Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate Pf6N2E2_1380 Alcohol dehydrogenase (EC 1.1.1.1); Acetaldehyde dehydrogenase (EC 1.2.1.10)
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1380 Length = 392 Score = 261 bits (666), Expect = 3e-74 Identities = 139/377 (36%), Positives = 212/377 (56%) Query: 7 FIPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYD 66 F+ + GA + N +G + LIVTD + G DV+ +L+ + I +Y Sbjct: 16 FVSPEIMFGAGCRHNVGNYAKTFGARKVLIVTDPGVIAAGWVADVEASLQAQGIDYCVYS 75 Query: 67 GTQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGIALVAANGGDIRDYEGVDRS 126 PNP E V G L +EN+CD ++++GGGSP DC KGI +V A+G +I ++EGVD Sbjct: 76 AVSPNPRVEEVMLGADLYRENHCDVIVAVGGGSPMDCGKGIGIVVAHGRNILEFEGVDTL 135 Query: 127 AKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMPKS 186 P P+I I TTAGT++++++F II+++ +K +IV K P +S+ D + M Sbjct: 136 HVPSPPLILIPTTAGTSADVSQFVIISNQQERMKFSIVSKAAVPDVSLIDPETTLSMDPF 195 Query: 187 LTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSNAKAREAMAYA 246 L+A TG+DAL HAIEA+VS P+TD AL+A+ +I NL + + ++ RE + Sbjct: 196 LSACTGIDALVHAIEAFVSTGHGPLTDPHALEAMRLINSNLVQMIANPADIALREKIMLG 255 Query: 247 QFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSKVAAARLRDCAAA 306 AG+AF+NA LG VHAM+H LGGF +LPHG+CNAVL+ HV FN A R + A Sbjct: 256 SMQAGLAFSNAILGAVHAMSHSLGGFLDLPHGLCNAVLVEHVVAFNYNSAPERFKVIAET 315 Query: 307 MGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEEDFAVLATNALKDACGFTN 366 +G++ G N + + + L + L V D L+ +A+ D C TN Sbjct: 316 LGIDCRGLNHRQIRTRLVEHLIALKHTIGFHETLGLHGVSTSDIPFLSQHAMHDPCILTN 375 Query: 367 PIQATHEEIVAIYRAAM 383 P +++ ++ +Y A+ Sbjct: 376 PRESSQRDVEVVYGEAL 392 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: 364 Number of extensions: 21 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: 392 Length adjustment: 30 Effective length of query: 353 Effective length of database: 362 Effective search space: 127786 Effective search space used: 127786 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