Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate H281DRAFT_03803 H281DRAFT_03803 alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Burk376:H281DRAFT_03803 Length = 387 Score = 197 bits (500), Expect = 5e-55 Identities = 126/354 (35%), Positives = 192/354 (54%), Gaps = 7/354 (1%) Query: 33 RTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNCDSV 92 R +VTD L K G+ L + + D +P V + + V Sbjct: 36 RLCVVTDGFLHKSGLLDPALADLAAHGWNATVIDDVIADPPEHIVLEATARARSAGAEIV 95 Query: 93 ISLGGGSPHDCAKGIALVAANGGD-IRDYEGVDRSAKPQLPMIAINTTAGTASEMTRFCI 151 + LGGGS D AK IA +A + + GV++ +LP++ + TTAGT SE+T I Sbjct: 96 LGLGGGSSMDVAKLIAALAPQQQQQLSEMYGVNKVTVQRLPLVQMPTTAGTGSEVTAVSI 155 Query: 152 IT-DEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSLTAATGMDALTHAIEAYVSI-AAT 209 +T EAR KM +V + L++ D+ L +G+P + TAATG+DA+ HAIEAY S Sbjct: 156 VTVGEAR--KMGVVAPQLIADLAILDAELTLGLPVAATAATGIDAMVHAIEAYTSAHLKN 213 Query: 210 PITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQFLAGMAFNNASLGYVHAMAHQL 269 P++D A+KA+ +++ NL A EDG+N AREAM AG AF N+ + VHA+A+ + Sbjct: 214 PVSDMLAIKALELLSRNLLPACEDGNNRDAREAMLLGATFAGQAFANSPVAAVHALAYPI 273 Query: 270 GGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAAMGVNVTGKNDAEGAEACINAIRE 329 GG Y++PHG+ NA++LPHV FN+ AA + A + TG + + +A I + Sbjct: 274 GGIYHVPHGLSNALVLPHVLRFNADSAADLYAELADVVVPGTTG-SARDKTQALIENLER 332 Query: 330 LAKKVDIPAGLRDLNVKEEDFAVLATNA-LKDACGFTNPIQATHEEIVAIYRAA 382 + + IPA LRD+ ++ E +A++A L+ NP + + +AIY AA Sbjct: 333 MIAETAIPARLRDVGIEREGLGRMASDAMLQTRLLVNNPRPVSEADALAIYNAA 386 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: 342 Number of extensions: 17 Number of successful extensions: 4 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: 387 Length adjustment: 30 Effective length of query: 353 Effective length of database: 357 Effective search space: 126021 Effective search space used: 126021 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