Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate 6939184 Sama_3278 threonine dehydratase (RefSeq)
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__SB2B:6939184 Length = 531 Score = 385 bits (990), Expect = e-111 Identities = 220/506 (43%), Positives = 310/506 (61%), Gaps = 14/506 (2%) Query: 97 YLVDILASPVYDVAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSR 156 YL IL S VYDVA +PL KLS RLG Y+KRED Q V SFKLRGAYN +S L++ Sbjct: 24 YLQKILLSSVYDVAKVTPLSHMGKLSARLGQEIYLKREDMQPVHSFKLRGAYNRISQLTQ 83 Query: 157 EELDKGVITASAGNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGDVVLYGKTF 216 E ++GV+ ASAGNHAQGVAL+ A IVMPTTTP IKIDAVR GG+V+L+G++F Sbjct: 84 PECERGVVCASAGNHAQGVALSASSRGIDAVIVMPTTTPDIKIDAVRRRGGNVLLHGESF 143 Query: 217 DEAQTHALELSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKDIHAVFIPVGGGGLIAG 276 D+A HA L++ +G YI PFDD VI GQGT+ E+ +Q +D+ VF+PVGGGGL+AG Sbjct: 144 DQANAHAQHLAQTEGRVYIAPFDDEAVIAGQGTVAQEMLQQQRDLELVFVPVGGGGLVAG 203 Query: 277 VATFFKQIAPNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAKC 336 +A ++K + P+ KIIGVEP AA + ++ G V LS V FADGVAV +G F Sbjct: 204 IAAYYKAVRPSVKIIGVEPEDAACLKAAMAAGEPVTLSQVGLFADGVAVKRIGAEPFRIA 263 Query: 337 QELIDGMVLVANDGISAAIKDVYDEGRNILETSGAVAIAGAAAY--------CEFYKIKN 388 + +D +V V++D I AA+KD++++ R I E +GA+++AG Y E K Sbjct: 264 KHYVDEVVTVSSDEICAAVKDIFEDTRAIAEPAGALSLAGLKKYLAQTTPALAEAGK-PA 322 Query: 389 ENIVAIASGANMDFSKLHKVTELAGLGSGKEALLATFMVEQQGSFKTFVGLVGSLNFTEL 448 + AI SGAN++F L V+E LG KEA+LA + E GSF F L+G TE Sbjct: 323 RKVAAILSGANVNFHSLRYVSERCELGEQKEAVLAVKVPEVPGSFLKFCELLGKRAMTEF 382 Query: 449 TYRFTSERKNALILYRVNVD-KESDLEKMIEDMKSSNMTTLNLSHNELVVDHLKHLVGG- 506 YRF S R +A++ + + +S+L+++I + S +LS +E H++++VGG Sbjct: 383 NYRF-SGRDSAVVFAGIRLSGGQSELKEIIASLTSGGFEVQDLSSDETAKLHVRYMVGGH 441 Query: 507 -SANISDEIFGEFIVPEKAETLKTFLDAFSPRWNITLCRYRNQGDINASLLMGFQVPQAE 565 + +S+ +F F PE L FL RWNI+L YRN G +L GF+VP+ + Sbjct: 442 PTEPLSERLF-SFEFPEYPGALLKFLTTLGSRWNISLFHYRNHGAAFGRVLAGFEVPEGD 500 Query: 566 MDEFKNQADKLGYPYELDNYNEAFNL 591 + F +LG+ ++ + ++ A+ L Sbjct: 501 NEAFGRFLTELGFVWQEETHSPAYRL 526 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: 688 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: 531 Length adjustment: 36 Effective length of query: 559 Effective length of database: 495 Effective search space: 276705 Effective search space used: 276705 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