GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Halioglobus japonicus S1-36

Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate WP_102106165.1 C0029_RS05670 enoyl-CoA hydratase

Query= SwissProt::Q0AVM1
         (260 letters)



>NCBI__GCF_002869505.1:WP_102106165.1
          Length = 264

 Score =  142 bits (359), Expect = 5e-39
 Identities = 82/227 (36%), Positives = 133/227 (58%), Gaps = 3/227 (1%)

Query: 6   IILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKSFVAG 65
           +I+ + E +A+L +NRP + NAL+   L  +  A++ +++DP V  +++TG G K+F  G
Sbjct: 13  LIVSQGEGVALLELNRPDSFNALSVSLLDALVAALSTLSEDPTVSAIVLTGRG-KAFSVG 71

Query: 66  ADIAFMQNLSA-MEAREFGALGQKVFRLIEAMEKPVIAAVNGFALGGGCELAMCCDFRIA 124
            D+  + + +  ME+ E G  G  V R     +KP+I AVNGFA+ GG E+A+ CDF  A
Sbjct: 72  VDLKELASGNGLMESGELGP-GGSVMRAFNGCQKPIIGAVNGFAVTGGFEIALACDFLYA 130

Query: 125 ASNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLVNKVVQ 184
           A +A+F      +G+ PG+G +Q+LPRLVG   A+++ +T +   A +A   GLVN+V  
Sbjct: 131 AESARFADTHARVGLIPGWGLSQKLPRLVGINRAREISFTGNYFGAADAEAWGLVNRVCS 190

Query: 185 PEELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEAD 231
             +LL E    A +I +    A+   KA  NEG +  +  A+ +E +
Sbjct: 191 DNDLLAEALDTAHQIATALPEALFAIKAMMNEGWEDTLGHALVMEGE 237


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: 164
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: 260
Length of database: 264
Length adjustment: 25
Effective length of query: 235
Effective length of database: 239
Effective search space:    56165
Effective search space used:    56165
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 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