Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate BWI76_RS11535 BWI76_RS11535 putative oxidoreductase, Zn-dependent and NAD(P)-binding protein
Query= curated2:Q72L62 (343 letters) >FitnessBrowser__Koxy:BWI76_RS11535 Length = 358 Score = 160 bits (404), Expect = 6e-44 Identities = 114/361 (31%), Positives = 185/361 (51%), Gaps = 31/361 (8%) Query: 1 MRALAKLAPE-EGLTLVDRPVPEPGPGEILVRVEAASICGTDLHIWKWDAWARGRIRPPL 59 M+ALA+ G ++D P P GP ++++ ++AA+ICG D+ + D+ G + Sbjct: 1 MKALARFGKAFGGYKMIDVPEPVCGPDDVVIEIKAAAICGADMKHYNVDS---GSDQFNS 57 Query: 60 VTGHEFSGVVEAVGPGVKRPQVGDHV-SLESHVVCHACPACRTGNYHVCLNTKILGVDRD 118 + GHEF+G + VG VK +VG V S S VC CPAC G++ C LG+D + Sbjct: 58 IRGHEFAGAIVRVGDKVKDWKVGQRVVSDNSGHVCGVCPACEQGDFLCCAEKVNLGLDNN 117 Query: 119 ---GGFAEYVVVPAE-------NAWVNPKDLPFEVAAILEPFGNAVHTVYAGSG-VSGKS 167 GGF++Y +VP E W P + +E AA+L+P NA ++ S + G+ Sbjct: 118 TWGGGFSKYCLVPGEILKIHRHALWEIPPGVDYEDAAVLDPICNAYKSLAQQSKFLPGQD 177 Query: 168 VLITGAGPIGLMAAMVARASGAGPILV---SDPNPYRLAFARPY-ADRLVNPLEEDLLEV 223 V++ G GP+GL + +AR GA I++ + R A+ A +VN ED++ Sbjct: 178 VVVFGTGPLGLFSVQMARIMGAVNIVMVGLEEDVAVRFPIAKALGATAVVNASTEDVVAR 237 Query: 224 VRRVTGS-GVEVLLEFSGNEAAIHQGLMALIPGGEARILGIPSDPIRFDLAGELVMRGIT 282 + + G + +++E SG A+ Q + L P GE +G+ P+ F + IT Sbjct: 238 CQAICGKDNLGLVIECSGANIALKQSIEMLRPNGEVVRVGMGFQPLDFSI------NDIT 291 Query: 283 AFG--IAGRRLWQT--WMQGTALVYSGRVDLSPLITHRLPLSRYREAFGLLASGQAVKVI 338 + I G + + W L+ SG + + P+ITHR+ LS++RE F + A+KVI Sbjct: 292 TWNKSIIGHMAYDSTSWRNAIRLLASGAIKVKPMITHRIGLSQWREGFDAMVDKTAIKVI 351 Query: 339 L 339 + Sbjct: 352 M 352 Lambda K H 0.321 0.140 0.432 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: 362 Number of extensions: 21 Number of successful extensions: 7 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: 343 Length of database: 358 Length adjustment: 29 Effective length of query: 314 Effective length of database: 329 Effective search space: 103306 Effective search space used: 103306 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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