GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdh in Sphingomonas indica Dd16

Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate WP_085218348.1 B9N75_RS08190 3-hydroxybutyrate dehydrogenase

Query= uniprot:A0A4R8NY47
         (263 letters)



>NCBI__GCF_900177405.1:WP_085218348.1
          Length = 261

 Score =  114 bits (285), Expect = 2e-30
 Identities = 80/257 (31%), Positives = 118/257 (45%), Gaps = 12/257 (4%)

Query: 16  SLAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDAAVAPR--FF 73
           SL GK  +ITG  SGIG A  +   G GA +         + A +    +     R  + 
Sbjct: 2   SLKGKAALITGSTSGIGLAYAKTLAGAGAHIMLNGFGDRDAIAKIQREIEGLSGARTDYS 61

Query: 74  PCNLMNLEALRATFTEIETVMGGVDILINNAANDDRHKSEDVTPAYWDERLAVNLRHQFF 133
             +L N  A+ A   + ++ +GGVDILINNA        ++     W+  +A+NL   F 
Sbjct: 62  DADLTNPAAIEAMIGQAKSSLGGVDILINNAGMQHVAPVDEFPIDKWNAIIALNLSAAFH 121

Query: 134 CAQAVLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGVRV 193
             +  +P M+E+K G I++  S    +  P+ + Y+ AK GI G+T  +A +    G+ V
Sbjct: 122 AIRLAVPHMKEKKWGRIISTASAHSLVASPNKSAYVAAKHGIAGLTKTVALEVATHGITV 181

Query: 194 NAIIPGAI----------RTPRQTLLWHTPEEEAKILAAQCLPVRVDPHDVAALALFLSS 243
           N I PG +           T +   L         +LAAQ     V P  VA+LAL+L S
Sbjct: 182 NCISPGYVWTQLVEDQIPDTMKSRGLTREQVMNDVLLAAQPTKQFVTPEQVASLALYLCS 241

Query: 244 DSGAKCTGREYYVDAGW 260
           D  A  TG    +D GW
Sbjct: 242 DDAAAITGANLSMDGGW 258


Lambda     K      H
   0.322    0.137    0.417 

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: 171
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: 263
Length of database: 261
Length adjustment: 25
Effective length of query: 238
Effective length of database: 236
Effective search space:    56168
Effective search space used:    56168
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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