Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate AZOBR_RS28580 AZOBR_RS28580 alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__azobra:AZOBR_RS28580 Length = 387 Score = 214 bits (544), Expect = 4e-60 Identities = 124/380 (32%), Positives = 197/380 (51%), Gaps = 1/380 (0%) Query: 4 STFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSV 63 S+F P+ V G + +++ ++ TR ++ D L + ++ L + Sbjct: 7 SSFSCPTKIVFGVGAHEQLPDVLREWNATRLFVLLDPALADSAIFRRIEGLLTSNGVALS 66 Query: 64 IYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGV 123 ++ G +P P V A + +E + +++++GGGS D AK + ++ NGG I DYEG+ Sbjct: 67 VFTGIEPEPGDRTVQAAYERCREQDAQALLAIGGGSTIDVAKAVGILMTNGGRIADYEGI 126 Query: 124 DRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPL-LSVNDSSLMIG 182 ++ A LP+IA+ TTAGT SE++ C+ITD AR KMAI +P +++ D + Sbjct: 127 EKFAIRPLPLIAVPTTAGTGSEVSGACVITDTARKTKMAIRHAAFSPAQVAILDPLAVGS 186 Query: 183 MPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREA 242 MP + A G+DA HA E+Y+S AT +DA L A+T+IA ++ V D +N A Sbjct: 187 MPAHVAAHAGIDAFVHAFESYLSKRATVFSDAVNLHAMTLIAGSIRPFVADRTNVPAALD 246 Query: 243 MAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRD 302 M LA M+F LG VH MA +G + +PHG+ NAV LP+ FN R+ Sbjct: 247 MLCGSALAAMSFGVTGLGNVHCMAMSVGALFPVPHGLANAVCLPYAAAFNVSAKPERMAR 306 Query: 303 CAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDAC 362 A +GV+ G + AEA ++ +R L + IP LRD+ V E+ +A + Sbjct: 307 IAEILGVDTAGLPLDQAAEAAVDGLRTLCADLGIPPRLRDVGVTEDRLDEMARRSYAADY 366 Query: 363 GFTNPIQATHEEIVAIYRAA 382 NP + + ++RAA Sbjct: 367 NRWNPRHTSEPDFQDLFRAA 386 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: 316 Number of extensions: 10 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: 387 Length adjustment: 30 Effective length of query: 353 Effective length of database: 357 Effective search space: 126021 Effective search space used: 126021 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