Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate WP_022528034.1 L248_RS00395 acetoin reductase
Query= reanno::BFirm:BPHYT_RS16120 (260 letters) >NCBI__GCF_000469325.1:WP_022528034.1 Length = 255 Score = 170 bits (431), Expect = 2e-47 Identities = 103/251 (41%), Positives = 145/251 (57%), Gaps = 4/251 (1%) Query: 8 KVAILTGAASGIGEAVARRYLDEGARCVLVDV--KPADSFGDSLRATYGDRVLTVSADVT 65 K AI+TG GIG +A + +G V+ D+ K A S + ++A D L V ADV+ Sbjct: 3 KTAIVTGGGQGIGRGIALQLAKDGFNVVVGDLNEKTAASVAEEIKALGVDS-LPVVADVS 61 Query: 66 RRDDIQRIVASTLERFGQIDILFNNAALFDMRPILEESWDVFDRLFAVNVKGMFFLMQAV 125 Q +V + ++F ID+L NNA + + I E + F+R+F +NV +FF ++AV Sbjct: 62 DEASFQNLVETAHKQFPTIDVLVNNAGIALVATIQETTTAEFERIFRINVNSVFFGIKAV 121 Query: 126 AQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPHKINVNGIA 185 M QG GGKIIN SS AG +G L+ Y ATK A+ TQ+AA LA I VNG A Sbjct: 122 TPIMQAQG-GGKIINASSIAGHQGIELLGPYSATKFAIRGLTQAAAQELAKDHITVNGYA 180 Query: 186 PGVVDTPMWNEVDALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAALFLASADADY 245 PG+V TPMW+ +D + P+G ++ + + LGR P+D+ G FLAS+ +DY Sbjct: 181 PGIVLTPMWDLIDKRMSEIHGVPIGASRQKFIDGIALGRGEQPEDVAGLVSFLASSKSDY 240 Query: 246 ITAQTLNVDGG 256 IT QT+ VDGG Sbjct: 241 ITGQTIVVDGG 251 Lambda K H 0.321 0.135 0.393 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: 134 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: 260 Length of database: 255 Length adjustment: 24 Effective length of query: 236 Effective length of database: 231 Effective search space: 54516 Effective search space used: 54516 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 (21.9 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