Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 8500233 DvMF_0990 iron-containing alcohol dehydrogenase (RefSeq)
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Miya:8500233 Length = 386 Score = 260 bits (665), Expect = 4e-74 Identities = 144/354 (40%), Positives = 202/354 (57%), Gaps = 1/354 (0%) Query: 30 GFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNC 89 G +R L+V+D + G V + L + I + G NP V G ++ + C Sbjct: 32 GASRCLVVSDQGVAAAGHTDAVARTLRDEGIACATFLGVSENPRDTEVMQGSEVFRAEGC 91 Query: 90 DSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRSAKPQLPMIAINTTAGTASEMTRF 149 D+++++GGGSP DCAKGI +V ANGG I DYEGVD KP P++ + TTAG+++++++F Sbjct: 92 DAIVAVGGGSPMDCAKGIGIVVANGGHILDYEGVDAIPKPMPPLVCVPTTAGSSADVSQF 151 Query: 150 CIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSLTAATGMDALTHAIEAYVSIAAT 209 II D R +K+AIV K P +++ D + P+ LTAATG+DALTHA+EAY S A + Sbjct: 152 AIIRDTPRRVKIAIVSKANVPDVALVDPLTTLTKPRELTAATGLDALTHAVEAYASNAHS 211 Query: 210 PITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQFLAGMAFNNASLGYVHAMAHQL 269 P+TD AL+AV I L ++D N AR MA AG+AF+NA LG VHA++H L Sbjct: 212 PVTDMFALEAVRGIGSALFDVLDDLGNRDARARMALGSMNAGLAFSNAILGAVHALSHSL 271 Query: 270 GGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAAMGV-NVTGKNDAEGAEACINAIR 328 GG +LPHG CNA+LLP V N A R R A A+GV + D E +A + Sbjct: 272 GGLLDLPHGECNALLLPFVVRRNYVAAPQRYRRVAEALGVADALAAPDDEVRDALFARLG 331 Query: 329 ELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFTNPIQATHEEIVAIYRAA 382 + ++ GL V + A LA AL+D C TNP+ E+ +Y A Sbjct: 332 AMRRRAGFDKGLAQYGVTRDQLAELARLALEDPCLSTNPVPLDARELEQLYAEA 385 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: 408 Number of extensions: 18 Number of successful extensions: 2 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: 386 Length adjustment: 30 Effective length of query: 353 Effective length of database: 356 Effective search space: 125668 Effective search space used: 125668 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