GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HDOP-hydrol in Brucella inopinata BO1

Align FAA hydrolase family protein (characterized, see rationale)
to candidate WP_008507772.1 BIBO1_RS12805 fumarylacetoacetate hydrolase family protein

Query= uniprot:A0A2E7P912
         (281 letters)



>NCBI__GCF_000182725.1:WP_008507772.1
          Length = 281

 Score =  398 bits (1022), Expect = e-116
 Identities = 182/276 (65%), Positives = 226/276 (81%), Gaps = 1/276 (0%)

Query: 1   MKLLRYGPVGQEKPGVLDQSGKIRDLSAYIKDVNGAVLDDASLDKIRKLDLESLPAVEGS 60
           MK LRYG  GQEKPG+LD  G IRDLSA++ D++GA LD  +L K+  LD+ SLP VEG+
Sbjct: 1   MKFLRYGATGQEKPGLLDADGTIRDLSAHVSDLSGAALDPDALAKLGALDVNSLPKVEGN 60

Query: 61  PRIGACVGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKK 120
           PRIG CV   GKFICIGLNY+DHAAE+   +P+EP++F K TSA+VGPNDD+ IPRGS+K
Sbjct: 61  PRIGPCVAGTGKFICIGLNYSDHAAETGAAVPSEPIIFMKATSAIVGPNDDLVIPRGSQK 120

Query: 121 TDWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTWDKGKGCDTFGP 180
           TDWEVELG++IGK   Y+ E+DA+ +VAGYC ++DVSER +QIER G W KGK CDTFGP
Sbjct: 121 TDWEVELGIIIGKTAKYVSEEDALDYVAGYCTIHDVSERAFQIERQGQWTKGKSCDTFGP 180

Query: 181 IGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVIS 240
            GPWLVT+DE+ADP+ L MWL+V+G+  QNG++ TMI+GV H+VSYLS+FMSLQPGD+IS
Sbjct: 181 TGPWLVTKDEIADPENLAMWLKVNGETMQNGSSRTMIYGVRHLVSYLSQFMSLQPGDIIS 240

Query: 241 TGTPPGVGMGVKPEAVYLRAGQTMRLGIDGLGEQQQ 276
           TGTPPGVGMG+KP   YL+AG  + LGI+GLG Q+Q
Sbjct: 241 TGTPPGVGMGMKPPR-YLKAGDVVELGIEGLGSQKQ 275


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: 368
Number of extensions: 6
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: 281
Length of database: 281
Length adjustment: 26
Effective length of query: 255
Effective length of database: 255
Effective search space:    65025
Effective search space used:    65025
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