GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Pseudomonas fluorescens FW300-N2C3

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate AO356_30295 AO356_30295 fatty-acid oxidation protein subunit alpha

Query= BRENDA::D3RXI0
         (252 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_30295
          Length = 703

 Score = 90.5 bits (223), Expect = 8e-23
 Identities = 64/173 (36%), Positives = 93/173 (53%), Gaps = 10/173 (5%)

Query: 6   IKVEKDERVARIKIANPPVNVLDMETMKEIISAIDEVEG---VDVIVFSGEGKSFSAGAE 62
           +  E +  VA I + NPPVN L  E    II A+        V  IV  G G++F AGA+
Sbjct: 7   VSYEVEGVVAVITVNNPPVNALTPEMRGSIIDAVTHANADPAVAAIVLMGGGQNFIAGAD 66

Query: 63  IKEHFPDKAPEMIRWFTQLIDKVLRCKAI-TVAAVKGFALGGGFELAIACDFVLASKNAK 121
           I++    KA  +    T +    L   A  TVAA+ G+ALGGG E A+AC + +A   AK
Sbjct: 67  IRQF--GKARTIT---TSMSAAALDASAKPTVAAIHGYALGGGLEHALACHYRIALPTAK 121

Query: 122 LGVPEITLAHYP-PVAIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKV 173
           LG+PE+ L   P       LPR++G   A +L+++   I A  A +IGL++++
Sbjct: 122 LGLPEVALGLIPGGGGTQRLPRLVGAAVATDLLVSSRHIHAPEALQIGLISQI 174


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: 362
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: 252
Length of database: 703
Length adjustment: 31
Effective length of query: 221
Effective length of database: 672
Effective search space:   148512
Effective search space used:   148512
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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