Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate Ac3H11_2042 Threonine dehydratase biosynthetic (EC 4.3.1.19)
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2042 Length = 519 Score = 417 bits (1072), Expect = e-121 Identities = 231/506 (45%), Positives = 315/506 (62%), Gaps = 12/506 (2%) Query: 97 YLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSR 156 YL IL + VYDVA+ES LE A+ LS RL +KRED+Q VFSFKLRGAYN M++L+ Sbjct: 10 YLKKILTARVYDVAVESALEPAKSLSRRLHNKVLLKREDQQPVFSFKLRGAYNKMAHLTP 69 Query: 157 EELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVVLYGKTF 216 E+L +GVI ASAGNHAQGVA++ +L A +VMPTTTPQ+K+DAV+ LGG+VVL+G+++ Sbjct: 70 EQLQRGVICASAGNHAQGVAMSAHKLGTRAVVVMPTTTPQLKVDAVKTLGGEVVLHGESY 129 Query: 217 DEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLK-----DIHAVFIPVGGG 271 +A HA L ++ GL ++ PFDDP VI GQGTI EI RQL+ + AVF+ +GGG Sbjct: 130 SDAYEHAARLQKEQGLTFVHPFDDPLVIAGQGTIAMEILRQLQSLGSNQLDAVFVAIGGG 189 Query: 272 GLIAGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEY 331 GL++GVA + K + P K+IGV+ + +M S++ RV L +V F+DG AV LVGE Sbjct: 190 GLVSGVANYIKAVRPEIKVIGVQMNDSDAMIQSVNAHQRVTLPDVGLFSDGTAVKLVGEE 249 Query: 332 TFAKCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENI 391 TF Q L+D V V D + AAIKD++ + R+I+E +GA+A+A Y +K K E Sbjct: 250 TFRVAQGLVDEFVTVDTDAVCAAIKDIFVDTRSIVEPAGALAVAAIKQYVATHKTKGETY 309 Query: 392 VAIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSL-----NFT 446 AI GANM+F +L V E A +G +EAL A + E++GSF+ F +VG L N T Sbjct: 310 AAILCGANMNFDRLRFVAERAEVGEEREALFAVTIPEERGSFRRFCEVVGGLPGGPRNVT 369 Query: 447 ELTYRFTSERKNALILYRVNVDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGG 506 E YR S+ A + + + + + EK+ ++ L+L+H+EL +HL+HLVGG Sbjct: 370 EFNYRI-SDAAQAHVFVGITTNGKGESEKIAKNFGRHGFEALDLTHDELAKEHLRHLVGG 428 Query: 507 -SANISDEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAE 565 SA DE F PE+ L FL P WNI+L YRNQG +L+G QVP + Sbjct: 429 HSALAQDERLMRFTFPERPGALLKFLSLMQPTWNISLFHYRNQGADYGRILVGIQVPPED 488 Query: 566 MDEFKNQADKLGYPYELDNYNEAFNL 591 F LGYPY + N A+ L Sbjct: 489 TATFDAFLATLGYPYVEETLNPAYRL 514 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: 678 Number of extensions: 32 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: 595 Length of database: 519 Length adjustment: 36 Effective length of query: 559 Effective length of database: 483 Effective search space: 269997 Effective search space used: 269997 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: 53 (25.0 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