Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 5209439 Shew_1910 bifunctional acetaldehyde-CoA/alcohol dehydrogenase (RefSeq)
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__PV4:5209439 Length = 872 Score = 201 bits (511), Expect = 7e-56 Identities = 146/413 (35%), Positives = 215/413 (52%), Gaps = 44/413 (10%) Query: 8 IPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDG 67 +PS SL A+ ++D R LIVTD L G + K L+ + + + ++ Sbjct: 456 LPSSIYFRRGSLPIALEELSDK--KRALIVTDKYLFNNGYCDETIKILKSQGLETEVFYE 513 Query: 68 TQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGI-----------ALVAANGGD 116 + +PT V G + K D +I+LGGGSP D AK I A +A D Sbjct: 514 VEADPTLAIVNQGASVAKSFQPDVIIALGGGSPMDAAKIIWVMYEHPEVDFADLALRFMD 573 Query: 117 IRD----YEGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLL 172 IR + + + AK M+AI TT+GT SE+T F ++TDE +K I D +TP + Sbjct: 574 IRKRIYKFPKLGKKAK----MVAIPTTSGTGSEVTPFAVVTDEQTGMKYPIADYELTPNM 629 Query: 173 SVNDSSLMIGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVE 232 ++ D +L++ MPKSLTA G+DA+THA+EAYVS+ A +D AL+A+ ++ + LP + Sbjct: 630 AIVDPNLVMDMPKSLTAFGGIDAITHALEAYVSVMANEYSDGQALQALDLLVKYLPDSYA 689 Query: 233 DGSNAK-AREAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVF 291 G+ A ARE + +AG+AF NA LG H+MAH+LG ++L HG+ NA+L+ +V F Sbjct: 690 LGAQAPVAREKVHNGATIAGIAFANAFLGICHSMAHKLGAEFHLAHGLANALLISNVIRF 749 Query: 292 N-----SKVAA-------------ARLRDCAAAMGVNVTGKNDAEGAEACINAIRELAKK 333 N +K AA A++ + G G +D E EA + I EL K Sbjct: 750 NATDLPTKQAAFSQYDRPKALCRYAKIAEHLKLKGATGEGISDEEKVEALLEKIDELKKT 809 Query: 334 VDIPAGLRDLNVKEEDFAV----LATNALKDACGFTNPIQATHEEIVAIYRAA 382 + IPA +++ V E DF LA +A D C NP E+ AI A+ Sbjct: 810 IGIPASIQEAGVNEADFFAKLDELAEDAFDDQCTGANPRYPLIAELKAILTAS 862 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: 628 Number of extensions: 26 Number of successful extensions: 4 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: 872 Length adjustment: 36 Effective length of query: 347 Effective length of database: 836 Effective search space: 290092 Effective search space used: 290092 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: 53 (25.0 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