Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 8499560 DvMF_0330 iron-containing alcohol dehydrogenase (RefSeq)
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Miya:8499560 Length = 380 Score = 234 bits (597), Expect = 3e-66 Identities = 141/385 (36%), Positives = 208/385 (54%), Gaps = 9/385 (2%) Query: 1 MAASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNI 60 M + F IP + + G SL G +R L+V+D L G V L + Sbjct: 1 MRITKFAIPEI-IFGHGSLDHLAPCARRLGASRVLLVSDKGLESSGWVERVMDILSGNGL 59 Query: 61 FSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDY 120 V + NP V G ++ +E D VI+LGGGSP D AKGI + NGG I DY Sbjct: 60 EWVYFADCSSNPRDHQVHEGAQIYREERADVVIALGGGSPMDTAKGIGTIVGNGGRINDY 119 Query: 121 EGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLM 180 EG ++ +P PMI + TTAG+ S++++FCIITD R +KM+I+ + + P +S+ D ++ Sbjct: 120 EGANKIMRPLPPMIFLPTTAGSGSDISQFCIITDVERRLKMSIISRSLVPNVSIIDPQVL 179 Query: 181 IGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAR 240 + + L A+ +DA HA+E+Y+S+ A+P TD AL+A+ +I NL AVE + A Sbjct: 180 LTKSEELIIASAIDAFAHAVESYLSLLASPFTDHQALRAMELIMANLMPAVE-RRDPHAL 238 Query: 241 EAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARL 300 E ++ A AGM+F+NA LG H++AH LGG +++ HG+ + VLLPHV +N V+ RL Sbjct: 239 EQLSIASTAAGMSFSNAGLGIGHSLAHSLGGMFDVLHGLVHPVLLPHVMRYNLPVSVDRL 298 Query: 301 RDCAAAMGVNVTGKNDAEG---AEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNA 357 AA+G V G A A A I + E + +P L L +A A Sbjct: 299 ----AAIGRIVVGPRVASAESIARAGIERLGEFFAGLGVPVRLGQLLPDRSALETIARTA 354 Query: 358 LKDACGFTNPIQATHEEIVAIYRAA 382 + DAC TNP T ++++ I A Sbjct: 355 VHDACTLTNPRAVTWQDLLTICEEA 379 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: 326 Number of extensions: 19 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: 380 Length adjustment: 30 Effective length of query: 353 Effective length of database: 350 Effective search space: 123550 Effective search space used: 123550 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