Align sorbitol-6-phosphate dehydrogenase; EC 1.1.1.140 (characterized)
to candidate Ga0059261_2655 Ga0059261_2655 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= CharProtDB::CH_091827 (259 letters) >FitnessBrowser__Korea:Ga0059261_2655 Length = 259 Score = 130 bits (326), Expect = 4e-35 Identities = 87/255 (34%), Positives = 136/255 (53%), Gaps = 6/255 (2%) Query: 5 AVVIGGGQTLGAFLCHGLAAEGYRVAVVDIQSDKAANVAQEINAEYGESMAYGFGADATS 64 AV+ GG + +G + A+EG + + I++D + A++ A YG + D T Sbjct: 9 AVISGGNKGIGLAIAERFASEGANIVIGAIEADLSP--AEQALAGYGTGVV-AQRCDVTK 65 Query: 65 EQSVLALSRGVDEIFGRVDLLVYSAGIAKAAFISDFQLGDFDRSLQVNLVGYFLCAREFS 124 V AL E FG VD+ V +AG+ A + D G++D +L VN G FLC +E Sbjct: 66 ADDVRALFEAA-EAFGGVDIAVQNAGVITIAKVEDLTEGEWDLNLAVNTKGAFLCCQEAI 124 Query: 125 RLMIRDGIQGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSLML 184 R + G GR+I S + G Y+A+KFG VG+TQSLA ++A GITV+++ Sbjct: 125 RRLRARGKPGRLINTASGQARDGFIFTPHYAASKFGVVGMTQSLAKEVATQGITVNAICP 184 Query: 185 GNLLKSPMFQSLLPQYATKLG-IKPDQVEQYYIDKVPLKRGCDYQDVLNMLLFYASPKAS 243 G ++ + M+ ++ +G P + + ++ +P+KR DV ++ F AS AS Sbjct: 185 G-IIHTDMWDYNDREWGRLMGDYAPGALMEEWVQGIPMKRAGTGADVAALVAFLASADAS 243 Query: 244 YCTGQSINVTGGQVM 258 Y TGQ+INV GG +M Sbjct: 244 YITGQTINVDGGLIM 258 Lambda K H 0.320 0.137 0.391 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: 174 Number of extensions: 6 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: 259 Length of database: 259 Length adjustment: 24 Effective length of query: 235 Effective length of database: 235 Effective search space: 55225 Effective search space used: 55225 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 2021. 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