Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate 3607519 Dshi_0931 Alcohol dehydrogenase GroES domain protein (RefSeq)
Query= curated2:Q65JE7 (346 letters) >FitnessBrowser__Dino:3607519 Length = 339 Score = 125 bits (313), Expect = 2e-33 Identities = 95/273 (34%), Positives = 140/273 (51%), Gaps = 17/273 (6%) Query: 25 PKIDKHEVLIKVKAASICGTDVHIYNWDEWAKSRVKPPYVFGHEFSGEVVQVGENVTTVK 84 P + +L+K++A +C TD+H D K +PP++ GHE G VV+VG NVT+VK Sbjct: 24 PTVTDGNILVKIEACGVCHTDLHAARGDWPVKP--EPPFIPGHEGVGVVVEVGHNVTSVK 81 Query: 85 EGEYVSAE-THIVCGKCLPCLTGKEHVCK-KTLILGVDTDGCFAEYVKMPAANIWKNPAG 142 EG+ V H CG C C+TG E +C+ + G +G FAEYV+ + P Sbjct: 82 EGDRVGVPWLHHACGHCTACVTGWETLCRTEPEYTGYTVNGGFAEYVEADPTYVGHLPDK 141 Query: 143 MPEDLASIQEPLGNAVHTVLTGMT-----AGVKVAVVGCGPIGLMAVAVAKASGAAQVIA 197 + D A P+ A TV G+ G V + G G +G +AV A+A G VIA Sbjct: 142 L--DFAP-AAPILCAGVTVYKGLKECDLHPGQTVVISGIGGLGHLAVQYARAMG-LHVIA 197 Query: 198 IDKNEYRLDLALQMGATDIISVEKEDPLKNVSALTNGEGADLVCEMSGHPTAIRQSLKMA 257 +D E +L LA +GA I+ +DP+ V+ L EG LV +S TA Q + M Sbjct: 198 VDVAEDKLALARDLGAGVAINAATQDPVAEVARLGGAEGV-LVTAVSN--TAFSQGVGML 254 Query: 258 ANGGRVHVLSLPEHPVCIDMTNDIVFKGLTVQG 290 A GG + ++ LP +++ D+V T++G Sbjct: 255 APGGTMSLVGLPPGDFPLNIF-DVVLNRKTIRG 286 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: 315 Number of extensions: 18 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: 339 Length adjustment: 29 Effective length of query: 317 Effective length of database: 310 Effective search space: 98270 Effective search space used: 98270 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