Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate WP_009563248.1 RSPH17029_RS14480 threonine ammonia-lyase IlvA
Query= SwissProt::P25306 (595 letters) >NCBI__GCF_000015985.1:WP_009563248.1 Length = 415 Score = 193 bits (491), Expect = 1e-53 Identities = 127/400 (31%), Positives = 204/400 (51%), Gaps = 9/400 (2%) Query: 108 DVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSREELD-KGVITA 166 D+ E+PL+ + LS R G + ++KRED V S+KLRGA+ M + D + + A Sbjct: 17 DLFPETPLQRNDHLSARYGADIWLKREDLTPVRSYKLRGAFTAMRKVRDARPDQRSFVCA 76 Query: 167 SAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGD---VVLYGKTFDEAQTHA 223 SAGNHAQGVA A + I MP TTPQ KI R GG+ +VL G FD+ A Sbjct: 77 SAGNHAQGVAYACRHFGVKGTIFMPVTTPQQKIAKTRTFGGEAVEIVLTGDYFDQTLAAA 136 Query: 224 LELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQL-KDIHAVFIPVGGGGLIAGVATFFK 282 + ++ PFDDP VI+GQ ++G E+ QL + V +PVGGGGL +GV F + Sbjct: 137 QAWCAEQKAHFLAPFDDPDVIEGQASVGVELLEQLGRAPDLVVLPVGGGGLASGVTAFLR 196 Query: 283 QIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAKCQEL-ID 341 AP T VEP G AS+ +L G L V++F DG AVA +G+ F+ + D Sbjct: 197 SEAPETDFRFVEPAGGASLLAALEAGGPTALPRVNSFVDGAAVARLGQLPFSMLDWVRPD 256 Query: 342 GMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIVAIASGANMD 401 + L D I + ++ + +LE +GA+++ + +I+ +V + SG N D Sbjct: 257 QVHLAPEDRICITMLEMLNVEGIVLEPAGALSVDVLPELAD--RIRGRTVVCVTSGGNFD 314 Query: 402 FSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVG-SLNFTELTYRFTSERKNAL 460 F +L +V E A SG + M ++ G+ + F+ ++G + Y S R Sbjct: 315 FERLPEVKERAQRYSGLKKYFILRMPQRPGALREFLMMLGPDDDIARFEYLKKSARNFGS 374 Query: 461 ILYRVNVDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHL 500 +L + + + ++ M+ + + +++ ++ + + L Sbjct: 375 VLIGIETREAGNFARLTAVMEEAGLNYRDITGDDALAEFL 414 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: 502 Number of extensions: 29 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: 415 Length adjustment: 34 Effective length of query: 561 Effective length of database: 381 Effective search space: 213741 Effective search space used: 213741 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 Apr 10 2024. 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