Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate GFF3713 Psest_3782 Alcohol dehydrogenase, class IV
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__psRCH2:GFF3713 Length = 388 Score = 252 bits (643), Expect = 1e-71 Identities = 142/377 (37%), Positives = 213/377 (56%), Gaps = 5/377 (1%) Query: 8 IPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDG 67 +P + +GA + ++ + G R LIVTD M+ +LG + L E I S + Sbjct: 7 LPRLMEVGAGASQQLARVLKELGCNRPLIVTDRMMVELGYVARIAGQLGEAGIASQCFAD 66 Query: 68 TQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRSA 127 T P PT ++ AG++++++ + DS+++LGGGSP D AK I ++ GG++RDY + Sbjct: 67 TLPEPTAASIRAGVEMVRQGDFDSIVALGGGSPIDSAKAIGILGKFGGEMRDYRFPRDVS 126 Query: 128 KPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKSL 187 + LP+IAI TTAGT SE TRF IITDE KM P+ ++ D L + +P + Sbjct: 127 EAGLPLIAIPTTAGTGSEATRFTIITDETSDEKMLCAGLGFMPIAALIDYELTLSLPPRV 186 Query: 188 TAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYAQ 247 TA TG+DALTHAIEAYVS A+ +DA AL+A+ ++A NL A + N AREAM Sbjct: 187 TADTGIDALTHAIEAYVSRKASLYSDAQALEAMRLLAPNLRAAFHEPGNRAAREAMMLGA 246 Query: 248 FLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAAM 307 LAG+AF+NAS+ VH M+ +G F+++PHG+ NA+LLP + F+ A R DCA AM Sbjct: 247 TLAGIAFSNASVALVHGMSRPIGAFFHVPHGLSNAMLLPAITAFSIPAAPERYADCARAM 306 Query: 308 GVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDF----AVLATNALKDACG 363 GV + + + +R + +++ +P+ + E F +A AL Sbjct: 307 GVAAQTDSVGVANDKLLAELRAINQELQVPSP-EQFGISRERFFELRETMARQALASGSP 365 Query: 364 FTNPIQATHEEIVAIYR 380 NP T EI+ +Y+ Sbjct: 366 GNNPRVPTEAEIIDLYK 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: 372 Number of extensions: 15 Number of successful extensions: 1 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: 388 Length adjustment: 30 Effective length of query: 353 Effective length of database: 358 Effective search space: 126374 Effective search space used: 126374 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