GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DKDP-dehydrog in Methylocystis bryophila S285

Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_085771999.1 B1812_RS13135 glucose 1-dehydrogenase

Query= uniprot:A0A4P7ABK7
         (254 letters)



>NCBI__GCF_002117405.1:WP_085771999.1
          Length = 249

 Score =  129 bits (323), Expect = 7e-35
 Identities = 81/252 (32%), Positives = 136/252 (53%), Gaps = 14/252 (5%)

Query: 6   GRLAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELAS-----IAGVETHL 60
           G+L+GK  ++T    GIG ++ +LFA EGA ++ T   K  L+   +       GV+  +
Sbjct: 2   GKLSGKVAVVTGGNSGIGLSTAQLFAAEGAHLVVTGRRKAELDTAVAEIGHGAVGVQGDV 61

Query: 61  LDVTDDDAIKALV-AKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRA 119
             + D DA+ A V +K G +D+LF  AG      ++   ++ +D  F++N K +  T++ 
Sbjct: 62  SKLADLDALYAEVKSKFGRIDILFANAGVCELAPLVGVSEEHFDKVFDINVKGLLFTVQK 121

Query: 120 VLPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAI 179
            LP  L    GSI+ + S+ ++  G+     Y A+KAAV    ++  ++   + IR N I
Sbjct: 122 ALP--LFADGGSII-LNSSVANTTGIPAFGVYSATKAAVRSFARTWTSELKDRNIRVNVI 178

Query: 180 CPGTIESPSLNQRISTQAKETGKSEDEVRAAFVARQPMGRIGKAEEVAALALYLASDESN 239
            PG IE+P    ++   A++      E  A   A+ P+GR GK EE+A  AL+LASD+++
Sbjct: 179 SPGPIETPIFG-KVGLSAEQL----QEFDAQISAKVPLGRFGKPEEIAKAALFLASDDAS 233

Query: 240 FTTGSIHMIDGG 251
           +  G+   +DGG
Sbjct: 234 YVAGADLYVDGG 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: 160
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: 249
Length adjustment: 24
Effective length of query: 230
Effective length of database: 225
Effective search space:    51750
Effective search space used:    51750
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 Apr 09 2024. 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