GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-dehydrog in Shewanella amazonensis SB2B

Align SDR family oxidoreductase (characterized, see rationale)
to candidate 6936328 Sama_0517 D-beta-hydroxybutyrate dehydrogenase (RefSeq)

Query= uniprot:A0A4P7ABK7
         (254 letters)



>FitnessBrowser__SB2B:6936328
          Length = 266

 Score =  135 bits (339), Expect = 1e-36
 Identities = 85/265 (32%), Positives = 136/265 (51%), Gaps = 13/265 (4%)

Query: 1   MSASTGRLAGKTVLITAAAQGIGRASTELFAREGARVIA-----TDISKTHLEELASIAG 55
           MS     L GK  LIT +  GIG A+ ++ A +G  +I       D  ++   + A+   
Sbjct: 1   MSGGQRSLEGKVGLITGSTSGIGLATAQVLAEQGCNLILHGLLPEDEGQSMAADFAAQYR 60

Query: 56  VETHL--LDVTDDDAIKALVAK----VGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLN 109
           + T     D+   ++I   +A+    +G++D+L N AG     ++     + W+    +N
Sbjct: 61  IRTFFSNADLRQPESIHRFMAEGTKALGSIDILINNAGIQHTDSVASFPIEKWNDIIAIN 120

Query: 110 AKAMFHTIRAVLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADF 169
             + FHT++  +P M  K+ G I+NIAS    V  V N+ AY A+K  +VGLTK VA + 
Sbjct: 121 LSSAFHTMQQAVPAMAQKRWGRIINIASVHGLVASV-NKAAYCAAKHGIVGLTKVVAIEC 179

Query: 170 VSQGIRCNAICPGTIESPSLNQRISTQAKETGKSEDEVRAAFV-ARQPMGRIGKAEEVAA 228
             QGI  NAICPG +++P +N++I   A   G    E R   V A+QP+  +    ++  
Sbjct: 180 AEQGITVNAICPGWVDTPLINKQIEAVANTKGLDYHEARYQLVTAKQPLPEMLDPRQIGE 239

Query: 229 LALYLASDESNFTTGSIHMIDGGWS 253
            AL+L  D +   TG+   +DGGW+
Sbjct: 240 FALFLCGDAARGITGASLAMDGGWT 264


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: 147
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: 266
Length adjustment: 24
Effective length of query: 230
Effective length of database: 242
Effective search space:    55660
Effective search space used:    55660
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 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