Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate AO353_25145 AO353_25145 butanediol dehydrogenase
Query= SwissProt::Q8U259 (348 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25145 Length = 364 Score = 170 bits (430), Expect = 6e-47 Identities = 111/314 (35%), Positives = 159/314 (50%), Gaps = 25/314 (7%) Query: 23 DVP---KPGPGEVLIKILATSICGTDLHIYEWNE--------WAQTRIRPPQIMGHEVAG 71 DVP P G V I++ ICG+DLH Y T I+ I+GHE G Sbjct: 26 DVPLPIAPPAGWVQIRVQWCGICGSDLHEYVAGPVFIPVDAPHPLTGIKGQCILGHEFCG 85 Query: 72 EVVEVGPGVEGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDTDGVFAEYAVV 131 E+VE+G GV+G VG+ V+ + CG CY C G Y++C+N G+ +G FAE V Sbjct: 86 EIVELGAGVQGFSVGEPVAADACQHCGTCYYCTHGLYNICENLAFTGLMNNGAFAELVNV 145 Query: 132 PAQNVWKNPKNIPPEYATLQEPLGNAVDTV-LAGPIAGKSVLITGAGPLGLLGIAVAKAS 190 PA ++K P N P E L EPL + V AG + G++V++ GAG +GL I AKA+ Sbjct: 146 PANLLYKLPANFPAEAGALIEPLAVGMHAVKKAGSLLGQNVVVVGAGTIGLCTIMCAKAA 205 Query: 191 GAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLEFSGAPKAL 250 GA VI E S R+ A +VGA +V++P E D + EV +T G G DV E G Sbjct: 206 GAAQVITLEMSGARKAKALEVGATHVLDPNECDALAEVRRLTGGLGADVSFECIGNKHTA 265 Query: 251 EQGLQAVTPAGRVSLLGLFPGKVSIDFNNLI-----IFKALTVYGITGRHLWETWYTVSR 305 + + + AG+ L+G+F +F L+ + AL G + V Sbjct: 266 KLAIDLIRKAGKCVLVGIFEEPSEFNFFELVATEKQVLGALAYNG--------EFADVIA 317 Query: 306 LLQSGKLNIDPIIT 319 + G+L+I P++T Sbjct: 318 FIADGRLDITPLVT 331 Lambda K H 0.318 0.138 0.417 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: 319 Number of extensions: 23 Number of successful extensions: 3 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: 348 Length of database: 364 Length adjustment: 29 Effective length of query: 319 Effective length of database: 335 Effective search space: 106865 Effective search space used: 106865 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 (21.7 bits) S2: 49 (23.5 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