Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate PP_0662 PP_0662 putative Threonine synthase
Query= curated2:P29363 (469 letters) >FitnessBrowser__Putida:PP_0662 Length = 462 Score = 382 bits (982), Expect = e-110 Identities = 199/463 (42%), Positives = 290/463 (62%), Gaps = 8/463 (1%) Query: 1 MRYISTRGQAPALNFEDVLLAGLASDGGLYVPENLPRFTLEEIASWVGLPYHELAFRVMR 60 M+Y STRG ++F LL+GLA DGGLYVP ++P F+ +EIASW LP+ ELA+RVM Sbjct: 1 MQYTSTRGNETRVDFRTALLSGLADDGGLYVPTSVPVFSPQEIASWSWLPFDELAWRVMA 60 Query: 61 PFVAGSIADADFKKILEETYGVFAHDAVAPLRQLNGNEWVLELFHGPTLAFKDFALQLLG 120 PFV ++ + + ++ ++Y F H +APL+QL NEW+L+LFHGPT + KDFA QL Sbjct: 61 PFVGDTLDEPTLRSLVSDSYRGFRHRGIAPLQQLGHNEWILQLFHGPTRSSKDFAAQLQA 120 Query: 121 RLLDHVLAKRGERVVIMGATSGDTGSAAIEGCRRCDNVDIFIMHPHNRVSEVQRRQMTTI 180 R + H L ERV+++GA++GDT AAIE R C + ++P + M + Sbjct: 121 RFVRHFLGAECERVMLVGASNGDTAVAAIEALRHCPAAGLLALYPSAGTPADRAAVMRSA 180 Query: 181 LGDNIHNIAIEGNFDDCQEMVKASFADQGFLKGTRLVAVNSINWARIMAQIVYYFHAALQ 240 D++ +A++G+FDDCQ +V A D G V+ NS NW ++AQIV+YFHAALQ Sbjct: 181 ASDSVSCVAVDGSFDDCQSLVSALLRDWP-CPGLIPVSFNSTNWVGVLAQIVFYFHAALQ 239 Query: 241 LGAPHRSVAFSVPTGNFGDIFAGYLARNMGLPVSQLIVATNRNDILHRFMSGNRYDKDTL 300 LG R V FS+PT +F +I+AG++A+ MGLP++Q+IV+TNRND LHRF+ NRY + + Sbjct: 240 LGGGIRPVGFSIPTASFAEIYAGFIAQKMGLPINQIIVSTNRNDALHRFIHCNRYSRGST 299 Query: 301 HPSLSPSMDIMVSSNFERLLFDLHGRNGKAVAELLDAFKASGKLSVEDQRWTEARKLFDS 360 +LSP MD + SN ER +++L+ R+G A L++ F+A G+LS+ +++W AR LFDS Sbjct: 300 SQTLSPVMDFSLFSNLERFVWELYDRDGGATRALMEHFEACGELSIGNRQWLHARMLFDS 359 Query: 361 LAVSDEQTCETIAEVYRSSGELLDPHTAIGVRAARECRRSLSVPMVTLGTAHPVKFPEAV 420 AV D E I ++ +G +DPH A GV A R RR++ P+VTLG P K + Sbjct: 360 YAVDDALIREEIVTLFHETGSAVDPHAATGVFAGRLHRRNIGAPIVTLGQFAPEKSAGLL 419 Query: 421 EKAGI--GQAPALPAHLADLFEREERCTVLPNELAKVQAFVSQ 461 + G G+ PA A + + P++LA V A +++ Sbjct: 420 AELGAWHGEVPAGAVGTAG-----DGPLLAPDDLAGVHALLTR 457 Lambda K H 0.322 0.137 0.407 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: 559 Number of extensions: 20 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: 469 Length of database: 462 Length adjustment: 33 Effective length of query: 436 Effective length of database: 429 Effective search space: 187044 Effective search space used: 187044 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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