Align sorbitol-6-phosphate dehydrogenase (characterized)
to candidate BWI76_RS07645 BWI76_RS07645 short-chain dehydrogenase/reductase
Query= CharProtDB::CH_091826 (259 letters) >FitnessBrowser__Koxy:BWI76_RS07645 Length = 265 Score = 130 bits (327), Expect = 3e-35 Identities = 85/261 (32%), Positives = 138/261 (52%), Gaps = 9/261 (3%) Query: 3 QVAVVIGGGQTLGAFLCEGLAQAGYHVAVADLNESNANRLADTINSRYGAGRAYGFKVDA 62 + V+ G + +GA + E A+ G ++ + N + A+T+ RY A +VD Sbjct: 8 KTVVITGACRGIGAGIAERFARDGANLVMVS-NAERVHETAETLRQRYQAD-ILSLQVDV 65 Query: 63 TDEASVEALARAVDETFGRADLLVYSAGVAKAAPITQFRLTDFDLSLQVNLVGYFLCSRE 122 TDEA V++L FG D+ + +AGV + DF+ L VN G +LC RE Sbjct: 66 TDEAQVQSLYEQAAARFGAIDVSIQNAGVITIDYYDRMPKADFEKVLAVNTTGVWLCCRE 125 Query: 123 FSKLMIRDGIKGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITVHSL 182 +K M++ G +I +S G+ G + Y+A+K G +G+TQSLA +LA + ITV++ Sbjct: 126 AAKYMVKQN-HGSLINTSSGQGRQGFIYTPHYAASKMGVIGITQSLAHELAPWNITVNAF 184 Query: 183 MLGNLLKSPMFQSLLPQYAEKLGITPE-----EVEPYYVDKVPLKRGCDYQDVLNVLLFY 237 G +++S M+ + E L + E+ +V+ +P+KR +DV ++ F Sbjct: 185 CPG-IIESEMWDYNDRVWGEILSTEQKRYGKGELMAEWVEGIPMKRAGKPEDVAGLVAFL 243 Query: 238 ASDKAAYCTGQSINVTGGQVM 258 ASD A Y TGQ+IN+ GG +M Sbjct: 244 ASDDARYLTGQTINIDGGLIM 264 Lambda K H 0.319 0.136 0.387 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: 197 Number of extensions: 14 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: 265 Length adjustment: 25 Effective length of query: 234 Effective length of database: 240 Effective search space: 56160 Effective search space used: 56160 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 (21.7 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