GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudomonas simiae WCS417

Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate GFF2094 PS417_10680 enoyl-CoA hydratase

Query= SwissProt::Q0AVM1
         (260 letters)



>FitnessBrowser__WCS417:GFF2094
          Length = 263

 Score =  138 bits (347), Expect = 1e-37
 Identities = 87/263 (33%), Positives = 137/263 (52%), Gaps = 14/263 (5%)

Query: 6   IILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKSFVAG 65
           ++ + +  +A + +NR    NAL+  TL  +   +   N DPAV ++++TG+G +SF AG
Sbjct: 7   VLTQVQAGVAWITLNRGPQRNALDIPTLKHLHALLDTFNTDPAVRVVVLTGNG-RSFCAG 65

Query: 66  ADIAFMQNLSAMEAREFGAL--------GQKVFRLIEAMEKPVIAAVNGFALGGGCELAM 117
           AD+A     +A EAR  GAL           +   +  ++KP IAA+NG A+G G +L +
Sbjct: 66  ADLA---EWAAAEAR--GALETYGWTDTAHALMTRLHTLDKPTIAAINGTAVGAGMDLTL 120

Query: 118 CCDFRIAASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIG 177
           CCD R+AA +A+F      +  +P  G +  LPRL+G   AK+LL+  ++ +AD A   G
Sbjct: 121 CCDLRVAAQSARFKAGYTSMAYSPDAGASWHLPRLIGSEQAKRLLFLDELWSADRALAAG 180

Query: 178 LVNKVVQPEELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEADAFGLCF 237
           LV +VV  + L      +A R+ +    A   +K    +G +  +   +  E  A  LC 
Sbjct: 181 LVGEVVTDDHLHAHTNALATRLANGPTFAFAQTKTLIRDGAERSLPAQLQAELAAGLLCG 240

Query: 238 ATQDQKEGMTAFLEKRKANFISK 260
            + D  E + A LEKR   F  K
Sbjct: 241 RSADGTEALRASLEKRLPIFSGK 263


Lambda     K      H
   0.319    0.136    0.378 

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: 123
Number of extensions: 4
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: 260
Length of database: 263
Length adjustment: 25
Effective length of query: 235
Effective length of database: 238
Effective search space:    55930
Effective search space used:    55930
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 (21.8 bits)
S2: 47 (22.7 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