Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate RR42_RS02315 RR42_RS02315 threonine dehydratase
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__Cup4G11:RR42_RS02315 Length = 508 Score = 425 bits (1093), Expect = e-123 Identities = 233/503 (46%), Positives = 323/503 (64%), Gaps = 6/503 (1%) Query: 97 YLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSR 156 YL IL + VYDVA E+ L A LS R G + KRED Q VFSFKLRGAYN M++LS Sbjct: 7 YLRKILTAKVYDVAQETDLTYANLLSARTGNKVWFKREDTQPVFSFKLRGAYNKMASLSP 66 Query: 157 EELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGD---VVLYG 213 EEL +GVI ASAGNHAQGVAL+ RL C A I MP TTPQ+KIDAVR GG+ +VL+G Sbjct: 67 EELKRGVIAASAGNHAQGVALSAARLKCKALIAMPVTTPQVKIDAVRERGGEWVEIVLHG 126 Query: 214 KTFDEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKD-IHAVFIPVGGGG 272 ++ +A HA L +K L +I PFDDP VI GQGTI EI RQ +HAVF+ +GGGG Sbjct: 127 DSYSDAYNHAAVLEKKHKLTFIHPFDDPEVIAGQGTIAMEILRQHPGPLHAVFVAIGGGG 186 Query: 273 LIAGVATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYT 332 LI+G+A++ K + P K+IGV+ + +M S+ G RV+L V F+DG AV LVG+ T Sbjct: 187 LISGIASYIKAVRPEIKVIGVQTVDSDAMKRSVDAGKRVELKEVGLFSDGTAVKLVGKET 246 Query: 333 FAKCQELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIV 392 F +EL+D ++LV D I A +KDV+ + R+ILE +GA+A+AG Y E K+K +++V Sbjct: 247 FRITRELVDEIILVDTDAICAGLKDVFQDTRSILEPAGAMAVAGLKLYAEREKLKGQHLV 306 Query: 393 AIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTELTYRF 452 AIA GANM+F +L V E A +G +EA+ A + E++GSFK F +G+ N TE YR Sbjct: 307 AIACGANMNFDRLRFVAERAEVGEAREAVFAVSIPEERGSFKRFCEQLGTRNVTEFNYRI 366 Query: 453 TSERKNALILYRVNVDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGGSANIS- 511 +++ A I V + ++ EK+ + TL+LS++EL H++++VGG + ++ Sbjct: 367 -ADKSMAHIFVGVQIASRAENEKIAAGFRRHGFDTLDLSNDELAKQHIRYMVGGHSPLAH 425 Query: 512 DEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAEMDEFKN 571 DE+ F PE+ L FL + SP WNI+L YRNQG +++L+G QVP+ E F++ Sbjct: 426 DELLYRFEFPERPGALMRFLSSMSPNWNISLFHYRNQGGDTSNILVGIQVPKNEKRAFRD 485 Query: 572 QADKLGYPYELDNYNEAFNLVVS 594 LGY + + N + L +S Sbjct: 486 FLATLGYVHWEETENPVYKLFLS 508 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: 696 Number of extensions: 37 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: 508 Length adjustment: 36 Effective length of query: 559 Effective length of database: 472 Effective search space: 263848 Effective search space used: 263848 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