GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Methylocystis bryophila S285

Align Galactitol 2-dehydrogenase; GDH; Sorbitol dehydrogenase; SorbD; EC 1.1.1.16; EC 1.1.1.- (characterized)
to candidate WP_085771999.1 B1812_RS13135 glucose 1-dehydrogenase

Query= SwissProt::A9CES4
         (256 letters)



>NCBI__GCF_002117405.1:WP_085771999.1
          Length = 249

 Score =  157 bits (396), Expect = 3e-43
 Identities = 96/251 (38%), Positives = 141/251 (56%), Gaps = 8/251 (3%)

Query: 2   RLNNKVALITGAARGIGLGFAQAFAAEGAKVIIADIDIARATTSAAAIGPAAKAVKLDVT 61
           +L+ KVA++TG   GIGL  AQ FAAEGA +++     A   T+ A IG  A  V+ DV+
Sbjct: 3   KLSGKVAVVTGGNSGIGLSTAQLFAAEGAHLVVTGRRKAELDTAVAEIGHGAVGVQGDVS 62

Query: 62  DLAQIDAVVKAVDEEFGGIDILVNNAAIFDMAPINGITEESYERVFDINLKGPMFMMKAV 121
            LA +DA+   V  +FG IDIL  NA + ++AP+ G++EE +++VFDIN+KG +F    V
Sbjct: 63  KLADLDALYAEVKSKFGRIDILFANAGVCELAPLVGVSEEHFDKVFDINVKGLLF---TV 119

Query: 122 SNVMIARARGGKIINMASQAGRRGEALVTLYCASKAAIISATQSAALALVKHGINVNAIA 181
              +   A GG II  +S A   G     +Y A+KAA+ S  ++    L    I VN I+
Sbjct: 120 QKALPLFADGGSIILNSSVANTTGIPAFGVYSATKAAVRSFARTWTSELKDRNIRVNVIS 179

Query: 182 PGVVDGEHWEVVDAHFAKWEGLKPGEKKAAVAKSVPIGRFATPDDIKGLAVFLASADSDY 241
           PG ++   +  V     + +     E  A ++  VP+GRF  P++I   A+FLAS D+ Y
Sbjct: 180 PGPIETPIFGKVGLSAEQLQ-----EFDAQISAKVPLGRFGKPEEIAKAALFLASDDASY 234

Query: 242 ILAQTYNVDGG 252
           +      VDGG
Sbjct: 235 VAGADLYVDGG 245


Lambda     K      H
   0.319    0.133    0.376 

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: 144
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: 256
Length of database: 249
Length adjustment: 24
Effective length of query: 232
Effective length of database: 225
Effective search space:    52200
Effective search space used:    52200
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 (21.8 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