Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_078716111.1 B5D49_RS02645 iron-containing alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >NCBI__GCF_900167125.1:WP_078716111.1 Length = 382 Score = 268 bits (685), Expect = 2e-76 Identities = 156/384 (40%), Positives = 225/384 (58%), Gaps = 3/384 (0%) Query: 1 MAASTFFIPSVNVIGADSLTDAMNMMADYGFTRTLIVTD-NMLTKLGMAGDVQKALEERN 59 M+ F P + G ++ A G +R LIVT + T+ G V +L E Sbjct: 1 MSTYIFQTPPRIIFGNGAVAQVGRETARLG-SRALIVTGKSSSTRTGSLEAVTASLNEAG 59 Query: 60 IFSVIYDGTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRD 119 + V++ + +P+ + V AG L +EN CD ++ LGGGSP D AKGI L+ + GDIRD Sbjct: 60 VHPVLFAEVESDPSIQTVEAGAALARENQCDVIVGLGGGSPLDAAKGIVLLLTHPGDIRD 119 Query: 120 YEGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSL 179 Y P +P+I+I TTAGTASE+TRF +ITD + IKM++ + P +++ D L Sbjct: 120 YTSQPADG-PGMPLISIPTTAGTASEITRFTVITDTEQKIKMSLQGTALIPSVALLDPQL 178 Query: 180 MIGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKA 239 + MP+ +TAATGMDALTHAIEAY+S ATP++D AL+A+ +I NL AV+ N A Sbjct: 179 TVTMPQHVTAATGMDALTHAIEAYISKLATPMSDLHALEAIRLIGANLIKAVDSPDNMAA 238 Query: 240 REAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAAR 299 REAM Q AG+AF+NAS+ VH+M+ LG + + HG NA+LLP V FN AA R Sbjct: 239 REAMLRGQMHAGLAFSNASVALVHSMSRPLGALFGIAHGQANAMLLPVVMDFNRSAAADR 298 Query: 300 LRDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALK 359 R A A+G NV + + A+ + ++ EL ++ + L V+E+D A LA +A++ Sbjct: 299 YRHIAEALGENVQELSARDAAKTTVLSVEELFEETGLEQHLSAYGVQEKDIARLAKDAME 358 Query: 360 DACGFTNPIQATHEEIVAIYRAAM 383 A NP +A E + AIY + + Sbjct: 359 SASTAFNPRKADLESVAAIYHSLL 382 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: 325 Number of extensions: 12 Number of successful extensions: 2 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 Apr 09 2024. 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