GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-dehydrog in Salinicoccus carnicancri Crm

Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_017548686.1 C792_RS0106680 glucose 1-dehydrogenase

Query= uniprot:A0A4P7ABK7
         (254 letters)



>NCBI__GCF_000330705.1:WP_017548686.1
          Length = 243

 Score =  134 bits (338), Expect = 1e-36
 Identities = 88/252 (34%), Positives = 138/252 (54%), Gaps = 20/252 (7%)

Query: 6   GRLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIAGVETHLL--DV 63
           GR+ GK V++T    G+G +  + F  EGA+V+ TD+ +     L    G ++  +  DV
Sbjct: 2   GRVNGKVVIVTGGTGGMGASHVKKFVSEGAQVVFTDLDEGAGRVLQDEMGPQSLFIKQDV 61

Query: 64  TDDDAIKALVAK----VGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRA 119
           TD ++   ++ +    +G V+VL N AG   +       +  +D    +N KA+F  ++A
Sbjct: 62  TDSESWNKVIVETEKNLGPVNVLVNNAGVNYSEETEAFPEDEYDRVIEVNQKAVFLGMKA 121

Query: 120 VLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAI 179
           V+P M    +GSI+NI+S    ++G     AY ASK AV G+TK  A +    GIR N++
Sbjct: 122 VIPSMKKAASGSIINISSIGG-IRGRMESVAYSASKFAVTGMTKVGALELGKYGIRVNSV 180

Query: 180 CPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESN 239
            P  + +   ++  ST  K           A  + +P+GR+   EEV+AL LYLASDES+
Sbjct: 181 HPSLVNTGLFSE--STGGK-----------AVASDRPLGRVLTKEEVSALVLYLASDESS 227

Query: 240 FTTGSIHMIDGG 251
           +TTG+ H+IDGG
Sbjct: 228 YTTGAEHVIDGG 239


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: 158
Number of extensions: 12
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: 243
Length adjustment: 24
Effective length of query: 230
Effective length of database: 219
Effective search space:    50370
Effective search space used:    50370
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.

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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