GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-dehydrog in Leeuwenhoekiella blandensis MED217

Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_009780166.1 MED217_RS08850 3-oxoacyl-[acyl-carrier-protein] reductase

Query= uniprot:A0A4P7ABK7
         (254 letters)



>NCBI__GCF_000152985.1:WP_009780166.1
          Length = 248

 Score =  122 bits (305), Expect = 9e-33
 Identities = 80/254 (31%), Positives = 136/254 (53%), Gaps = 22/254 (8%)

Query: 8   LAGKTVLITAAAQGIGRASTELFAREGARVIATDISKT----HLEELASIAGVET--HLL 61
           L GK  +IT A++GIG    ++FA+ GA V  T  S       LE+  +  GV+   +  
Sbjct: 4   LEGKNTIITGASRGIGNGIAKVFAQNGANVAFTYSSSAGPAEELEKELTAMGVKAKAYKS 63

Query: 62  DVTDDDAIKALVAKVG----TVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTI 117
           D +  +A + L+ ++     ++DVL N AG      ++   ++ +D    +N K++F+  
Sbjct: 64  DASSFEACQDLIKQISEDFDSIDVLVNNAGITKDNLLMRMGEEDFDKVLEVNLKSIFNMT 123

Query: 118 RAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCN 177
           +AV   ML ++ GSI+N++S    +KG A +  Y ASKA ++G +KS+A +  S+ IR N
Sbjct: 124 KAVQRTMLKQRHGSIINMSSVVG-IKGNAGQANYAASKAGIIGFSKSMALELGSRNIRTN 182

Query: 178 AICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDE 237
            + PG IE+           + T K +++V A +    P+ R G  E++A   ++L SD 
Sbjct: 183 VVAPGFIET-----------EMTAKLDEKVVAGWRDAIPLKRGGTPEDIANACVFLGSDM 231

Query: 238 SNFTTGSIHMIDGG 251
           S + TG +  +DGG
Sbjct: 232 SAYVTGQVLQVDGG 245


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: 125
Number of extensions: 7
Number of successful extensions: 3
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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