GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaJ in Sphingobium czechense LL01

Align 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized)
to candidate WP_066609234.1 V473_RS20820 3-oxoacid CoA-transferase subunit B

Query= BRENDA::P0A102
         (213 letters)



>NCBI__GCF_001046645.1:WP_066609234.1
          Length = 212

 Score =  194 bits (492), Expect = 1e-54
 Identities = 105/207 (50%), Positives = 135/207 (65%), Gaps = 4/207 (1%)

Query: 8   SRTEMAQRVAADIQEGAYVNLGIGAPTLVANYLGDK-EVFLHSENGLLGMGPSPAPGEED 66
           +R +MA + A ++Q+G YVNLGIG PTLVANY+ D  EV L SENGLLG+GP P   E D
Sbjct: 4   TREQMAAQAAGELQDGFYVNLGIGIPTLVANYVPDDIEVVLQSENGLLGIGPFPYDDEVD 63

Query: 67  DDLINAGKQHVTLLTGGAFFHHADSFSMMRGGHLDIAVLGAFQVSVKGDLANWHTGAEGS 126
            DLINAGKQ VT L   +FF  ADSF+M+RGGH+D+A+LGA +V+  GDLANW T     
Sbjct: 64  PDLINAGKQTVTTLPTSSFFSSADSFAMIRGGHIDLAILGAMEVAGNGDLANW-TVPGKM 122

Query: 127 IPAVGGAMDLATGARQVFVMMDHLTKTGESKLVPECTYPLTGIACVSRIYTDLA--VLEV 184
           I  +GGAMDL  G R+V V+M H  K G  K+V  CT PLTG   V  I +D    +L+ 
Sbjct: 123 IKGMGGAMDLVAGVRRVVVVMSHTDKAGNPKIVDRCTLPLTGTGVVDAIVSDFGRFILDR 182

Query: 185 TPEGLKVVEICADIDFDELQKLSGVPL 211
               L   E+  D+D + +Q  +G+P+
Sbjct: 183 DSGELIAQELADDLDLEFVQGRTGIPV 209


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: 185
Number of extensions: 11
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: 212
Length adjustment: 21
Effective length of query: 192
Effective length of database: 191
Effective search space:    36672
Effective search space used:    36672
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 24 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