GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Shewanella loihica PV-4

Align SDR family oxidoreductase (characterized, see rationale)
to candidate 5209125 Shew_1603 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)

Query= uniprot:A0A4P7ABK7
         (254 letters)



>FitnessBrowser__PV4:5209125
          Length = 248

 Score =  134 bits (336), Expect = 2e-36
 Identities = 85/250 (34%), Positives = 132/250 (52%), Gaps = 18/250 (7%)

Query: 8   LAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETH--LLDVTD 65
           L GK  L+T A++GIGRA  E     GA VI T  S+     +    G + H  +L+VTD
Sbjct: 7   LTGKVALVTGASRGIGRAVAETLVEAGALVIGTATSERGAAAIQEYLGDKGHGLVLNVTD 66

Query: 66  DDAIKALVA----KVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVL 121
            ++I  L A    KVG VD+L N AG      ++   +  W    + N  +++ T + VL
Sbjct: 67  SESIDHLFASIKEKVGEVDILVNNAGITRDNLLMRMKEDEWTDIIDTNLTSLYRTSKQVL 126

Query: 122 PGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICP 181
             M+ K++G I+NI S   ++ G A +  Y A+KA ++G TKS+A +  S+ I  NAI P
Sbjct: 127 RAMMKKRSGRIINIGSVVGTM-GNAGQTNYCAAKAGLIGFTKSLAREVASRQITVNAIAP 185

Query: 182 GTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESNFT 241
           G I           Q   T +  +E +   +++ PM R+G+ +E+A   L+LASD + + 
Sbjct: 186 GFI-----------QTDMTDELTEEQQKGIMSQVPMERLGQPQEIANAVLFLASDSAAYI 234

Query: 242 TGSIHMIDGG 251
           TG    ++GG
Sbjct: 235 TGETLHVNGG 244


Lambda     K      H
   0.316    0.129    0.359 

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: 141
Number of extensions: 5
Number of successful extensions: 4
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: 254
Length of database: 248
Length adjustment: 24
Effective length of query: 230
Effective length of database: 224
Effective search space:    51520
Effective search space used:    51520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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