GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Acidovorax sp. GW101-3H11

Align Crotonyl-CoA hydratase; EC 4.2.1.150 (characterized)
to candidate Ac3H11_4989 Enoyl-CoA hydratase (EC 4.2.1.17)

Query= SwissProt::Q0AVM1
         (260 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4989
          Length = 266

 Score =  133 bits (335), Expect = 3e-36
 Identities = 82/255 (32%), Positives = 127/255 (49%), Gaps = 1/255 (0%)

Query: 6   IILEKEEKLAVLYINRPKAMNALNKDTLLEIKDAVTAVNDDPAVELLIITGSGDKSFVAG 65
           ++LE+E  +A L  NRP+A+NA++         AV  V  DPAV  +++ G+G + F+AG
Sbjct: 13  LLLEREGAIATLRFNRPEALNAIDVPMANAFLAAVQTVAADPAVRAVVLCGNG-RGFMAG 71

Query: 66  ADIAFMQNLSAMEAREFGALGQKVFRLIEAMEKPVIAAVNGFALGGGCELAMCCDFRIAA 125
            D+A ++      A +          L+  M  PV+A V+G A G G  L +  D+ IAA
Sbjct: 72  GDLATLRADPVQSAIDILTPLNAALLLLAQMNAPVVAQVHGVAAGAGLSLLLMADYVIAA 131

Query: 126 SNAKFGQPEVGLGITPGFGGTQRLPRLVGPGMAKQLLYTADVINADEAFRIGLVNKVVQP 185
              +     + LG +   G +  LPR+VG   A ++    D   AD+A R+GLVN+VV  
Sbjct: 132 EGTRLNLAYINLGTSCDVGASWALPRIVGVRQALEIALLGDAFTADDALRLGLVNRVVPA 191

Query: 186 EELLPEVKKIAGRILSKGQLAVRLSKAAANEGMQTDIDRAMSIEADAFGLCFATQDQKEG 245
            EL      +A R+ S   LA    K      M   +   ++ E DAF  C  T+D + G
Sbjct: 192 AELDSATAALAQRLASGPTLAYGAMKRLMRASMDHTLPEQLAAEKDAFVHCAGTEDFRAG 251

Query: 246 MTAFLEKRKANFISK 260
           + AF  ++ A+F  +
Sbjct: 252 VEAFHLRQSASFAGR 266


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: 161
Number of extensions: 8
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: 266
Length adjustment: 25
Effective length of query: 235
Effective length of database: 241
Effective search space:    56635
Effective search space used:    56635
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