Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate Ga0059261_0846 Ga0059261_0846 Zn-dependent alcohol dehydrogenases, class III
Query= curated2:Q72L62 (343 letters) >FitnessBrowser__Korea:Ga0059261_0846 Length = 361 Score = 128 bits (321), Expect = 3e-34 Identities = 107/366 (29%), Positives = 166/366 (45%), Gaps = 33/366 (9%) Query: 1 MRALAKLAPEEGLTLVDRPVPEPGPGEILVRVEAASICGTDLHIWKWDAWARGRIRPPLV 60 ++A + L + D + +PGP E+L+R A +C +DLH A + P + Sbjct: 1 VKAAVLFEAKRPLEIHDITIDKPGPREVLIRTAACGVCRSDLHFVDG---AYPHVMPT-I 56 Query: 61 TGHEFSGVVEAVGPGVKRPQVGDHVSLESHVVCHACPACRTGNYHVCLN----------- 109 GHE SGVVEAVG V R + GDHV V C +C C +G +C++ Sbjct: 57 PGHEASGVVEAVGSEVTRLRPGDHVITFFTVFCGSCEFCVSGRPSLCVDGSTKRPKEGEP 116 Query: 110 -------TKILGVDRDGGFAEYVVVPAENAWVNPKDLPFEVAAILEPFGNAVHT----VY 158 T I FAE ++V KD+P + AA+L G AV T ++ Sbjct: 117 KLRLPDGTPIAQFLNLSAFAEQMLVHENACVAISKDMPLDRAALL---GCAVITGAGAIF 173 Query: 159 AGSGVS-GKSVLITGAGPIGLMAAMVARASGAGPILVSDPNPYRLAFARPY-ADRLVNPL 216 S V+ G++V + G G IGL A A+ +GAG I+ DP P + AR A + + + Sbjct: 174 RDSKVTPGETVAVIGCGGIGLSAVNAAKIAGAGKIIAIDPVPEKREIARKMGATHVFDAM 233 Query: 217 EEDLLEVVRRVTGSGVEVLLEFSGNEAAIHQGLMALIPGGEARILGIPSDPIRFDLAGEL 276 +DL++ V ++T GV+ +E G L GG A ILG+ + + G Sbjct: 234 ADDLVKQVAKLTDGGVDYAIEAVGRPNTAELAWNLLRRGGTATILGMIAPGQSVSIPGPT 293 Query: 277 VMRGITAFG-IAGRRLWQTWMQGTALVY-SGRVDLSPLITHRLPLSRYREAFGLLASGQA 334 + G G + G + + +Y G +DL ++ R+ L AF L G A Sbjct: 294 FLTGKKLQGSLLGSMRFPVDLPRLVQMYLDGLLDLDTMVAERIRLEDINHAFDNLRKGDA 353 Query: 335 VKVILD 340 V+ +++ Sbjct: 354 VRSVIE 359 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: 374 Number of extensions: 21 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: 343 Length of database: 361 Length adjustment: 29 Effective length of query: 314 Effective length of database: 332 Effective search space: 104248 Effective search space used: 104248 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