Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate AZOBR_RS16135 AZOBR_RS16135 sorbitol dehydrogenase
Query= SwissProt::Q8U259 (348 letters) >FitnessBrowser__azobra:AZOBR_RS16135 Length = 334 Score = 140 bits (352), Expect = 6e-38 Identities = 87/256 (33%), Positives = 133/256 (51%), Gaps = 7/256 (2%) Query: 21 EVDVPKPGPGEVLIKILATSICGTDLHIYEWNEWAQTRIRPPQIMGHEVAGEVVEVGPGV 80 EV P PGPGEVL+ I ++CG+DL ++ + P+I GHE+ GE+ VG GV Sbjct: 12 EVAEPTPGPGEVLLAIRHVALCGSDLSTFKG---LNPLVSLPRIPGHEIGGEIAAVGEGV 68 Query: 81 EG-IEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDTDGVFAEYAVVPAQNVWKN 139 VG V + CG C +C++G+ + C++ + GV +G AE V+P + N Sbjct: 69 PAEYTVGRRAIVIPYTACGTCPSCRKGRVNACRSNRTLGVQQNGGLAERIVLPYGKLILN 128 Query: 140 PKNIPPEYATLQEPLGNAVDTVLAGPI-AGKSVLITGAGPLGLLGIAVAKASGAYPVIVS 198 + P + L EPL G + A +VL+ G G +G+ IA + GA VI Sbjct: 129 D-TLAPRHLALVEPLSVGFHAAARGRVEAADTVLVLGCGMIGMGAIAGSVHRGA-TVIAV 186 Query: 199 EPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLEFSGAPKALEQGLQAVT 258 + E + LA++ GA + I+ +EDV + ++T+G+G DV +E G P Q + V+ Sbjct: 187 DIGEAKTGLARRYGAAHTIDAGKEDVAARIAELTNGDGADVVIEAVGLPATFTQAIDLVS 246 Query: 259 PAGRVSLLGLFPGKVS 274 AGRV +G VS Sbjct: 247 FAGRVVYIGYAKEPVS 262 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: 259 Number of extensions: 13 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: 334 Length adjustment: 29 Effective length of query: 319 Effective length of database: 305 Effective search space: 97295 Effective search space used: 97295 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