GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bch in Pseudomonas simiae WCS417

Align 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial; 3-hydroxyisobutyryl-coenzyme A hydrolase; HIB-CoA hydrolase; HIBYL-CoA-H; EC 3.1.2.4 (characterized)
to candidate GFF2714 PS417_13845 enoyl-CoA hydratase

Query= SwissProt::Q5XIE6
         (385 letters)



>FitnessBrowser__WCS417:GFF2714
          Length = 257

 Score =  103 bits (258), Expect = 4e-27
 Identities = 68/193 (35%), Positives = 106/193 (54%), Gaps = 9/193 (4%)

Query: 37  VLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKGAGGKAFCAG 96
           +LLE +G  G+ITLNRP+ LNAL+  ++ ++   L   E DP    I++ G+  KAF AG
Sbjct: 6   ILLEVQGRVGLITLNRPQALNALNAQLVSELNQALDGLEADPQIGCIVLTGSR-KAFAAG 64

Query: 97  GDIKALSEAKKAGQTLSQDLFREEYILNNAIASCQKPYVALIDGITMGGGVGLSVHGQFR 156
            DIK ++E     Q    DLF +    ++ +A+ +KP +A ++G  +GGG  L++   F 
Sbjct: 65  ADIKEMAELTYP-QIYLDDLFSD----SDRVANRRKPIIAAVNGFALGGGCELALMCDFI 119

Query: 157 VATERSLFAMPETGIGLFPDVGGGYFLPRLQGKL-GYFLALTGFRLKGRDVHRAGIATHF 215
           +A + + F  PE  +G+ P +GG   L R  GK     + LTG  +   +  R GI    
Sbjct: 120 LAGDGAKFGQPEINLGVLPGMGGTQRLTRAVGKAKAMEMCLTGRFIDAVEAERCGIVARI 179

Query: 216 VDSEKLHVLEEEL 228
           V +++L  LEE L
Sbjct: 180 VPADEL--LEEAL 190


Lambda     K      H
   0.320    0.136    0.394 

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: 181
Number of extensions: 9
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: 385
Length of database: 257
Length adjustment: 27
Effective length of query: 358
Effective length of database: 230
Effective search space:    82340
Effective search space used:    82340
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: 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