Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate WP_017549841.1 C792_RS0112730 zinc-binding alcohol dehydrogenase family protein
Query= BRENDA::Q6ECH5 (336 letters) >NCBI__GCF_000330705.1:WP_017549841.1 Length = 338 Score = 147 bits (372), Expect = 3e-40 Identities = 98/324 (30%), Positives = 166/324 (51%), Gaps = 14/324 (4%) Query: 1 MEALVLTGKKQLEIEDIKEPEIKP-DEVLIHTAYAGICGTDKALYAGLPGSASAVPPIVL 59 M+A+ + QL I ++++P I+ DEV++ GICG+D +Y G S P V+ Sbjct: 1 MKAIQVEKPGQLNIVELEKPVIENGDEVIVKIKNVGICGSDVHIYHGSNPFTSY--PRVI 58 Query: 60 GHENSGVVTKVGSEVTNVKPGDRVTVDPNIYCGQCKYCRTQRPELCEHLDAVGVTRNGGF 119 GHE SG+V +VG VT++ PGD V ++P YCG+C CR +P +C+ L+ GV R+GG Sbjct: 59 GHEVSGIVEQVGEAVTSLAPGDLVALEPITYCGECYACRNGQPNVCDSLEVFGVHRDGGM 118 Query: 120 EEYFTAPAKVVYPIPDDVSLKAAAVVEPISCAMHGVDLLETHPYQKALVLGDGFEGQLFA 179 EY A + +P +VS +AAA++EP++ + V+G G G Sbjct: 119 AEYLKADENNWHKVPGNVSEEAAALMEPMTIGAQATYRGDVREGDTVFVIGAGPTGIACL 178 Query: 180 QILKARGIHEVTLAGRSDEKLENNRKHFGVKTIDT----TKEEI----PADAYDIVVEAV 231 K RG +V ++ + +L+ + TI +EEI + ++V++AV Sbjct: 179 LQAKQRGA-KVFISDFNQNRLDYAKSIGADATIQPDGVHVEEEINRLTNGELANVVIDAV 237 Query: 232 GLPATQEQALAAAARGAQVLMFGVGNPDDKFSVNTYDVFQKQLTIQGAFVNPYTFEDSIA 291 GLP T +QA+ A+ +V+ G + S+ + + +K+L + G+ + + F I Sbjct: 238 GLPQTFQQAVELASIAGRVVTLGFN--EQPSSIPSLLLTKKELKVAGSRLQTHQFPKVID 295 Query: 292 LLSSGVVDPLPLFSHELDLDGVED 315 + G +DP + S +D + D Sbjct: 296 QVGRGEIDPTQIISQRYSMDQIHD 319 Lambda K H 0.316 0.136 0.393 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: 263 Number of extensions: 15 Number of successful extensions: 3 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: 336 Length of database: 338 Length adjustment: 28 Effective length of query: 308 Effective length of database: 310 Effective search space: 95480 Effective search space used: 95480 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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