Align L-threonine 3-dehydrogenase (EC 1.1.1.103) (characterized)
to candidate Ga0059261_2605 Ga0059261_2605 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= reanno::Phaeo:GFF3379 (342 letters) >FitnessBrowser__Korea:Ga0059261_2605 Length = 341 Score = 454 bits (1169), Expect = e-132 Identities = 218/342 (63%), Positives = 268/342 (78%), Gaps = 2/342 (0%) Query: 1 MKALEKSHPREGLWMVQAPVPEIGPDEVLIKIRTTGICGTDIHIWNWDEWASHTVPVPMI 60 M+ L K H REG+W +APVP GPD++LI++R T ICGTD+HI+NWD+WA+ T+PVPMI Sbjct: 1 MRGLAKLHAREGIWETEAPVPTPGPDDILIRVRRTAICGTDLHIYNWDDWAARTIPVPMI 60 Query: 61 TGHEFAGEIVEIGRNVT-DLAVGQRCSGEGHLIQTDSRQSRAGKFHLDPGTRGIGVNEQG 119 GHEF+GEIVEIG VT L +GQR SGEGH+I DS +RAG+FHLDPGT G+GVN QG Sbjct: 61 VGHEFSGEIVEIGEAVTRPLCIGQRVSGEGHIIDFDSSAARAGRFHLDPGTVGVGVNRQG 120 Query: 120 AFAQYLKLPAFNVVPLPEDIPDEIGAILDPLGNAVHTALSFDLLGEDVLITGAGPIGVMA 179 AFA YL +PAFNVVPLP+D+ D++GA+LDP GNAVHTA FDL+GEDVL+TGAGPIG+MA Sbjct: 121 AFADYLCIPAFNVVPLPDDVSDDVGALLDPFGNAVHTAQQFDLMGEDVLVTGAGPIGIMA 180 Query: 180 AAVARHAGARHVVITDINPDRLALAEHVVPAVRAVNVAEEDLQDVVRELGLKQGFDVGLE 239 AAVAR AGAR VVITDINP RL LA + VR VN EEDL++V+ G+ GF V LE Sbjct: 181 AAVARRAGARSVVITDINPYRLDLAARLAD-VRPVNTLEEDLREVMAAEGIDDGFAVALE 239 Query: 240 MSGSQAALDQMVEALVMGGKIALLGIPPGKSPVDWSRIVFKAITIKGVYGREMFETWYKM 299 MSG+ A++Q + AL MGG +A+LGIP G V WS I+ KA+TI+GVYGREMF TW KM Sbjct: 240 MSGAPVAINQAIGALRMGGGLAMLGIPGGSMDVAWSDIILKALTIRGVYGREMFGTWQKM 299 Query: 300 IAMLQNGLDVSRVITHRFDVEDFAEGFAAMKSGRSGKVVLRW 341 +++ GLD+S +ITHR D DF +GF AM++GR+GKVVL W Sbjct: 300 FGLIRGGLDLSPLITHRLDARDFQQGFDAMRAGRAGKVVLSW 341 Lambda K H 0.320 0.139 0.421 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: 433 Number of extensions: 17 Number of successful extensions: 3 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: 342 Length of database: 341 Length adjustment: 29 Effective length of query: 313 Effective length of database: 312 Effective search space: 97656 Effective search space used: 97656 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