Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate Pf6N2E2_668 2,3-butanediol dehydrogenase, R-alcohol forming, (R)- and (S)-acetoin-specific (EC 1.1.1.4)
Query= SwissProt::Q8U259 (348 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_668 Length = 364 Score = 172 bits (436), Expect = 1e-47 Identities = 119/351 (33%), Positives = 174/351 (49%), Gaps = 26/351 (7%) Query: 1 MSEKMVAIMKTKPEYGAELVEV-DVP---KPGPGEVLIKILATSICGTDLHIYEWNE--- 53 +S K M+ +G + V DVP P G V I++ ICG+DLH Y Sbjct: 3 VSIKPTRSMRAAVWHGRNDIRVEDVPLPVSPPAGWVQIRVQWCGICGSDLHEYVAGPVFI 62 Query: 54 -----WAQTRIRPPQIMGHEVAGEVVEVGPGVEGIEVGDYVSVETHIVCGKCYACKRGQY 108 T I+ I+GHE GE+VE+G GVEG VG+ V+ + CG CY C G Y Sbjct: 63 PVDAPHPLTGIKGQCILGHEFCGEIVELGAGVEGFSVGEPVAADACQHCGTCYYCTHGLY 122 Query: 109 HVCQNTKIFGVDTDGVFAEYAVVPAQNVWKNPKNIPPEYATLQEPLGNAVDTV-LAGPIA 167 ++C+N G+ +G FAE VPA ++K P + P E L EPL + V AG + Sbjct: 123 NICENLAFTGLMNNGAFAELVNVPANLLYKLPADFPAEAGALIEPLAVGMHAVKKAGSLL 182 Query: 168 GKSVLITGAGPLGLLGIAVAKASGAYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKE 227 G++V++ GAG +GL I AKA+GA VI E S R+ A +VGA +VI+P E D + E Sbjct: 183 GQNVVVVGAGTIGLCTIMCAKAAGAAQVIALEMSGARKAKALEVGASHVIDPNECDALAE 242 Query: 228 VMDITDGNGVDVFLEFSGAPKALEQGLQAVTPAGRVSLLGLFPGKVSIDFNNLI-----I 282 V +T G G DV E G + + + AG+ L+G+F +F L+ + Sbjct: 243 VRRLTGGLGADVSFECIGNKHTAKLAIDLIRKAGKCVLVGIFEEPSQFNFFELVSTEKQV 302 Query: 283 FKALTVYGITGRHLWETWYTVSRLLQSGKLNIDPIITHKYKGFDKYEEAFE 333 AL G + V + G+L+I P++T + + + + FE Sbjct: 303 LGALAYNG--------EFADVIAFIADGRLDISPLVTGRIQLEEIVGQGFE 345 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: 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