GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Burkholderia phytofirmans PsJN

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase monomer (EC 4.2.1.100) (characterized)
to candidate BPHYT_RS28015 BPHYT_RS28015 enoyl-CoA hydratase

Query= metacyc::MONOMER-18320
         (256 letters)



>FitnessBrowser__BFirm:BPHYT_RS28015
          Length = 382

 Score = 70.1 bits (170), Expect = 6e-17
 Identities = 58/194 (29%), Positives = 91/194 (46%), Gaps = 10/194 (5%)

Query: 6   ILFEKKDKVATITLNVPNS-NWLTIPMMKEINEALMDVKKDPTIQLLVFDHAGDKAFCDG 64
           ILF   ++VA ITLN P + N L+  M++E+   +   + D  I  LV   AG K FC G
Sbjct: 19  ILFRVVNRVAIITLNRPAALNALSHAMVRELAVLVEHCRTDDGIVALVLKGAGAKGFCAG 78

Query: 65  VDVADH---VPEKVDEMIDLFHGMFRNMAAMDVTS---VCLVNGRSLGGGCELMAFCDIV 118
            DV +            +  F   +R   A+       V L++G ++GGG  L     + 
Sbjct: 79  GDVREVQRLAKNNDSRWLAFFVDEYRLDYALHTFPKPVVALLDGIAMGGGMGLGQGARLR 138

Query: 119 IASEKAKIGQPEINLAVFPPVAAAWFPKIMGLKKAMELILTGKIISAKEAEAIGLVNVVL 178
           I +E++KI  PE  +   P V A  F  +M  +  + + LTG  +S  +A  + L ++ +
Sbjct: 139 IVTERSKIAMPETRIGFLPDVGATRFLSVMPAELELYVGLTGATLSGADALRLQLADLCV 198

Query: 179 PVE---GFREAAQK 189
           P E    F E  Q+
Sbjct: 199 PAEWLASFEERLQR 212


Lambda     K      H
   0.322    0.136    0.401 

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: 186
Number of extensions: 9
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: 256
Length of database: 382
Length adjustment: 27
Effective length of query: 229
Effective length of database: 355
Effective search space:    81295
Effective search space used:    81295
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 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