GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-dehydrog in Echinicola vietnamensis KMM 6221, DSM 17526

Align SDR family oxidoreductase (characterized, see rationale)
to candidate Echvi_4610 Echvi_4610 3-oxoacyl-(acyl-carrier-protein) reductase

Query= uniprot:A0A4P7ABK7
         (254 letters)



>FitnessBrowser__Cola:Echvi_4610
          Length = 248

 Score =  145 bits (365), Expect = 1e-39
 Identities = 95/255 (37%), Positives = 142/255 (55%), Gaps = 22/255 (8%)

Query: 6   GRLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTH----LEELASIAGVETHLL 61
           G L GKT LIT A++GIGRA    +A+EGA V  T +S       LE+  +  GV+    
Sbjct: 2   GLLTGKTALITGASKGIGRAIALKYAQEGANVAFTFLSSVEKGQALEKELAEFGVKAKGF 61

Query: 62  --DVTDDDAIKALVAKV----GTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFH 115
             D +D  A + LV +V    G +DVL N AG      ++  +++AWD   N+N K+ F+
Sbjct: 62  RSDASDFKAAEELVNEVVKEFGALDVLINNAGVTRDNLLMRMNEEAWDDVMNINLKSCFN 121

Query: 116 TIRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIR 175
           T++A    ++ +KAGSI+NI S    +KG A +  Y ASKA ++G TKSVA +  S+GIR
Sbjct: 122 TVKAATRTLMKQKAGSIINITSVV-GIKGNAGQANYAASKAGIIGFTKSVALELGSRGIR 180

Query: 176 CNAICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLAS 235
            NA+ PG IE+           + T   +++    +    PM R G+ EEVA   ++L S
Sbjct: 181 SNAVAPGFIET-----------EMTEVLDEKTVQGWRDAIPMKRGGQPEEVANACVFLGS 229

Query: 236 DESNFTTGSIHMIDG 250
           D S++ +G +  +DG
Sbjct: 230 DMSSYVSGQVIQVDG 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: 156
Number of extensions: 7
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