GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Shewanella oneidensis MR-1

Align BadK (characterized)
to candidate 202993 SO3908 enoyl-CoA hydratase/isomerase family protein (NCBI ptt file)

Query= metacyc::MONOMER-943
         (258 letters)



>FitnessBrowser__MR1:202993
          Length = 245

 Score =  111 bits (277), Expect = 2e-29
 Identities = 75/237 (31%), Positives = 120/237 (50%), Gaps = 3/237 (1%)

Query: 14  VGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIASMAAW 73
           V II+ NRPD  NAL+  +   L   L+  +AD+ I A ++ G    F +G D+A     
Sbjct: 12  VRIISFNRPDKRNALDLNMYKQLTEYLIEGEADNDIRAFMLHGEDNCFTSGNDVADFL-- 69

Query: 74  SYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKFALPEI 133
             SD+  ++   R    + +++KP++AAV+G A G G  + L CD+V A  SAKF LP +
Sbjct: 70  KNSDLGPNHPAVRFLFCLLELKKPLVAAVSGAAVGIGTTVLLHCDLVYADNSAKFQLPFV 129

Query: 134 KLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETVAL 193
            L L+P AG +  LP  +G  KA ++ L     +A  A R  +++ V+  + L       
Sbjct: 130 NLALVPEAGASLLLPELVGYQKAAELLLLGESFDANTAHRLNIINDVIAQEELLAYAFNQ 189

Query: 194 ATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLEK 250
           A  +A    P  + +   L R  ++ +   +  E  +  AR  S +A+   QAFL+K
Sbjct: 190 AKKLAN-QPPQALQITRQLMRPHKNRVQHQMHQELEQFGARLKSDEAKARFQAFLKK 245


Lambda     K      H
   0.321    0.135    0.389 

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: 91
Number of extensions: 4
Number of successful extensions: 1
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: 245
Length adjustment: 24
Effective length of query: 234
Effective length of database: 221
Effective search space:    51714
Effective search space used:    51714
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: 46 (22.3 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