GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Stenotrophomonas chelatiphaga DSM 21508

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_057507562.1 ABB28_RS04910 enoyl-CoA hydratase

Query= BRENDA::D3RXI0
         (252 letters)



>NCBI__GCF_001431535.1:WP_057507562.1
          Length = 265

 Score =  114 bits (285), Expect = 2e-30
 Identities = 79/253 (31%), Positives = 130/253 (51%), Gaps = 9/253 (3%)

Query: 6   IKVEKDERVARIKIANPPVN---VLDMETMKEIISAIDEVEGVDVIVFSGEG-KSFSAGA 61
           +KVE D  VA I + NPP +   V  +  ++++++A++    +  +V SGEG K FSAGA
Sbjct: 12  LKVEADGHVAVITLHNPPAHTWTVHSLAALRDLVAALNADRSIYALVISGEGEKFFSAGA 71

Query: 62  EIKEHFPDK---APEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASK 118
           ++ +        A E  R F +  + +   + +++AA+ G+A+GGG E A+ACD  +  +
Sbjct: 72  DLNQFASGDRGAAREAARRFGEAFEALSGFRGVSIAAINGYAMGGGLECALACDLRIIEE 131

Query: 119 NAKLGVPEITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDE 177
           +A++ +PE T+   P       LPR++G   A  +IL GE I A+ A  IGL  +     
Sbjct: 132 HAQVALPEATVGLLPCAGGTQNLPRLVGEGWAKRMILLGERIDADTAVRIGLAEQKAGKG 191

Query: 178 NFEESVNDFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVEG 237
             +    ++     ++S  ++    K L+ ST     +   V        L  S D VEG
Sbjct: 192 EAKALALEWAKKAGKQSPTSIAAC-KTLVQSTRTGTHAAALVAEREAFVDLFDSADQVEG 250

Query: 238 LKAFLEKRKPEWK 250
           + AFLEKR  +WK
Sbjct: 251 VSAFLEKRSAQWK 263


Lambda     K      H
   0.318    0.136    0.382 

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: 150
Number of extensions: 9
Number of successful extensions: 4
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: 252
Length of database: 265
Length adjustment: 24
Effective length of query: 228
Effective length of database: 241
Effective search space:    54948
Effective search space used:    54948
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: 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