Align mannitol dehydrogenase (EC 1.1.1.255) (characterized)
to candidate SMa1296 SMa1296 alcohol dehydrogenase
Query= BRENDA::Q38707 (365 letters) >FitnessBrowser__Smeli:SMa1296 Length = 340 Score = 160 bits (406), Expect = 4e-44 Identities = 107/322 (33%), Positives = 161/322 (50%), Gaps = 13/322 (4%) Query: 36 GEKDVRLKVLFCGVCHSDHHMIHNNWGFTTYP-IVPGHEIVGVVTEVGSKVEKVKVGDNV 94 G V +K GVCH+D H +W P +PGHE VG V ++G++V ++K GD V Sbjct: 26 GPGQVLIKYEATGVCHTDLHAAKGDWPVRPNPPFIPGHEGVGYVAKLGAEVTRLKEGDRV 85 Query: 95 GIGCLVGSCRSCESCCDNRESHCENTIDTYGSIYFDGTMTHGGYSDTMVADEHFILRWPK 154 G+ L +C C C E+ C + +T S+ DGT G +AD F+ R P Sbjct: 86 GVPWLHTACGCCTPCRTGWETLCGSQQNTGYSV--DGTFAQYG-----LADPDFVGRLPA 138 Query: 155 NLPLDSGAPLLCAGITTYSPLKYYGLDKPGTKIGVVGLGGLGHVAVKMAKAFGAQVTVID 214 L AP+LCAG+T Y LK + +PG + V G+GGLGH+AV+ AKA G V D Sbjct: 139 RLEFGPAAPVLCAGVTVYKGLKETEV-RPGEWVLVSGIGGLGHMAVQYAKAMGMHVAAAD 197 Query: 215 ISESKRKEALEKLGADSFL---LNSDQEQMKGARSSLDGIIDTVPVNHPLAPLFDLLKPN 271 I K A EKLGAD + E+++ L G + T + + +L+ Sbjct: 198 IFPDKLALA-EKLGADLVVDARAPDAVEEVQRRTGGLHGALVTAVSPKAMEQAYSMLRSK 256 Query: 272 GKLVMVGAPEKPFELPVFSLLKGRKLLGGTINGGIKETQEMLDFAAKHNITADVEVIPMD 331 G + +VG P LPVF + R + G+I G ++ +E L+FA + + A ++ Sbjct: 257 GTMALVGLPPGQICLPVFDTVLKRITVRGSIVGTRQDLEEALEFAGEGKVAAHFSWDKIE 316 Query: 332 YVNTAMERLVKSDVRYRFVIDI 353 +N ER+ + + R V+D+ Sbjct: 317 NINAIFERMEEGKIDGRIVLDL 338 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: 275 Number of extensions: 14 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: 340 Length adjustment: 29 Effective length of query: 336 Effective length of database: 311 Effective search space: 104496 Effective search space used: 104496 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