Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 208394 DVU2885 alcohol dehydrogenase, iron-containing
Query= ecocyc::EG12293-MONOMER (383 letters) >MicrobesOnline__882:208394 Length = 397 Score = 186 bits (472), Expect = 1e-51 Identities = 125/389 (32%), Positives = 200/389 (51%), Gaps = 11/389 (2%) Query: 5 TFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVI 64 TF +P+ V GA L + + ++ + + G V L + ++ Sbjct: 5 TFHVPTRIVFGAGRLEELGRLPLPGVKPLVVVGAGGSMRRHGHLDRVLALLRQNGCEPML 64 Query: 65 YDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDY---- 120 ++ +PNP+ +V G + + N CD ++ LGGGSP D AK IAL AANGG DY Sbjct: 65 FERVRPNPSLVHVDEGACVARANGCDFIVGLGGGSPIDAAKAIALAAANGGSYWDYIQSG 124 Query: 121 -EGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSL 179 G P LP++AI TTAGT +E + ++T + K+ + P+LS+ D +L Sbjct: 125 TGGRRTPQHPALPVVAIPTTAGTGTEADPWTVVTRDETQEKIGWGNDSTYPVLSIVDPAL 184 Query: 180 MIGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKA 239 I +P +TA TGMDA HA+EAY+S++ P +D AL+AV+++A+ LP AV G + + Sbjct: 185 TITVPPRITAMTGMDAFFHAVEAYLSLSRQPSSDLLALEAVSLLAQFLPQAVRQGDSVEV 244 Query: 240 REAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFY-NLPHGVCNAVL-LPHVQVFNSKVAA 297 R +++A AG+ + +S H+M H L ++ +LPHG +L LP +V ++V Sbjct: 245 RSMVSWASTAAGLCESLSSCIAHHSMEHALSAYHPDLPHGAGLVMLSLPFFEVM-ARVQP 303 Query: 298 ARLRDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDI-PAGLRDLNVKEEDFAVLATN 356 R D AA MG+ + G A+ A + +R L + V + L D + + LA N Sbjct: 304 KRCADLAATMGMPLHGLPPAQQGMAFVEGLRLLIRAVGLDDLRLADHGITAAEIPALAKN 363 Query: 357 ALK--DACGFTNPIQATHEEIVAIYRAAM 383 A + A P+ E++ AI+ A+ Sbjct: 364 ARETMGALFPLTPVDLRPEDVEAIFAKAL 392 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: 325 Number of extensions: 12 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: 397 Length adjustment: 30 Effective length of query: 353 Effective length of database: 367 Effective search space: 129551 Effective search space used: 129551 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