHVTLLTGGAFFHHADSFSMMRGGHLDIAVLGAFQVSVKGDLANWHTGAEGS 126
            DLINAGKQ +T L   ++F  ADSF+M+RGGH+ +++LG  QVS  GDLANW    +  
Sbjct: 64  ADLINAGKQTITELDSSSYFSSADSFAMIRGGHIALSILGGMQVSENGDLANWMVPGK-M 122

Query: 127 IPAVGGAMDLATGARQVFVMMDHLTKTGESKLVPECTYPLTGIACVSRIYTDLAVLEV-- 184
           +  +GGAMDL  G ++V V+MDH  K+G  KL+ +C+ PLTG   V  + T+L V E+  
Sbjct: 123 VKGMGGAMDLVAGVKRVVVVMDHCEKSGAPKLLKQCSLPLTGAGVVDLLITELGVFEINR 182

Query: 185 --TPEGLKVVEICADIDFDELQ 204
             TP  +K++E+   +  DE++
Sbjct: 183 GKTP--VKLIELAPGVTVDEVK 202


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: 173
Number of extensions: 8
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: 213
Length adjustment: 22
Effective length of query: 191
Effective length of database: 191
Effective search space:    36481
Effective search space used:    36481
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