Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Cla h 8; EC 1.1.1.138 (characterized)
to candidate BPHYT_RS28235 BPHYT_RS28235 short-chain dehydrogenase
Query= SwissProt::P0C0Y5 (267 letters) >FitnessBrowser__BFirm:BPHYT_RS28235 Length = 260 Score = 121 bits (303), Expect = 2e-32 Identities = 90/257 (35%), Positives = 128/257 (49%), Gaps = 16/257 (6%) Query: 18 LKGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITY-------ASRAQGAEENVKELEKT 70 LK KVV+VTG G +G+G A CA GA VAI Y R E V E+E Sbjct: 3 LKDKVVIVTG--GSRGIGRAIAVACAAEGADVAINYWGDNDVSYGRRSAVAEVVAEIE-A 59 Query: 71 YGIKAKAYKCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSGILDGSVEAWNHVVQ 130 G + A + V + E+ ++LV+ V FG++D +NAG LD E V Sbjct: 60 LGRRVIAIEGNVAARETGQQLVRHTVEAFGKVDVLASNAGICPFHAFLDMPPEVLESTVA 119 Query: 131 VDLNGTFHCAKAVGHHFKERGT-GSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSL 189 V+LNG F+ +A K +GT G++V T+S+S + QT Y KAG + +S Sbjct: 120 VNLNGAFYVTQAAAQQMKLQGTGGAIVATSSISALVGG--GMQTHYTPTKAGVHSLMQSC 177 Query: 190 ANEWRDFA-RVNSISPGYIDTGLS--DFVPKETQQLWHSMIPMGRDGLAKELKGAYVYFA 246 A + R NS+ PG I T L+ D + + + IP+GR G +++ + A Sbjct: 178 AVALGPYGIRCNSVMPGTIATDLNAQDLADEAKKAYFEKRIPLGRLGRPEDVADCVTFLA 237 Query: 247 SDASTYTTGADLLIDGG 263 SD + Y TGA LL+DGG Sbjct: 238 SDRARYVTGAALLVDGG 254 Lambda K H 0.316 0.131 0.383 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: 178 Number of extensions: 13 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: 260 Length adjustment: 25 Effective length of query: 242 Effective length of database: 235 Effective search space: 56870 Effective search space used: 56870 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: 41 (21.6 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