GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaJ in Nocardioides daejeonensis MJ31

Align 3-oxoadipate CoA-transferase (subunit 1/2) (EC 2.8.3.6) (characterized)
to candidate WP_110206713.1 DNK54_RS09440 3-oxoacid CoA-transferase subunit B

Query= BRENDA::P0A102
         (213 letters)



>NCBI__GCF_003194585.1:WP_110206713.1
          Length = 236

 Score =  223 bits (569), Expect = 2e-63
 Identities = 114/206 (55%), Positives = 146/206 (70%), Gaps = 2/206 (0%)

Query: 7   LSRTEMAQRVAADIQEGAYVNLGIGAPTLVANYL-GDKEVFLHSENGLLGMGPSPAPGEE 65
           L+  E+A+ +A DI EG+++NLGIG PT +A++L  +  V LH+ENG+LGMGP+    + 
Sbjct: 28  LTMDELAEVIARDIPEGSFLNLGIGQPTKIADHLPAELGVILHTENGMLGMGPAADGDQI 87

Query: 66  DDDLINAGKQHVTLLTGGAFFHHADSFSMMRGGHLDIAVLGAFQVSVKGDLANWHTGAEG 125
           D DL NAGK  VT L G ++FHHADSF+MMRGGHLD+ VLGA+QV+  GDLANWHTG   
Sbjct: 88  DPDLTNAGKVPVTELPGASYFHHADSFAMMRGGHLDVCVLGAYQVAANGDLANWHTGKPD 147

Query: 126 SIPAVGGAMDLATGARQVFVMMDHLTKTGESKLVPECTYPLTGIACVSRIYTDLAVLEVT 185
           +IPAVGGAMDLA GA+ V VMM    K G  KLV  C+YPLTG+ CVSR+YTD  + EV 
Sbjct: 148 AIPAVGGAMDLAIGAKDVLVMMTLFGKDGTPKLVRSCSYPLTGVGCVSRVYTDHGIFEVG 207

Query: 186 PEGLKVVEICADIDFDELQKLSGVPL 211
            E + VV     I   +L++  G+PL
Sbjct: 208 GESV-VVRATWGISVADLEERLGMPL 232


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: 224
Number of extensions: 12
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: 213
Length of database: 236
Length adjustment: 22
Effective length of query: 191
Effective length of database: 214
Effective search space:    40874
Effective search space used:    40874
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 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