Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate BPHYT_RS31860 BPHYT_RS31860 alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__BFirm:BPHYT_RS31860 Length = 393 Score = 197 bits (500), Expect = 6e-55 Identities = 127/386 (32%), Positives = 196/386 (50%), Gaps = 10/386 (2%) Query: 3 ASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFS 62 A+ + P + IG ++ + +G + LIVTD + K + + L +I Sbjct: 4 AALLYSPRLLDIGGGAVRRTAALCRRFGISHPLIVTDPYMIKSKLICVLTDTLSAASIEF 63 Query: 63 VIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVA-----ANGGDI 117 I+ T +PT E V G++LL N D+VI+ GGGSP D AK I ++A + Sbjct: 64 AIFSDTVADPTDEVVDVGVELLNSGNFDAVIAFGGGSPIDTAKAINILAHARRTEPSACM 123 Query: 118 RDYEGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDS 177 RDY+ + + LP+IAI TTAGT SE+TRF +ITD KM I P+ ++ D Sbjct: 124 RDYKMPELADHAALPLIAIPTTAGTGSEVTRFTVITDIGLDEKMLISGLGALPIAAIVDY 183 Query: 178 SLMIGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNA 237 L + MP LTA TG+D+ THA+EA+VS A +D A A+++I +L A + N Sbjct: 184 QLTLDMPPRLTADTGIDSFTHALEAFVSRHANANSDLFARSALSLIGTHLKTAYTEPHNH 243 Query: 238 KAREAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAA 297 AREAM AG+A + A + VH MA +G +++PHG+ NA++LP V ++ + A Sbjct: 244 AAREAMMLGATHAGIACSIAPVALVHGMARPIGAHFHVPHGLSNAMMLPAVTAYSLRSAL 303 Query: 298 ARLRDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDF----AVL 353 R + A G ND E + +RE+ + + +P+ R + + + ++ Sbjct: 304 PRYAEVARLAGFATASDNDEEAGLKLVEGLREMNRDLTVPSP-RAYGINPDGWHAKKTLM 362 Query: 354 ATNALKDACGFTNPIQATHEEIVAIY 379 A AL NP T +I +Y Sbjct: 363 AEQALASGSPANNPKVPTKADIETLY 388 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: 370 Number of extensions: 17 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: 393 Length adjustment: 30 Effective length of query: 353 Effective length of database: 363 Effective search space: 128139 Effective search space used: 128139 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