Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate BPHYT_RS24470 BPHYT_RS24470 zinc-binding dehydrogenase
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__BFirm:BPHYT_RS24470 Length = 350 Score = 343 bits (880), Expect = 4e-99 Identities = 178/343 (51%), Positives = 234/343 (68%), Gaps = 5/343 (1%) Query: 14 FGWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGHE 73 + +AA D T L+PF+ RR DV+++VLFCGVCHSD H N W T +P+VPGHE Sbjct: 5 YAYAATDATAPLAPFEIQRRELRAHDVQMEVLFCGVCHSDLHQARNEWKNTVFPVVPGHE 64 Query: 74 IVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHCEN-TIDTYGSI-YFDG 131 IVG VT VG V K K GD VG+GCLV SCR+C SC ++ E +CEN + TY + DG Sbjct: 65 IVGRVTAVGLDVTKYKAGDLVGVGCLVDSCRTCASCKEDLEQYCENGFVGTYNGVDRVDG 124 Query: 132 TMTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVG 191 T+GGYS +V DE F LR P+NL APLLCAGITTYSPL+ +G PG K+G+VG Sbjct: 125 QTTYGGYSTQLVVDEAFTLRVPENLDPAGVAPLLCAGITTYSPLRTWGAG-PGKKVGIVG 183 Query: 192 LGGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDGI 251 LGGLGH+ VK+A+A GA V + S SK ++A ++LGA +++ + +M+ +S D I Sbjct: 184 LGGLGHMGVKLARAMGAHVVLFTTSPSKIEDA-KRLGAHEVVISKNAGEMEAHLNSFDLI 242 Query: 252 IDTVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFELP-VFSLLKGRKLLGGTINGGIKETQ 310 ++TV H L P +LLK +G + +VGAPE P VF+L+ R+ L G++ GGI ETQ Sbjct: 243 VNTVAAQHDLNPFLNLLKRDGTMTLVGAPEHDHPSPQVFNLIFKRRRLAGSLIGGIAETQ 302 Query: 311 EMLDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDI 353 EMLDF +H IT+DVEVIPM +N A ER++KSDV+YRFVID+ Sbjct: 303 EMLDFCGEHGITSDVEVIPMQGINEAFERMLKSDVKYRFVIDL 345 Lambda K H 0.319 0.137 0.415 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: 370 Number of extensions: 23 Number of successful extensions: 5 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: 365 Length of database: 350 Length adjustment: 29 Effective length of query: 336 Effective length of database: 321 Effective search space: 107856 Effective search space used: 107856 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 (21.7 bits) S2: 49 (23.5 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