GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Sphingomonas koreensis DSMZ 15582

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate Ga0059261_2908 Ga0059261_2908 Enoyl-CoA hydratase/carnithine racemase

Query= BRENDA::O87873
         (258 letters)



>FitnessBrowser__Korea:Ga0059261_2908
          Length = 275

 Score = 95.9 bits (237), Expect = 8e-25
 Identities = 82/261 (31%), Positives = 122/261 (46%), Gaps = 25/261 (9%)

Query: 9   KVWLERDGSLLRLRLARP-KANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHFSFG 67
           +V + R G++  +RL RP K N +D  M  A+  A       P +RAV+L  EG  F  G
Sbjct: 12  RVSIGRAGAVADIRLRRPFKMNALDGPMFDALIAAAESVAVDPTIRAVVLSGEGKAFCAG 71

Query: 68  A---SVDEHMPDQCAQMLKSL-HGLVREMLDS-------PVPILVALRGQCLGGGLEVAA 116
               S+   M D+  Q ++S  HGL      +       PVP++ AL G   GGGL++  
Sbjct: 72  IDLESLQALMSDEGKQAMQSRSHGLANRYQQAALAWREVPVPVIAALHGVAFGGGLQIPL 131

Query: 117 AGNLLFAAPDAKFGQPEIRLGVFAP-AASCLLPPRVGQACAEDLLWSGRSIDGAEGHRIG 175
             ++  +APD KF   E+R G+    A + LL   V +    +L+++ R   G E   +G
Sbjct: 132 GADIRISAPDTKFSLMEVRWGIVPDMAGTVLLRSIVREDVLRELIYTARVFTGIEAASMG 191

Query: 176 LIDVLAEDPEAAALRWFDEHIARLSASSLRFAVRAARCDSVPRIKQKLDTVEALYLEE-- 233
           ++  LA +P  AAL      +A   A     AVRAA+   +    Q +    AL  E   
Sbjct: 192 IVTQLAANPHVAAL-----ELASSIAEQGPRAVRAAK--QLLNETQSVSPQVALLSESEA 244

Query: 234 ---LMASHDAVEGLKAFLEKR 251
              L+A  D +E L A  E+R
Sbjct: 245 QVGLLAGPDQIEALNAHAEQR 265


Lambda     K      H
   0.321    0.135    0.402 

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: 173
Number of extensions: 10
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: 258
Length of database: 275
Length adjustment: 25
Effective length of query: 233
Effective length of database: 250
Effective search space:    58250
Effective search space used:    58250
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: 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