GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaJ in Phaeobacter inhibens BS107

Align 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized)
to candidate GFF606 PGA1_c06200 probable succinyl-CoA:3-ketoacid-coenzyme A transferase subunit B

Query= BRENDA::P0A102
         (213 letters)



>FitnessBrowser__Phaeo:GFF606
          Length = 209

 Score =  197 bits (501), Expect = 1e-55
 Identities = 104/205 (50%), Positives = 138/205 (67%), Gaps = 2/205 (0%)

Query: 9   RTEMAQRVAADIQEGAYVNLGIGAPTLVANYLGDK-EVFLHSENGLLGMGPSPAPGEEDD 67
           R +MA R A ++Q+G YVNLGIG PTLV+N++ +   V L SENG+LGMGP P  GEED 
Sbjct: 5   RNQMAARAAQELQDGWYVNLGIGIPTLVSNHIPEGVNVTLQSENGMLGMGPFPVEGEEDA 64

Query: 68  DLINAGKQHVTLLTGGAFFHHADSFSMMRGGHLDIAVLGAFQVSVKGDLANWHTGAEGSI 127
           DLINAGKQ +T L   A+F  A SF+M+RGG + +A+LGA +V+  GDLANW    +  +
Sbjct: 65  DLINAGKQTITELPQTAYFDSAQSFAMIRGGKIAMAILGAMEVAENGDLANWMIPGK-LV 123

Query: 128 PAVGGAMDLATGARQVFVMMDHLTKTGESKLVPECTYPLTGIACVSRIYTDLAVLEVTPE 187
             +GGAMDL  G  +V V+MDH  K G+SK++ +CT PLTG   V RI T+L VL+V   
Sbjct: 124 KGMGGAMDLVAGVGRVVVVMDHTNKHGDSKVLTDCTLPLTGKGVVDRIITNLGVLDVVDG 183

Query: 188 GLKVVEICADIDFDELQKLSGVPLI 212
           GLK+VE    +  DEL+  +   +I
Sbjct: 184 GLKIVETAEGVSEDELRAATQATII 208


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: 171
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: 209
Length adjustment: 21
Effective length of query: 192
Effective length of database: 188
Effective search space:    36096
Effective search space used:    36096
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