GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-dehydrog in Dyadobacter tibetensis Y620-1

Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_025763370.1 X939_RS0111250 glucose 1-dehydrogenase

Query= uniprot:A0A4P7ABK7
         (254 letters)



>NCBI__GCF_000566685.1:WP_025763370.1
          Length = 257

 Score =  153 bits (386), Expect = 4e-42
 Identities = 89/256 (34%), Positives = 147/256 (57%), Gaps = 20/256 (7%)

Query: 7   RLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIA---GVETHLL-- 61
           RL  K  LIT  + GIGR +  LFAREGA+++ +D+++   ++ A +    G E + +  
Sbjct: 2   RLKNKVALITGGSGGIGRETALLFAREGAQIVVSDVNQEMGQQTADMIVEQGGEAYFIYS 61

Query: 62  DVTDDDAIKALVA----KVGTVDVLFNCAGYVAAG--NILECDDKAWDFSFNLNAKAMFH 115
           DV+ D   KA+VA    K G +++LFN AG + +   N +  ++  WD + N+NAK +F 
Sbjct: 62  DVSKDADCKAMVAFTEEKFGKLNILFNNAGIMHSDDDNAMTTEESVWDLTMNINAKGVFL 121

Query: 116 TIRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIR 175
             +  +P +     GS++N AS  + +     + AY ASK AV+ LT+ +A     + IR
Sbjct: 122 GCKYGIPALQRAGGGSVINTASFVAILGAATPQIAYTASKGAVLALTRELAVIHARENIR 181

Query: 176 CNAICPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLAS 235
            NA+CPG + +  L + ++T+ K+  +         +   PMGR G+A+E+A+  L+LAS
Sbjct: 182 VNALCPGPLRTELLMKFLNTEEKKQRR---------LVHVPMGRFGEAKEMASAVLFLAS 232

Query: 236 DESNFTTGSIHMIDGG 251
           DES + TG+  ++DGG
Sbjct: 233 DESTYVTGTDFLVDGG 248


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: 152
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: 257
Length adjustment: 24
Effective length of query: 230
Effective length of database: 233
Effective search space:    53590
Effective search space used:    53590
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 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