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.
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:
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