Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate GFF3437 PGA1_c34900 threonine dehydratase biosynthetic
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__Phaeo:GFF3437 Length = 408 Score = 191 bits (486), Expect = 4e-53 Identities = 129/389 (33%), Positives = 200/389 (51%), Gaps = 16/389 (4%) Query: 113 SPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSREELDKGV-ITASAGNH 171 +PL+ + LS+R G Y+KRED V S+K+RGA+N M R++L++ + + ASAGNH Sbjct: 22 TPLQRSALLSERFGAEIYLKREDLSPVRSYKIRGAFNAM----RKQLEQSLFVCASAGNH 77 Query: 172 AQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVV---LYGKTFDEAQTHALELSE 228 AQGVA + L I MP TTPQ KI R GGD V L G FD+ A + Sbjct: 78 AQGVAYMCRELGKRGVIFMPVTTPQQKIQKTRMFGGDSVEIHLVGDYFDDTLAAAQKWCA 137 Query: 229 KDGLKYIPPFDDPGVIKGQGTIGTEINRQLKDI-HAVFIPVGGGGLIAGVATFFKQIAPN 287 +G ++ PFDD VI+GQ +I EI QL V +PVGGGG+ +GVA +F Sbjct: 138 DEGGHFLSPFDDDDVIEGQSSIAVEIEAQLGAAPDHVILPVGGGGMSSGVARWF---GDR 194 Query: 288 TKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAKCQEL-IDGMVLV 346 + EP G A + +L GH V L +VDTF DG AV VG F +++ + ++ + Sbjct: 195 VHCLFAEPSGGACLRAALAAGHPVALDHVDTFVDGAAVGRVGARPFEVLKQVPLPDVLSI 254 Query: 347 ANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIVAIASGANMDFSKLH 406 A D I I ++ + +LE +GA+AI + I+ + +V + SG N DF +L Sbjct: 255 AEDRICTTILEMLNVEGVVLEPAGALAIEALRDVRSW--IRGKTVVCLTSGGNFDFERLP 312 Query: 407 KVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVG-SLNFTELTYRFTSERKNALILYRV 465 +V E A G + + ++ G+ K F+G++G + Y S R +L + Sbjct: 313 EVKERAQRYMGLKKYFLLRLPQRPGALKEFLGILGPEDDIARFEYMKKSARNFGSVLIGI 372 Query: 466 NVDKESDLEKMIEDMKSSNMTTLNLSHNE 494 + + + + ++ +++ +E Sbjct: 373 ETKRPENFADLYARLDAAGFAYTDITSDE 401 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: 504 Number of extensions: 31 Number of successful extensions: 6 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: 408 Length adjustment: 34 Effective length of query: 561 Effective length of database: 374 Effective search space: 209814 Effective search space used: 209814 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