Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate N515DRAFT_0565 N515DRAFT_0565 threonine dehydratase
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__Dyella79:N515DRAFT_0565 Length = 523 Score = 400 bits (1029), Expect = e-116 Identities = 223/499 (44%), Positives = 305/499 (61%), Gaps = 6/499 (1%) Query: 102 LASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSREELDK 161 LA+ VY+VA E+ LE A LS RLG +KRED+Q VFSFKLRGAYN M L + + Sbjct: 23 LAARVYEVARETALESAPLLSARLGQRVLLKREDQQPVFSFKLRGAYNKMVGLDAAQRAR 82 Query: 162 GVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGG---DVVLYGKTFDE 218 GVI ASAGNHAQGVALA +L A IVMP T PQ+KIDAVR LGG +VVL G ++ + Sbjct: 83 GVIAASAGNHAQGVALAAAKLGLRAVIVMPVTAPQVKIDAVRRLGGAWVEVVLAGDSYSD 142 Query: 219 AQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKD-IHAVFIPVGGGGLIAGV 277 AQ A L ++ G ++ PFDDP VI GQ T+G EI RQ +HAVF+PVGGGGL+AGV Sbjct: 143 AQAEAARLEQQHGYTFVHPFDDPAVIAGQATVGMEILRQHPGPLHAVFVPVGGGGLLAGV 202 Query: 278 ATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAKCQ 337 A + K + P K+IGV+ + +M SL +G RV L V FADG AV VG TFA CQ Sbjct: 203 AAYIKALRPEVKVIGVQTVDSDAMAQSLEQGERVTLDEVGLFADGTAVKRVGAETFALCQ 262 Query: 338 ELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIVAIASG 397 +D M+ V D I AAI+DV+ E R++ E SGA+A+AG Y +++ + +VAI SG Sbjct: 263 RHVDAMLRVDTDAICAAIRDVFQETRSVPEPSGALALAGLKQYAATHQLDDATLVAIVSG 322 Query: 398 ANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRFTSERK 457 AN++F +L V E A +G +EA+ A + E++GSF+ F +G + TE YR + Sbjct: 323 ANLNFDRLRFVAERAEVGEQREAVFAVTIPEERGSFRRFCATLGQRSITEFNYRI-GDAA 381 Query: 458 NALILYRVNVDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGGSANIS-DEIFG 516 +A I + + + + E + + L+L+ +EL HL+H++GG + ++ DE+ Sbjct: 382 SAHIFVGIQIRQRDEREALTAAFAAEGFGVLDLTDDELAKLHLRHMIGGRSPLAHDELLY 441 Query: 517 EFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFKNQADKL 576 F PE+ L FL P WNI+L YRN G +L+G QVP E F+ +L Sbjct: 442 RFEFPERPGALTRFLGHMHPDWNISLFHYRNHGADYGRILVGIQVPAGERAMFEQFLAQL 501 Query: 577 GYPYELDNYNEAFNLVVSE 595 GYP ++ N A+ L++ E Sbjct: 502 GYPCRDESGNPAYRLLLRE 520 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: 655 Number of extensions: 32 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: 523 Length adjustment: 36 Effective length of query: 559 Effective length of database: 487 Effective search space: 272233 Effective search space used: 272233 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