GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HDOP-hydrol in Pantoea rwandensis LMG 26275

Align FAA hydrolase family protein (characterized, see rationale)
to candidate WP_084936660.1 HA51_RS21730 fumarylacetoacetate hydrolase family protein

Query= uniprot:A0A2E7P912
         (281 letters)



>NCBI__GCF_002095475.1:WP_084936660.1
          Length = 278

 Score =  135 bits (339), Expect = 1e-36
 Identities = 92/279 (32%), Positives = 140/279 (50%), Gaps = 21/279 (7%)

Query: 6   YGPVGQEKPGVLDQSGKIRDLSAYIKDV--NGAVLDDASLDKIRKLDLESLPAVE--GSP 61
           YG V +E  GV+D   ++      +K +   GAV D  +          SLPA     + 
Sbjct: 16  YGIVREE--GVIDVGSRLGAECPDLKSLLQRGAVSDLEAFS--------SLPADHPYSAI 65

Query: 62  RIGACVGNIGKFICIGLNYADHAAESNLPIPAEPVVFNKWTSAVVGPNDDVKIPRGSKKT 121
           R    V N GK  C+G+NYAD   E    + A P +F ++  ++ G    +  P  +++ 
Sbjct: 66  RFLPVVENPGKVFCVGMNYADKRKEFAETLDA-PTLFVRFADSLAGHEQPLLKPATTQEF 124

Query: 122 DWEVELGVVIGKGGSYIDEKDAMSHVAGYCVVNDVSEREYQIERGGTW-DKGKGCDTFGP 180
           D+E EL V+IGK    +   DA+ HVAGY    D + R+ Q     TW   GK     G 
Sbjct: 125 DYEGELAVIIGKAAYQVKAADALQHVAGYSCFMDATVRDMQF----TWFTAGKNWQQTGG 180

Query: 181 IGPWLVTRDEVADPQKLGMWLEVDGKRYQNGNTSTMIFGVAHIVSYLSRFMSLQPGDVIS 240
            GPW+ T DE+ DPQ+L +   ++ +  QN  T++M+  VA I+ Y+S F  L PGDVI 
Sbjct: 181 FGPWMTTADEIPDPQQLAIKTWLNEREVQNDTTASMVHPVAKIIEYISAFSPLSPGDVII 240

Query: 241 TGTPPGVGMGVKPEAVYLRAGQTMRLGIDGLGEQQQKTI 279
           TG+P GVG    P  +++  G  + + I+ +G  +   +
Sbjct: 241 TGSPGGVGKKRTP-PLFMFPGDVIEVEIEKIGRLRHTVV 278


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: 232
Number of extensions: 14
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: 278
Length adjustment: 26
Effective length of query: 255
Effective length of database: 252
Effective search space:    64260
Effective search space used:    64260
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