Align L-threonine dehydrogenase (EC 1.1.1.103) (characterized)
to candidate WP_038857023.1 AFK65_RS11195 bifunctional acetaldehyde-CoA/alcohol dehydrogenase
Query= ecocyc::EG12293-MONOMER (383 letters) >NCBI__GCF_001277175.1:WP_038857023.1 Length = 892 Score = 199 bits (507), Expect = 2e-55 Identities = 129/383 (33%), Positives = 205/383 (53%), Gaps = 35/383 (9%) Query: 18 SLTDAMNMMADYGFTRTLIVTDNMLTKLGMAGDVQKALEERNIFSVIYDGTQPNPTTENV 77 SL A++ + G R +IVTD L G A + L+ + + ++ + +PT V Sbjct: 466 SLPIALDEVITDGHKRAMIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSVV 525 Query: 78 AAGLKLLKENNCDSVISLGGGSPHDCAKGIALV-----------AANGGDIRD--YEGVD 124 G +L+ D +I+LGGGSP D AK + ++ A DIR Y+ Sbjct: 526 RKGAELMNSFKPDVIIALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPK 585 Query: 125 RSAKPQLPMIAINTTAGTASEMTRFCIITDEARHIKMAIVDKHVTPLLSVNDSSLMIGMP 184 K + MIA+ TT+GT SE+T F ++TD+ K + D +TP +++ D++L++ MP Sbjct: 586 MGVKAK--MIAVTTTSGTGSEVTPFAVVTDDETGQKYPLADYALTPDMAIVDANLVMDMP 643 Query: 185 KSLTAATGMDALTHAIEAYVSIAATPITDACALKAVTMIAENLPLAVEDGS-NAKAREAM 243 KSL A G+DA+THA+EAYVS+ A+ +D AL+A+ ++ ENLP + +GS N ARE + Sbjct: 644 KSLCAFGGLDAVTHALEAYVSVLASEFSDGQALQALKLLKENLPASYHEGSKNPVARERV 703 Query: 244 AYAQFLAGMAFNNASLGYVHAMAHQLGGFYNLPHGVCNAVLLPHVQVFNSK--------- 294 A +AG+AF NA LG H+MAH+LG +++PHG+ NA+L+ +V +N+ Sbjct: 704 HSAATIAGIAFANAFLGVCHSMAHKLGSQFHIPHGLANALLISNVIRYNANDNPTKQTAF 763 Query: 295 ------VAAARLRDCAAAMGVNVTGKNDAEGAEACINAIRELAKKVDIPAGLRDLNVKEE 348 A R + A +G++ G A E + + + ++ IP +R+ V+E Sbjct: 764 SQYDRPQARRRYAEVADHLGLSAPGDRTAAKIEKLLAWLESIKAELGIPKSIREAGVQEA 823 Query: 349 DFAV----LATNALKDACGFTNP 367 DF L+ +A D C NP Sbjct: 824 DFLANVDKLSEDAFDDQCTGANP 846 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: 693 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: 892 Length adjustment: 36 Effective length of query: 347 Effective length of database: 856 Effective search space: 297032 Effective search space used: 297032 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 24 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