Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate GFF5024 PS417_25740 alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__WCS417:GFF5024 Length = 382 Score = 254 bits (649), Expect = 3e-72 Identities = 151/383 (39%), Positives = 220/383 (57%), Gaps = 3/383 (0%) Query: 1 MAASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNI 60 M+ S+F I + GA ++ + LIVTD L K G L ER+ Sbjct: 1 MSTSSFKIAHKLLTGAGAIEQLAAELTRLDVDNPLIVTDAALVKSGTVALALVHLGERSY 60 Query: 61 FSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDY 120 I+D P+P V +++ +E D +I LGGGS D AK +A A G + D Sbjct: 61 --EIFDRVLPDPEIAIVEDCMRVYREGGHDGLIGLGGGSAIDIAKSVAAYAGYHGALADL 118 Query: 121 EGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLM 180 GVD+ + P+IAI TTAGT SE+T I++D+A +K IV ++ P +++ + Sbjct: 119 FGVDQVPRKGPPLIAIPTTAGTGSEVTNVAILSDKAAQLKKGIVSDYLLPDVALISPQMT 178 Query: 181 IGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAR 240 + P+S+TAA+G+DAL HAIE+Y+S+ A+PITDA A+ A+ +IA LP A + +N +AR Sbjct: 179 LTCPRSVTAASGVDALVHAIESYLSLNASPITDALAIGAIKLIAHALPKAYANPANLQAR 238 Query: 241 EAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARL 300 + MA A +AGMAF NA +G VHA+A+ LGG +N+ HGV NA+LLP+V +N R+ Sbjct: 239 DDMATASLMAGMAFGNAGVGAVHALAYPLGGRFNIAHGVSNALLLPYVMHWNKLACVERM 298 Query: 301 RDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALK- 359 +D A AMGVNVTG + + A+ + A+ L V+IPAGL V E+ +A A Sbjct: 299 QDIAQAMGVNVTGLSVNDAADQAVEAMTRLCAAVEIPAGLHSFGVPEDAIPAMAVEAAGI 358 Query: 360 DACGFTNPIQATHEEIVAIYRAA 382 + NP + + +I IYRAA Sbjct: 359 ERLMRNNPRKLSAADIEKIYRAA 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: 361 Number of extensions: 17 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: 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