Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_046008144.1 OLEAN_RS03865 short chain dehydrogenase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >NCBI__GCF_000967895.1:WP_046008144.1 Length = 252 Score = 125 bits (313), Expect = 1e-33 Identities = 83/267 (31%), Positives = 136/267 (50%), Gaps = 26/267 (9%) Query: 6 NLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKH-------QSSGNYNFWPT 58 N +K++ +TG +GIG A QGA+V + DI+ D Q+ G F Sbjct: 3 NFADKVVLITGAGNGIGRATALAFAQQGASVVVADINRADGEETAAMITQAGGIATFMLC 62 Query: 59 DISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNI 118 D++ +V V+ ++ +G++D NNAG+ + K G +EA ++K++++ Sbjct: 63 DVTKDQDVQSMVEGTVETYGKLDIAFNNAGIEIEQ----SKLADG----DEATYDKIMDV 114 Query: 119 NQKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKEL 178 N KGV+ + ++KQ + IVN +S +GL + S Y+A+K A+ T+S + E Sbjct: 115 NVKGVWRCMKYQIPALLKQSTSAIVNTASIAGLGAAPKMSIYSASKHAVIGLTKSAAVEY 174 Query: 179 GKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEV 238 GK G+RV + P +++ R T+N + +E Y K+ P+GR G+ EV Sbjct: 175 GKKGLRVNAICPAVIDTEMFRRA--------TQN---DPQKEQYVKSLHPVGRIGQPDEV 223 Query: 239 ADFVCYLLSERASYMTGVTTNIAGGKT 265 A V YL S+ A + TGV I GG T Sbjct: 224 AAAVLYLCSDLAGFTTGVALPIDGGAT 250 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: 136 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: 252 Length adjustment: 24 Effective length of query: 243 Effective length of database: 228 Effective search space: 55404 Effective search space used: 55404 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 24 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