Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate RR42_RS09405 RR42_RS09405 butanediol dehydrogenase
Query= SwissProt::Q8U259 (348 letters) >FitnessBrowser__Cup4G11:RR42_RS09405 Length = 357 Score = 186 bits (472), Expect = 8e-52 Identities = 116/339 (34%), Positives = 180/339 (53%), Gaps = 15/339 (4%) Query: 21 EVDVP-KPGPGEVLIKILATSICGTDLHIYEW--------NEWAQTRIRPPQIMGHEVAG 71 EV VP KP G V I++ ICG+DLH Y + T ++ I+GHE +G Sbjct: 16 EVRVPDKPAEGWVKIRVHWCGICGSDLHEYVAGPVFIPVDHPHPLTGLKGQCILGHEFSG 75 Query: 72 EVVEVGPGVEGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDTDGVFAEYAVV 131 E+ E+G GV G +VG+ V+ + CGKCY C G Y++C++ G+ +G FAEY V Sbjct: 76 EIAELGAGVTGFKVGERVTADACQHCGKCYYCTHGLYNICESLAFTGLMNNGAFAEYVNV 135 Query: 132 PAQNVWKNPKNIPPEYATLQEPLGNAVDTV-LAGPIAGKSVLITGAGPLGLLGIAVAKAS 190 PA+ ++K P+N P E L EPL + V AG I G++V++ GAG +GL I AKA+ Sbjct: 136 PAELLYKLPENFPTEAGALIEPLAVGLHAVKKAGNIVGQTVVVVGAGTIGLCTIMCAKAA 195 Query: 191 GAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLEFSGAPKAL 250 GA +I E S R+ A +VGA+ VI+P E D + +V +T G G DV E G Sbjct: 196 GAGRIIALEMSSARKKKALEVGANVVIDPKECDAIAQVKALTGGYGADVSFECIGNKATA 255 Query: 251 EQGLQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALTVYGITGRHLWETWYT-VSRLLQS 309 + + + AG+ ++G+F + +F ++ T I G + + V R + Sbjct: 256 KLAIDVIRKAGKCVMVGIFEEPSAFNFFEIV----STEKEIIGSLAYNGEFADVIRFIAD 311 Query: 310 GKLNIDPIITHKYKGFDKYEEAFELMRAGKTGKVVFMLK 348 G++++ P+IT + D + FE + K G V +++ Sbjct: 312 GRIDVQPLITGRISLADIVSQGFEELVNNKDGNVKIIVQ 350 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: 323 Number of extensions: 19 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: 348 Length of database: 357 Length adjustment: 29 Effective length of query: 319 Effective length of database: 328 Effective search space: 104632 Effective search space used: 104632 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