Align Threonine dehydratase 2 biosynthetic, chloroplastic; SlTD2; Threonine deaminase 2; EC 4.3.1.17; EC 4.3.1.19 (characterized)
to candidate CA265_RS15860 CA265_RS15860 threonine dehydratase
Query= SwissProt::P25306 (595 letters) >FitnessBrowser__Pedo557:CA265_RS15860 Length = 416 Score = 250 bits (639), Expect = 7e-71 Identities = 141/397 (35%), Positives = 216/397 (54%), Gaps = 7/397 (1%) Query: 109 VAIESPLELAEKLSDRLGVNFYIKREDKQRVFSFKLRGAYNMMSNLSREELDKGVITASA 168 V +PLE LS N Y+KRED Q V S+KLRGAYN +S+L ++ L GV+ ASA Sbjct: 21 VVKRTPLEFNAGLSAHYNANIYLKREDLQIVRSYKLRGAYNKISSLPQDALINGVVCASA 80 Query: 169 GNHAQGVALAGQRLNCVAKIVMPTTTPQIKIDAVRALGGD---VVLYGKTFDEAQTHALE 225 GNHAQGVA + ++L I MP TP+ K+ GGD VVL G TFD+ AL Sbjct: 81 GNHAQGVAYSCKKLGIKGVIFMPEITPKQKVKQTYMFGGDNVEVVLVGDTFDDCLKEALA 140 Query: 226 LSEKDGLKYIPPFDDPGVIKGQGTIGTEINRQLKDIHAVFIPVGGGGLIAGVATFFKQIA 285 S + +IPPFDD VI+GQ T+G EI L D+ + +PVGGGGL +GV+ + K + Sbjct: 141 YSAEKSATFIPPFDDEKVIEGQATVGVEIYEDLPDLDMIVMPVGGGGLASGVSAYMKTVK 200 Query: 286 PNTKIIGVEPYGAASMTLSLHEGHRVKLSNVDTFADGVAVALVGEYTFAKCQELIDGMVL 345 P K++GVEP GA SM ++ G L +D F DG AV +G T+ C+EL+D M L Sbjct: 201 PEVKLVGVEPLGAPSMVTAMEYGGPFTLEEIDRFVDGAAVKRIGHITYEYCKELLDQMHL 260 Query: 346 VANDGISAAIKDVYDEGRNILETSGAVAIAGAAAYCEFYKIKNENIVAIASGANMDFSKL 405 + I I +Y+E ++E +GA+++A + +I + +V I SG N D ++ Sbjct: 261 IPEGKICTTILKLYNEDAIVVEPAGALSVAALDQLKD--QITGKTVVCIVSGGNNDIERM 318 Query: 406 HKVTELAGLGSGKEALLATFMVEQQGSFKTFVG--LVGSLNFTELTYRFTSERKNALILY 463 ++ E + L G + ++ G+ K FV L + T + + ++N L Sbjct: 319 QEIKEKSLLFEGLKHYFIVRFPQRPGALKLFVNEVLGPQDDITRFEFIKKTNKENGPALV 378 Query: 464 RVNVDKESDLEKMIEDMKSSNMTTLNLSHNELVVDHL 500 + + ++D +++ MK + L+ ++ + ++L Sbjct: 379 GIELSNKNDYASLLQRMKDFKFEIIELNQDQTLFEYL 415 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: 574 Number of extensions: 30 Number of successful extensions: 2 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: 416 Length adjustment: 34 Effective length of query: 561 Effective length of database: 382 Effective search space: 214302 Effective search space used: 214302 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: 52 (24.6 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