GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-dehydrog in Pseudomonas fluorescens FW300-N2E3

Align SDR family oxidoreductase (characterized, see rationale)
to candidate AO353_01660 AO353_01660 short-chain dehydrogenase

Query= uniprot:A0A4P7ABK7
         (254 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_01660
          Length = 253

 Score =  139 bits (349), Expect = 7e-38
 Identities = 94/254 (37%), Positives = 136/254 (53%), Gaps = 21/254 (8%)

Query: 9   AGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLE---ELASIAGVETHLL--DV 63
           +G+  L+T AA GIGRA+ + FA EG +V+  D+     E   EL   AG E   +  +V
Sbjct: 6   SGQVALVTGAAAGIGRATAQAFAAEGLKVVVADLDVAGGEGTAELIRAAGGEAVFVQCNV 65

Query: 64  TDDDAIKALVAKV----GTVDVLFNCAGY-VAAGNILECDDKAWDFSFNLNAKAMFHTIR 118
           T +  ++ L+AK     G +D  FN AG  +  G + E     +D    +N K ++  ++
Sbjct: 66  TQESDVQNLMAKAVSTYGRLDYAFNNAGIEIEKGKLAEGTLDEFDAIMGVNVKGVWLCMK 125

Query: 119 AVLPGMLAKKAGSIVNIASAASSVKGVANRFA-YGASKAAVVGLTKSVAADFVSQGIRCN 177
             LP MLA+  G+IVN AS A    G A + + Y ASK AV+GLTKS A ++  + IR N
Sbjct: 126 YQLPLMLAQGGGAIVNTASVAGL--GAAPKMSIYAASKHAVIGLTKSAAIEYAKKKIRVN 183

Query: 178 AICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDE 237
           A+CP  I++    +      K+   +         A  P+GRIGK EE+A+  LYL SD 
Sbjct: 184 AVCPAVIDTDMFRRAYEADPKKADFA--------AAMHPVGRIGKVEEIASAVLYLCSDG 235

Query: 238 SNFTTGSIHMIDGG 251
           + FTTG    +DGG
Sbjct: 236 AAFTTGHSLAVDGG 249


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: 138
Number of extensions: 10
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: 253
Length adjustment: 24
Effective length of query: 230
Effective length of database: 229
Effective search space:    52670
Effective search space used:    52670
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: 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