Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate SMa0263 SMa0263 alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Smeli:SMa0263 Length = 399 Score = 176 bits (445), Expect = 1e-48 Identities = 114/334 (34%), Positives = 172/334 (51%), Gaps = 29/334 (8%) Query: 33 RTLIVTDNMLTKLGMAGDVQ---KALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNC 89 R LIVTD T+L + D+ + LEE + ++ T P+ E+ Sbjct: 33 RALIVTD---TRLAVDADLLALVRRLEEAGLEVMVDSSTLPDVPVESAIVSAAAASGFAP 89 Query: 90 DSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRSAKPQLPMIAINTTAGTASEMTRF 149 D VI +GGGS D AK + L+ +GG +DY G P +P+IAI TTAGT SE+T Sbjct: 90 DLVIGIGGGSCLDMAKCVTLLLTHGGRPQDYYGEYAVPGPVMPLIAIPTTAGTGSEVTPV 149 Query: 150 CIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSLTAATGMDALTHAIEAYVSIAAT 209 +++D R +K+ I H+ P +S+ D L + P LTA G DALTHAIEA+ +I Sbjct: 150 AVLSDAERSLKVGISSPHLIPAVSICDPELTLSCPPGLTAIAGADALTHAIEAFTAIRRE 209 Query: 210 PI---------------TDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQFLAGMAF 254 P+ +D AL A+T++ + L A +DG++A ARE + LAG+AF Sbjct: 210 PVPGIAQQRVFVGKNELSDHFALSAITLLWQGLERACKDGADAGARETVMLGATLAGLAF 269 Query: 255 NNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAAMGVNVTGK 314 A HA+ + +G + HG+ A L+P+V +N+ + L A A G+ Sbjct: 270 GVAGTAAAHAIQYPVGALTHTAHGLGVACLMPYVMTWNAPLIRDELAQIAHAAGLG---- 325 Query: 315 NDAEGAEACINAIRELAKKVDIPAGLRDLNVKEE 348 G + I A+ L +++ IPA LRDL ++E+ Sbjct: 326 ----GPDEVIPALVSLFERIGIPATLRDLGLEED 355 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: 377 Number of extensions: 16 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: 399 Length adjustment: 31 Effective length of query: 352 Effective length of database: 368 Effective search space: 129536 Effective search space used: 129536 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