Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate PP_5149 PP_5149 threonine deaminase
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__Putida:PP_5149 Length = 504 Score = 419 bits (1078), Expect = e-121 Identities = 230/502 (45%), Positives = 316/502 (62%), Gaps = 6/502 (1%) Query: 94 LFQYLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSN 153 L QY+ IL S VYDVA+E+PL+ A +LS RLG +KRED Q VFSFK+RGAYN ++ Sbjct: 2 LEQYVKKILTSRVYDVAVETPLQSAGQLSKRLGNQILLKREDLQPVFSFKIRGAYNKLAQ 61 Query: 154 LSREELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVVLYG 213 LS EEL +GV+TASAGNHAQG+ALA + + A IVMP TTP+IK++ VR+ GG VVL+G Sbjct: 62 LSPEELARGVVTASAGNHAQGLALAAREMGIKATIVMPKTTPEIKVEGVRSRGGKVVLHG 121 Query: 214 KTFDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKD-IHAVFIPVGGGG 272 +F EA ++L+L ++ G Y+ P+DDP I GQGT+ EI RQ + A+F+PVGGGG Sbjct: 122 DSFPEALAYSLKLVDEKGFVYVHPYDDPHTIAGQGTVAMEILRQHPGRLDAIFVPVGGGG 181 Query: 273 LIAGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYT 332 LIAG+A + K + P KIIGVEP + + ++ G RV L V FADGVAVA +G++T Sbjct: 182 LIAGIAAYVKYLRPEIKIIGVEPDDSNCLQAAMAAGERVVLPQVGLFADGVAVAQIGQHT 241 Query: 333 FAKCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIV 392 F C+ +D +V V+ D I AAIKD+YD+ R+I E +GA+ +AG Y E Y + + +V Sbjct: 242 FDICRHHVDEVVTVSTDEICAAIKDIYDDTRSITEPAGALGVAGIKKYVELYGVSGQTLV 301 Query: 393 AIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYR- 451 AI SGAN++F +L V E A LG +EA++A + E+ GSFK F +G TE YR Sbjct: 302 AIDSGANVNFDRLRHVAERAELGEKREAIIAVTIPERPGSFKAFCEAIGKRQITEFNYRK 361 Query: 452 FTSERKNALILYRVNVDKESD-LEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGG-SAN 509 TS+ A I V E+D +++ + +L+ NEL H++H+VGG SA Sbjct: 362 HTSD--EAHIFVGVQTHPENDPRAALVQQLTEQGFPVTDLTDNELAKLHIRHMVGGHSAG 419 Query: 510 ISDEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEF 569 SDE+ F PE+ L FL+ RWNI++ YRN G + ++ G QVP+ E Sbjct: 420 ASDEMVLRFEFPERPGALFNFLNKLGGRWNISMFHYRNHGAADGRVVAGLQVPEDERHLV 479 Query: 570 KNQADKLGYPYELDNYNEAFNL 591 K+GYPY + N A+ L Sbjct: 480 PAALAKIGYPYWDETENPAYKL 501 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: 708 Number of extensions: 30 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: 504 Length adjustment: 36 Effective length of query: 559 Effective length of database: 468 Effective search space: 261612 Effective search space used: 261612 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