Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate SMa0512 SMa0512 IdnD L-idonate 5-dehydrogenase
Query= SwissProt::Q8U259 (348 letters) >FitnessBrowser__Smeli:SMa0512 Length = 343 Score = 164 bits (415), Expect = 3e-45 Identities = 109/307 (35%), Positives = 160/307 (52%), Gaps = 14/307 (4%) Query: 21 EVDVPKPGPGEVLIKILATSICGTDLHIYEWNEWAQTRIRPPQIMGHEVAGEVVEVGPGV 80 E V KPGPGEV I++ A ICG+DLH Y + R++ P I+GHEV+G V +G GV Sbjct: 16 ECAVEKPGPGEVEIRLAAGGICGSDLHYYNHGGFGTVRLKEPMILGHEVSGHVAALGEGV 75 Query: 81 EGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFG-----VDTDGVFAEYAVVPAQN 135 + +GD V+V CG C C +G + C + + +G G F E V A Sbjct: 76 SDLAIGDLVAVSPSRPCGACDYCLKGLPNHCFHMRFYGSAMPFPHIQGAFRERLVAKASQ 135 Query: 136 VWKNPKNIPPEYATLQEPLGNAVD-TVLAGPIAGKSVLITGAGPLGLLGIAVAKASGAYP 194 K + + A + EPL + T AG + GK VL+TG GP+G L I A+ +GA Sbjct: 136 CVK-AEGLSAGEAAMAEPLSVTLHATRRAGEMLGKRVLVTGCGPIGTLSILAARRAGAAE 194 Query: 195 VIVSEPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGV-DVFLEFSGAPKALEQG 253 ++ ++ SE A+ VGAD +N E+ ++ ++ G DV E SGA AL G Sbjct: 195 IVAADLSERALGFARAVGADRTVNLSEDR--DGLVPFSENKGTFDVLYECSGAQPALVAG 252 Query: 254 LQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALTVYGITGRHLWETWYTVSRLLQSGKLN 313 +QA+ P G + LGL G +++ I K L + G H E + T +L+Q G ++ Sbjct: 253 IQALRPRGVIVQLGL-GGDMALPM-MAITAKELDLRGSFRFH--EEFATAVKLMQGGLID 308 Query: 314 IDPIITH 320 + P+ITH Sbjct: 309 VKPLITH 315 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: 241 Number of extensions: 14 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: 343 Length adjustment: 29 Effective length of query: 319 Effective length of database: 314 Effective search space: 100166 Effective search space used: 100166 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