Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate 201293 SO2136 aldehyde-alcohol dehydrogenase (NCBI ptt file)
Query= ecocyc::EG12293-MONOMER (383 letters) >FitnessBrowser__MR1:201293 Length = 866 Score = 199 bits (507), Expect = 2e-55 Identities = 140/389 (35%), Positives = 207/389 (53%), Gaps = 31/389 (7%) Query: 8 IPSVNVIGADSLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDG 67 +PS SL A+ ++D R LIVTD L G + K L+ + + + ++ Sbjct: 456 LPSSIYFRRGSLPIALEELSDK--KRALIVTDPFLFNQGYCDETLKILKAQGLETEVFYE 513 Query: 68 TQPNPTTENVAAGLKLLKENNCDSVISLGGGSPHDCAKGI-----------ALVAANGGD 116 + +PT V G K+ D +I+LGGGSP D AK I A +A D Sbjct: 514 VEADPTLATVRQGAKVANSFKPDVIIALGGGSPMDAAKIIWVMYEHPDVDFADLALRFMD 573 Query: 117 IRDYEGVDRSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVND 176 IR + M+AI TT+GT SE+T F ++TDE K I D +TP +++ D Sbjct: 574 IRKRIYKFPKMGVKATMVAIPTTSGTGSEVTPFAVVTDEQTGKKYPIADYQLTPNMAIVD 633 Query: 177 SSLMIGMPKSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGSN 236 +L++ MPKSLTA G+DA+THA+EAYVS+ A +D AL+A+ ++ + LP A + G+ Sbjct: 634 PNLVMDMPKSLTAFGGIDAITHALEAYVSVMANEYSDGQALQALDLLCKYLPDAYQLGAA 693 Query: 237 AK-AREAMAYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFN--- 292 + ARE + +AG+AF NA LG H+MAH+LG ++L HG+ NA+L+ +V FN Sbjct: 694 SPIAREKVHNGATIAGIAFANAFLGICHSMAHKLGAEFHLAHGLANALLISNVIRFNATD 753 Query: 293 --SKVAA--------ARLRDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRD 342 +K AA A R A A + + G +DA+ E + I +L K + IPA +++ Sbjct: 754 LPTKQAAFSQYDRPKALCRYAAIADHLALGGNSDAQKVEKLLEKIEQLKKTLGIPASIQE 813 Query: 343 LNVKEEDFA----VLATNALKDACGFTNP 367 V E DF +LA +A D C NP Sbjct: 814 AGVNEADFLAKLDMLAEDAFDDQCTGANP 842 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: 650 Number of extensions: 27 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: 866 Length adjustment: 36 Effective length of query: 347 Effective length of database: 830 Effective search space: 288010 Effective search space used: 288010 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