Align sorbitol-6-phosphate dehydrogenase; EC 1.1.1.140 (characterized)
to candidate BWI76_RS23705 BWI76_RS23705 3-oxoacyl-ACP reductase
Query= CharProtDB::CH_091827 (259 letters) >FitnessBrowser__Koxy:BWI76_RS23705 Length = 244 Score = 108 bits (271), Expect = 8e-29 Identities = 82/259 (31%), Positives = 133/259 (51%), Gaps = 21/259 (8%) Query: 2 NQVAVVIGGGQTLGAFLCHGLAAEGYRVAVVD--IQSDKAANVAQEINAEYGESMAYGFG 59 ++ A+V G + +G + LA EG RV + D + AA +E A+ A Sbjct: 5 SKTAIVTGAARGIGFGIAQVLAREGARVIIADRDAHGEAAAASLRESGAQ-----ALFIS 59 Query: 60 ADATSEQSVLALSRGVDEIFGRVDLLVYSAGIAKAAFISDFQLGDFDRSLQVNLVGYFLC 119 + + V AL +E FG VD++V +AGI + A + D+D + VNL G FLC Sbjct: 60 CNIGDKAQVEALFSQAEEAFGAVDIVVNNAGINRDAMLHKLSEADWDTVIDVNLKGTFLC 119 Query: 120 AREFSRLMIRDGIQGRIIQINSKSGKVGSKHNSGYSAAKFGGVGLTQSLALDLAEYGITV 179 ++ + + +R+ GRII I S S +G+ + YSA+K G VG+T++ +LA+ G+TV Sbjct: 120 MQQ-AAIRMRERGAGRIINIASASW-LGNVGQTNYSASKAGVVGMTKTACRELAKKGVTV 177 Query: 180 HSLMLGNLLKSPMFQSLLPQYATKLGIKPDQVEQYYIDKVPLKRGCDYQDVLNMLLFYAS 239 +++ G + + M + + P+ V Q I+K+P + +DV + F AS Sbjct: 178 NAICPG-FIDTDMTRGV-----------PENVWQIMINKIPAGYAGEAKDVGECVAFLAS 225 Query: 240 PKASYCTGQSINVTGGQVM 258 A Y G+ INV GG V+ Sbjct: 226 DGARYINGEVINVGGGMVL 244 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: 140 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: 259 Length of database: 244 Length adjustment: 24 Effective length of query: 235 Effective length of database: 220 Effective search space: 51700 Effective search space used: 51700 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 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