GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HDOP-hydrol in Rhodococcus qingshengii djl-6-2

Align FAA hydrolase family protein (characterized, see rationale)
to candidate WP_050656959.1 C1M55_RS12530 fumarylacetoacetate hydrolase family protein

Query= uniprot:A0A2E7P912
         (281 letters)



>NCBI__GCF_002893965.1:WP_050656959.1
          Length = 257

 Score =  143 bits (360), Expect = 4e-39
 Identities = 77/185 (41%), Positives = 113/185 (61%), Gaps = 4/185 (2%)

Query: 72  KFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKTDWEVELGVVI 131
           K ICIG NYADH AE     PA+PV+F K  +++VGP   + +P  S +  +E EL VVI
Sbjct: 59  KVICIGKNYADHIAEMGGEAPADPVIFLKPNTSIVGPGAPIVLPPTSNEVHFEGELAVVI 118

Query: 132 GKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGPIGPWLVTRDEV 191
           G+    +    A+S V GY + NDVS R++Q    G W + KG DTF P+GPW+ T  + 
Sbjct: 119 GQPCKDVPAAKALSVVLGYTIANDVSARDHQ-RHDGQWTRAKGHDTFCPLGPWIETSLDA 177

Query: 192 ADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVISTGTPPGVGMGV 251
           +D   + +  EV+G+  Q+ +T+ ++  +  I+ ++S  M+L PGDVI TGTP GVG  V
Sbjct: 178 SD---VDIRTEVNGQVKQDSSTAFLLHDIPKIIEWISAVMTLLPGDVILTGTPAGVGPIV 234

Query: 252 KPEAV 256
             ++V
Sbjct: 235 DGDSV 239


Lambda     K      H
   0.316    0.138    0.419 

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: 229
Number of extensions: 7
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: 281
Length of database: 257
Length adjustment: 25
Effective length of query: 256
Effective length of database: 232
Effective search space:    59392
Effective search space used:    59392
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: 42 (22.0 bits)
S2: 47 (22.7 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