Align L-threonine 3-dehydrogenase; TDH; L-threonine dehydrogenase; EC 1.1.1.103 (characterized)
to candidate GFF1391 Psest_1428 Threonine dehydrogenase and related Zn-dependent dehydrogenases
Query= SwissProt::Q8U259 (348 letters) >FitnessBrowser__psRCH2:GFF1391 Length = 362 Score = 172 bits (435), Expect = 2e-47 Identities = 108/322 (33%), Positives = 167/322 (51%), Gaps = 15/322 (4%) Query: 24 VPKPG---PGEVLIKILATSICGTDLHIYEWNE--------WAQTRIRPPQIMGHEVAGE 72 VP PG PG V I++ ICG+DLH Y T I+ I+GHE GE Sbjct: 23 VPLPGAPQPGWVQIRVHWCGICGSDLHEYLAGPVFIPVDAPHPLTGIKGQCILGHEFCGE 82 Query: 73 VVEVGPGVEGIEVGDYVSVETHIVCGKCYACKRGQYHVCQNTKIFGVDTDGVFAEYAVVP 132 +V +G GVEG GD V+ + CG+C CK GQY++C+ G+ +G FAE+ VP Sbjct: 83 IVAIGEGVEGYAPGDKVAADACQHCGQCRFCKTGQYNLCEQLAFTGLMNNGAFAEFVNVP 142 Query: 133 AQNVWKNPKNIPPEYATLQEPLGNAVDTV-LAGPIAGKSVLITGAGPLGLLGIAVAKASG 191 A+ +++ P+ P E L EPL + V AG + G++V++ GAG +GL I AKA+G Sbjct: 143 AELLYRLPEGFPLEAGALIEPLAVGMHAVKKAGSLLGETVVVVGAGTIGLCTIMCAKAAG 202 Query: 192 AYPVIVSEPSEFRRNLAKKVGADYVINPFEEDVVKEVMDITDGNGVDVFLEFSGAPKALE 251 A VI E S R+ A +VGA++VI+P E D + E+ +T G G V E G + Sbjct: 203 AGQVIALEMSAARKAKALEVGANWVIDPSECDAIAEIKALTGGYGAGVSFECIGHKATAK 262 Query: 252 QGLQAVTPAGRVSLLGLFPGKVSIDFNNLIIFKALTVYGITGRHLWETWYTVSRLLQSGK 311 + + AGR ++G+F +F ++ + + + + V L+ G+ Sbjct: 263 LAIDVIRKAGRCVMVGIFEEPSEFNFFEIVATEKQVIGSLA---YAGEFADVIALIDDGR 319 Query: 312 LNIDPIITHKYKGFDKYEEAFE 333 +++ P+IT + + E+ FE Sbjct: 320 IDVTPLITGRIGLDNILEQGFE 341 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: 332 Number of extensions: 19 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: 362 Length adjustment: 29 Effective length of query: 319 Effective length of database: 333 Effective search space: 106227 Effective search space used: 106227 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