Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate BPHYT_RS27390 BPHYT_RS27390 hydroxyacid dehydrogenase
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__BFirm:BPHYT_RS27390 Length = 353 Score = 322 bits (824), Expect = 1e-92 Identities = 170/347 (48%), Positives = 227/347 (65%), Gaps = 7/347 (2%) Query: 13 AFGWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGH 72 A G+AA T LS F F RR+ DV ++VL+CGVCHSD H NNWG YPIVPGH Sbjct: 5 ARGYAATSATTPLSLFDFQRRSLRNDDVVIEVLYCGVCHSDLHTTRNNWGNARYPIVPGH 64 Query: 73 EIVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHCEN-TIDTYGSI-YFD 130 EIVG V E+G++ + VGD VG+GC+V SC+ C++C + E +CE+ TY + D Sbjct: 65 EIVGRVKELGAEATRFTVGDYVGVGCMVDSCQHCKTCRNGFEQYCESGATSTYNNTDRHD 124 Query: 131 GTMTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVV 190 + T GGYSD ++ E F+LR P NL L APLLCAGITTYSPL+++ + + G+++ V+ Sbjct: 125 QSRTQGGYSDQIIVSEKFVLRMPDNLDLKGAAPLLCAGITTYSPLRHWNVGE-GSRVAVI 183 Query: 191 GLGGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDG 250 GLGGLGH+A+K+A A GA VT+I S K +A LGA +L+SD EQM A+S D Sbjct: 184 GLGGLGHMAIKLASAMGADVTLITRSAGKETDA-RALGARDVVLSSDVEQMAAAKSRFDL 242 Query: 251 IIDTVPVNHPLAPLFDLLKPNGKLVMVG--APEKPFELPVFSLLKGRKLLGGTINGGIKE 308 IIDT+P H L P L G LV+VG P +P L ++ RK + G+ GGI E Sbjct: 243 IIDTIPYQHDLNPYVATLDSGGTLVLVGYFGPVEP-ALNSSPMVSKRKTVAGSFIGGIAE 301 Query: 309 TQEMLDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDIAN 355 TQEMLDF KH IT ++E+I + VN A +R+++SDV+YRFVID+ + Sbjct: 302 TQEMLDFCGKHGITCEIEMIDIQQVNEAFDRMLRSDVKYRFVIDLGS 348 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: 342 Number of extensions: 12 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: 353 Length adjustment: 29 Effective length of query: 336 Effective length of database: 324 Effective search space: 108864 Effective search space used: 108864 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