Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate SMc01582 SMc01582 alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Smeli:SMc01582 Length = 381 Score = 192 bits (488), Expect = 1e-53 Identities = 114/368 (30%), Positives = 185/368 (50%), Gaps = 13/368 (3%) Query: 9 PSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGT 68 P+ GA + + + G + L+VTD L + + LE + I+ Sbjct: 10 PTAVKFGAGRIKELADHCKALGIKKPLLVTDRGLAPMAITQQALDILEAGGLGRAIFADV 69 Query: 69 QPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVD---- 124 PNP N+ AG+K ++ D V++ GGGS D K +A +A + D+E + Sbjct: 70 DPNPNDRNLEAGVKAFRDGGHDGVVAFGGGSGLDLGKCVAFMAGQTRPVWDFEDIGDWWT 129 Query: 125 -RSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGM 183 S + P++A+ TTAGT SE+ R +IT+ A H+K I P +++ D L +GM Sbjct: 130 RASVEGIAPIVAVPTTAGTGSEVGRASVITNSASHVKKVIFHPKFLPGVTICDPELTVGM 189 Query: 184 PKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAM 243 PK +TA TGMDA H +EAY S P++ AL+ + ++ E LP A +DG++ +AR M Sbjct: 190 PKVITAGTGMDAFAHCLEAYSSPFYHPMSAGIALEGMRLVKEYLPRAYKDGADLEARANM 249 Query: 244 AYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDC 303 A + +AF LG +H+++H +G YN HG+ NAV++P V FN ++ Sbjct: 250 MSAAAMGAVAFQK-GLGAIHSLSHPVGAIYNTHHGMTNAVVMPPVLRFNRSAIEEKIGRA 308 Query: 304 AAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACG 363 AA +G+ A G + + + L +++ +P L L V + +A A+ D Sbjct: 309 AAYLGI-------AGGFDGFYDYVLRLREELGVPDKLSALGVGTDRIDEMAEMAIVDPTA 361 Query: 364 FTNPIQAT 371 NP++ T Sbjct: 362 GGNPVELT 369 Lambda K H 0.318 0.131 0.373 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: 369 Number of extensions: 19 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: 383 Length of database: 381 Length adjustment: 30 Effective length of query: 353 Effective length of database: 351 Effective search space: 123903 Effective search space used: 123903 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 (21.8 bits) S2: 50 (23.9 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