GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-dehydrog in Dechlorosoma suillum PS

Align SDR family oxidoreductase (characterized, see rationale)
to candidate Dsui_2538 Dsui_2538 acetoacetyl-CoA reductase

Query= uniprot:A0A4P7ABK7
         (254 letters)



>FitnessBrowser__PS:Dsui_2538
          Length = 246

 Score =  121 bits (304), Expect = 1e-32
 Identities = 82/253 (32%), Positives = 130/253 (51%), Gaps = 25/253 (9%)

Query: 11  KTVLITAAAQGIGRASTELFAREGARVIAT-----DISKTHLEELASIAGVETHLL---D 62
           K  L+T A  G+G A ++  A+EG +V+A      D  +  L E  + AG +  +L   D
Sbjct: 3   KVALVTGALGGLGTAISQALAKEGYKVVAAYHPEFDKKEEWLAEQEA-AGFKDFVLVPGD 61

Query: 63  VTDDDAIKALVA----KVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIR 118
           V+D ++ KA++A    K G +D+L N AG       ++ D   WD   N N  ++F+   
Sbjct: 62  VSDYESAKAMIAEAEAKAGPIDILVNNAGITRDKFFVKMDKGQWDAVINTNLNSLFNVTH 121

Query: 119 AVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNA 178
            V   M  +  G IVNI+S  + VKG A +  Y A+KA V+G TK++A +F ++G+  NA
Sbjct: 122 HVAAKMGERGWGRIVNISSV-NGVKGQAGQTNYSAAKAGVIGFTKALAQEFAAKGVTVNA 180

Query: 179 ICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDES 238
           I PG + +           K      +++    +   PM R+ K EE+ A  +YL S+ +
Sbjct: 181 IAPGYVAT-----------KMVTAIREDILKGIIDSVPMKRLAKPEEIGAAVVYLTSELA 229

Query: 239 NFTTGSIHMIDGG 251
            F TG+   I+GG
Sbjct: 230 GFVTGATLNINGG 242


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: 9
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: 246
Length adjustment: 24
Effective length of query: 230
Effective length of database: 222
Effective search space:    51060
Effective search space used:    51060
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