Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate H281DRAFT_00643 H281DRAFT_00643 3-oxoacyl-[acyl-carrier-protein] reductase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__Burk376:H281DRAFT_00643 Length = 246 Score = 132 bits (333), Expect = 5e-36 Identities = 86/268 (32%), Positives = 138/268 (51%), Gaps = 30/268 (11%) Query: 5 LNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDK-------HQSSGNYNFWP 57 + L K+ +TG GIG A + ++GA V D++ ++ G + + Sbjct: 1 MKLNGKVAIITGAGQGIGAATALKFASEGAVVIACDMNLDAVATVAHLCREAGGKADAFA 60 Query: 58 TDISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVN 117 D+++ ++V + V + +GRID +VNNAG+ L ++ F+ +++ Sbjct: 61 VDVTNRTQVDEMVAKVRGTYGRIDVVVNNAGITRDARL---------QKMTLQQFDDVID 111 Query: 118 INQKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKE 177 +N +GVF +QAV M++Q SGVI+N SS G+ G+ GQ+ YAA K + FT++WS+E Sbjct: 112 VNLRGVFHTAQAVVDTMIEQGSGVILNASSVVGVYGNYGQTNYAAAKFGVIGFTKTWSRE 171 Query: 178 LGKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTE 237 LG GIRV VAPG ++ L+T E+ L R + +PL R G+ E Sbjct: 172 LGPKGIRVNAVAPGFIDTPILKTIP-EDVLTKMR-------------DQVPLRRLGKPEE 217 Query: 238 VADFVCYLLSERASYMTGVTTNIAGGKT 265 +A +L S+ ASY+ G GG T Sbjct: 218 IASIYAFLASDEASYVNGAVIEATGGLT 245 Lambda K H 0.315 0.132 0.378 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: 138 Number of extensions: 7 Number of successful extensions: 4 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: 267 Length of database: 246 Length adjustment: 24 Effective length of query: 243 Effective length of database: 222 Effective search space: 53946 Effective search space used: 53946 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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