Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate GFF2063 HP15_2019 iron-containing alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__Marino:GFF2063 Length = 385 Score = 216 bits (551), Expect = 7e-61 Identities = 127/353 (35%), Positives = 199/353 (56%), Gaps = 4/353 (1%) Query: 33 RTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENVAAGLKLLKENNCDSV 92 + L+VTD L K G+ +L E + ++DG +P V A L +E D V Sbjct: 33 KVLLVTDPGLVKAGLLDVATNSLNEAGVKYELFDGVVADPPVSVVEAALADAREAGVDGV 92 Query: 93 ISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRSAKPQLPMIAINTTAGTASEMTRFCII 152 I GGGS D AK IAL+ + D GV ++ +LP+I I TTAGT SE+T II Sbjct: 93 IGFGGGSSMDVAKLIALLIGGEEKLDDVYGVGQAKGKRLPLIQIPTTAGTGSEVTPISII 152 Query: 153 TDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSLTAATGMDALTHAIEAYVSIAAT--P 210 T K +V + P +++ D+ L +G+P +TAATG+DA+ HAIE+Y S +A P Sbjct: 153 TVGETE-KKGVVAPQLLPDIALLDAELTLGLPAHVTAATGIDAMVHAIESYTSASANNNP 211 Query: 211 ITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQFLAGMAFNNASLGYVHAMAHQLG 270 ++ A A +A+ ++ N+ AV+DGSN KAR M LAG AF N+ + VHA+A+ +G Sbjct: 212 VSKALAREALRLLGANIETAVKDGSNVKARSDMLLGAMLAGQAFANSPVAAVHALAYPIG 271 Query: 271 GFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAAMGVNVTGKNDAEGAEACINAIREL 330 G +++PHG+ NA++LPHV FN+++ A + ++ G A+ A I+ + L Sbjct: 272 GIFHVPHGLSNALVLPHVMRFNTEICGEAYSILATDVFPDLAGTPAAKRANQFIDRLEAL 331 Query: 331 AKKVDIPAGLRDLNVKEEDFAVLATNALKDA-CGFTNPIQATHEEIVAIYRAA 382 + + + LR++ + E D A LA++++K NP + + + +AIY+AA Sbjct: 332 SADLGLEQTLREVGIGEADLATLASDSMKQTRLLVNNPREVSETDALAIYKAA 384 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: 350 Number of extensions: 8 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: 385 Length adjustment: 30 Effective length of query: 353 Effective length of database: 355 Effective search space: 125315 Effective search space used: 125315 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