Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate 3610092 Dshi_3473 threonine dehydratase (RefSeq)
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__Dino:3610092 Length = 413 Score = 181 bits (458), Expect = 7e-50 Identities = 125/394 (31%), Positives = 195/394 (49%), Gaps = 9/394 (2%) Query: 113 SPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSREELDKGVITASAGNHA 172 +PL++ LS+R G ++KRED V S+K+RGA+N +S E + ASAGNHA Sbjct: 22 TPLQMNIHLSERYGAEIWLKREDLSPVRSYKIRGAFNAISKRVAEGQTQ-FACASAGNHA 80 Query: 173 QGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGG---DVVLYGKTFDEAQTHALELSEK 229 QGVA A Q I MP TTP+ KID R GG D+ L G FD+ A + Sbjct: 81 QGVAYACQHFGVHGVIFMPVTTPRQKIDKTRIFGGTAIDIELVGDYFDDTLAAAQRYCTE 140 Query: 230 DGLKYIPPFDDPGVIKGQGTIGTEINRQLKDI-HAVFIPVGGGGLIAGVATFFKQIAPNT 288 ++ PFDD VI+GQ T+ E+ QL+ V +PVGGGGL +G+ +F+ Sbjct: 141 ASATFLSPFDDADVIEGQSTVAVELLEQLEGPPDMVILPVGGGGLSSGMKRYFEVCGVQV 200 Query: 289 KIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAKCQELIDGMVLVA- 347 + VEP GA S+ +L G LS VD F DG AVA +G F +++ VL A Sbjct: 201 DLRLVEPCGARSLAKALETGAPQTLSKVDNFVDGAAVARIGARPFEILRDVPPDHVLGAP 260 Query: 348 NDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIVAIASGANMDFSKLHK 407 D I + ++ + +LE +GA+A+ + I + +V + SG N DF +L + Sbjct: 261 EDRICHTMLEMLNVEGIVLEPAGALAVDVLDTLRD--SITGKRVVCVTSGGNFDFERLPE 318 Query: 408 VTELAGLGSGKEALLATFMVEQQGSFKTFVGLVG-SLNFTELTYRFTSERKNALILYRVN 466 V E + +G + + ++ G+ K F+G +G + Y S R +L + Sbjct: 319 VKERSLRYAGLKKYFILRLPQRPGALKEFLGFLGPDDDIARFEYLKKSARNFGSVLIGIE 378 Query: 467 VDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHL 500 E++ + ++ +++ + L+ + L Sbjct: 379 TKDAGAFEQLFARLDAAGFPFRDITEDALLAEFL 412 Lambda K H 0.317 0.135 0.382 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: 490 Number of extensions: 26 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: 595 Length of database: 413 Length adjustment: 34 Effective length of query: 561 Effective length of database: 379 Effective search space: 212619 Effective search space used: 212619 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: 52 (24.6 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