Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate CCNA_02929 CCNA_02929 sorbitol dehydrogenase
Query= curated2:Q65JE7 (346 letters) >FitnessBrowser__Caulo:CCNA_02929 Length = 346 Score = 128 bits (322), Expect = 2e-34 Identities = 103/336 (30%), Positives = 164/336 (48%), Gaps = 22/336 (6%) Query: 23 PIPKIDKHEVLIKVKAASICGTDVHIYNWDEWAKSRVKPPYVFGHEFSGEVVQVGENVTT 82 P P+ D+ + +++V A SICG+D+HIY+ +++ + GHE GEVV+VG V Sbjct: 20 PTPQSDR-DAIVQVTACSICGSDLHIYHGHGFSEDL---GFCVGHEAVGEVVEVGRGVQR 75 Query: 83 VKEGEYVSAETHIVCGKCLPCLTGKEHVCKK----TLILGVDTDGCFAEYVKMPAANIWK 138 +K G+ V + CG+C CL+G C+ L G AE V++PAA++ Sbjct: 76 LKVGDKVMLPAAVGCGRCRSCLSGVIQTCENGQGACYGLSARLQGSQAEAVRVPAADM-- 133 Query: 139 NPAGMPEDLASIQE-PLGNAVHTVLTG-----MTAGVKVAVVGCGPIGLMAVAVAKASGA 192 N +P+ ++ Q + +A+ T G + G VAV+G GPIGLMAV A GA Sbjct: 134 NAVPVPDGVSMDQALMMTDALATAWFGARNAEVRPGASVAVIGLGPIGLMAVESAYVMGA 193 Query: 193 AQVIAIDKNEYRLDLALQMGATDIISVEKEDPLKNVSALTNGEGADLVCEMSGHPTAIRQ 252 V AID R LA + GA I++ ++ L V T G G D V E G + Sbjct: 194 HVVYAIDPLPARRALAEEAGA---IALHPDEALARVREDTKGRGLDCVIEAVGGEATVDA 250 Query: 253 SLKMAANGGRVHVLSLPEHPVCIDMTNDIVFKGLTVQGITGRKMFETWRQVSGLLQSGTI 312 +L++ G V V+ + + GLT + + + E + L++SG + Sbjct: 251 ALRLVRPRGVVSVIGVQQAKRFAFPLERAFGAGLTFR-VGTCSVPEELPALFPLVRSGRL 309 Query: 313 QIKPVITHRFPMEEFEKGFELMRKGQCG--KVVLIP 346 + + I+HR P+ + + + L + G K+VL P Sbjct: 310 RPEKYISHRLPLSDGPEAYRLFESREAGALKMVLTP 345 Lambda K H 0.318 0.136 0.410 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: 283 Number of extensions: 15 Number of successful extensions: 5 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: 346 Length of database: 346 Length adjustment: 29 Effective length of query: 317 Effective length of database: 317 Effective search space: 100489 Effective search space used: 100489 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