Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate AO353_17425 AO353_17425 lactaldehyde reductase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__pseudo3_N2E3:AO353_17425 Length = 382 Score = 513 bits (1321), Expect = e-150 Identities = 260/379 (68%), Positives = 304/379 (80%) Query: 4 STFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSV 63 STFFIP+VN++G L +AMN + +YGF + LIVTD L K G+AG + + L ++I SV Sbjct: 3 STFFIPAVNIMGTGCLDEAMNAIRNYGFRKALIVTDAGLAKAGVAGLIAEKLAMQDIDSV 62 Query: 64 IYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGV 123 I+DG +PNP+ NV +GL+LL+ + CD VISLGGGSPHDCAKGIAL A NGG I DYEGV Sbjct: 63 IFDGAKPNPSIANVESGLELLQRSQCDCVISLGGGSPHDCAKGIALCATNGGKIADYEGV 122 Query: 124 DRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGM 183 D+SAKPQLP+IAINTTAGTASEMTRFCIITDE+RH+KMAIVD++VTPLLSVND +LM M Sbjct: 123 DQSAKPQLPLIAINTTAGTASEMTRFCIITDESRHVKMAIVDRNVTPLLSVNDPALMAAM 182 Query: 184 PKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAM 243 PK LTAATGMDALTHAIEAYVS AA PITDACALKA+ +I+ NL LAV DGS+ ARE M Sbjct: 183 PKGLTAATGMDALTHAIEAYVSTAANPITDACALKAIELISRNLRLAVHDGSDMIARENM 242 Query: 244 AYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDC 303 AYAQFLAGMAFNNASLG+VHAMAHQLGGFY+LPHGVCNAVLLPHVQ FN+ V A RL Sbjct: 243 AYAQFLAGMAFNNASLGFVHAMAHQLGGFYDLPHGVCNAVLLPHVQSFNAAVCAERLAVV 302 Query: 304 AAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACG 363 A A+G + G + EGA+A I AIR LA+ V+IP GLRDL K +D +LA NALKDACG Sbjct: 303 AQALGADTLGVSPEEGAQAAIVAIRALARDVEIPGGLRDLGAKLQDIPILAANALKDACG 362 Query: 364 FTNPIQATHEEIVAIYRAA 382 TNP A +I I+R+A Sbjct: 363 LTNPRAADQRQIEEIFRSA 381 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: 531 Number of extensions: 17 Number of successful extensions: 1 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: 382 Length adjustment: 30 Effective length of query: 353 Effective length of database: 352 Effective search space: 124256 Effective search space used: 124256 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