Align L-threonine 3-dehydrogenase; TDH; EC 1.1.1.103 (uncharacterized)
to candidate Ac3H11_3163 S-(hydroxymethyl)glutathione dehydrogenase (EC 1.1.1.284)
Query= curated2:Q65JE7 (346 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3163 Length = 371 Score = 124 bits (312), Expect = 3e-33 Identities = 109/370 (29%), Positives = 169/370 (45%), Gaps = 52/370 (14%) Query: 7 ALIKKPGEPGASFELVPIPKIDKHEVLIKVKAASICGTDVHIYNWDEWAKSRVKPPYVFG 66 A+ K GEP E+ P K EVLI++ +C TD + D+ P V G Sbjct: 6 AVAFKAGEPLKIVEIDVAPP-KKGEVLIRITDTGVCHTDAFTLSGDD---PEGLFPVVLG 61 Query: 67 HEFSGEVVQVGENVTTVKEGEYVSAETHIVCGKCLPCLTGKEHVC---KKTLILGVDTDG 123 HE +G VV+VGE VT+VK G++V CG+CL C +GK ++C + T GV DG Sbjct: 62 HEGAGIVVEVGEGVTSVKPGDHVIPLYTAECGECLFCKSGKTNLCVSVRATQGKGVMPDG 121 Query: 124 ------------------CFAEYVKMPAANIWK-NPAGMPEDL----ASIQEPLGNAVHT 160 F+EY + ++ K NP PE + + LG +T Sbjct: 122 TTRFSYNGQPIYHYMGCSTFSEYTVVAEVSLAKVNPQANPEQVCLLGCGVTTGLGAVKNT 181 Query: 161 VLTGMTAGVKVAVVGCGPIGLMAVAVAKASGAAQVIAIDKNEYRLDLALQMGATDIISVE 220 + G VAV G G IGL + AK + A ++IA+D N + DLA GATD I+ + Sbjct: 182 --AKVQEGDTVAVFGLGGIGLAVIQGAKLAKAGRIIAVDTNPSKFDLARTFGATDCINPK 239 Query: 221 KED-PLKNVSALTNGEGADLVCEMSGHPTAIRQSLKMAANGGRVHVL--------SLPEH 271 D P++ V G D E G+ +R +L+ A G V+ + Sbjct: 240 DFDKPIQQVIVEMTTWGVDHSFECIGNVNVMRAALECAHRGWGQSVIIGVAGAGQEISTR 299 Query: 272 PVCIDMTNDIVFKGLTVQGITGRKMFETWRQVSGLLQ---SGTIQIKPVITHRFPMEEFE 328 P + + G G+ GR ++ G+++ +G IQ++P +TH +++ Sbjct: 300 P--FQLVTGRKWLGTAFGGVKGRS------ELPGMVEDAMAGKIQLEPFVTHTMGLKDIN 351 Query: 329 KGFELMRKGQ 338 + F+LM +G+ Sbjct: 352 EAFDLMHEGK 361 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: 341 Number of extensions: 14 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: 371 Length adjustment: 29 Effective length of query: 317 Effective length of database: 342 Effective search space: 108414 Effective search space used: 108414 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