Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate GFF1243 Psest_1276 Zn-dependent alcohol dehydrogenases
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__psRCH2:GFF1243 Length = 351 Score = 332 bits (851), Expect = 9e-96 Identities = 174/345 (50%), Positives = 233/345 (67%), Gaps = 5/345 (1%) Query: 13 AFGWAARDTTGLLSPFKFSRRATGEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYPIVPGH 72 + G+AA D + L+P+ FSRR G DVR+++LFCGVCHSD H N W T YP VPGH Sbjct: 4 SIGYAALDPSTPLAPYSFSRREVGPNDVRIEILFCGVCHSDLHTARNEWNNTLYPSVPGH 63 Query: 73 EIVGVVTEVGSKVEKVKVGDNVGIGCLVGSCRSCESCCDNRESHCEN-TIDTY-GSIYFD 130 EIVG V+ VG+ V K K GD G+GCLV SCR+C SC + E +CEN + TY G + Sbjct: 64 EIVGRVSAVGANVSKFKAGDIAGVGCLVDSCRTCSSCGEGLEQYCENGFVGTYNGPAFGG 123 Query: 131 GTMTHGGYSDTMVADEHFILRWPKNLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVV 190 G T GGYSD +V DE ++LR L + APLLCAGITTYSPL+ + + PG K+GVV Sbjct: 124 GENTLGGYSDNIVVDEKYVLRINHTDNLAAVAPLLCAGITTYSPLRQWKVG-PGQKVGVV 182 Query: 191 GLGGLGHVAVKMAKAFGAQVTVIDISESKRKEALEKLGADSFLLNSDQEQMKGARSSLDG 250 GLGGLGH+AVK+A A GA+V + S KR++AL +LGA +++ ++++M +S D Sbjct: 183 GLGGLGHMAVKIANAMGAKVVLFTTSPDKREDAL-RLGAAEVVVSKNKDEMAAHANSFDF 241 Query: 251 IIDTVPVNHPLAPLFDLLKPNGKLVMVGAPEKPFELP-VFSLLKGRKLLGGTINGGIKET 309 I++TV H L +LLK + + +VGAP P P VF L+ R+ + G++ GGI ET Sbjct: 242 ILNTVAAPHNLDAFVNLLKRDATMTLVGAPASPHPSPSVFGLIFKRRRIAGSLIGGIAET 301 Query: 310 QEMLDFAAKHNITADVEVIPMDYVNTAMERLVKSDVRYRFVIDIA 354 QEMLDF A+H I +D+E+I M +N A ER++KSDV+YRFVID+A Sbjct: 302 QEMLDFCAEHGIVSDIEMIRMQDINDAYERMLKSDVKYRFVIDMA 346 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: 350 Number of extensions: 16 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: 351 Length adjustment: 29 Effective length of query: 336 Effective length of database: 322 Effective search space: 108192 Effective search space used: 108192 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