GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Escherichia coli BW25113

Align BadK (characterized)
to candidate 14182 b0036 crotonobetainyl CoA hydratase (RefSeq)

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



>FitnessBrowser__Keio:14182
          Length = 261

 Score =  129 bits (325), Expect = 5e-35
 Identities = 96/264 (36%), Positives = 135/264 (51%), Gaps = 9/264 (3%)

Query: 1   MSSNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTR 59
           MS +  LT   G +  ITL+RP   NA++      +G   L F  D  +   +I G   +
Sbjct: 1   MSESLHLTRN-GSILEITLDRPKA-NAIDAKTSFEMGEVFLNFRDDPQLRVAIITGAGEK 58

Query: 60  AFAAGADIASMAAWSYSDV-YGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACD 118
            F+AG D+ + A     D  +G        E I  + KPV+AAV G A+GGG ELALA D
Sbjct: 59  FFSAGWDLKAAAEGEAPDADFGPGGFAGLTE-IFNLDKPVIAAVNGYAFGGGFELALAAD 117

Query: 119 IVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVS 178
            ++   +A FALPE KLG++P +GG  RLP+ +  A   +M ++ R + AEEA R+G+V+
Sbjct: 118 FIVCADNASFALPEAKLGIVPDSGGVLRLPKILPPAIVNEMVMTGRRMGAEEALRWGIVN 177

Query: 179 RVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASA 238
           RVV    L D    LA  +   +  A+ ALKE      E  + E   + R  +   + S 
Sbjct: 178 RVVSQAELMDNARELAQQLVNSAPLAIAALKEIYRTTSEMPVEEAYRYIRSGVLKHYPSV 237

Query: 239 ----DAREGIQAFLEKRAPCFSHR 258
               DA EG  AF EKR P +  R
Sbjct: 238 LHSEDAIEGPLAFAEKRDPVWKGR 261


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: 106
Number of extensions: 6
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: 261
Length adjustment: 24
Effective length of query: 234
Effective length of database: 237
Effective search space:    55458
Effective search space used:    55458
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