Align threonine synthase; EC 4.2.3.1 (characterized)
to candidate Synpcc7942_1782 Synpcc7942_1782 threonine synthase
Query= CharProtDB::CH_107419 (405 letters) >FitnessBrowser__SynE:Synpcc7942_1782 Length = 430 Score = 277 bits (708), Expect = 5e-79 Identities = 161/403 (39%), Positives = 235/403 (58%), Gaps = 8/403 (1%) Query: 4 LKCIECGAEYSRDEVIYTCSKCDGLLDVIYDYSSIKIDMEKLKTECP--SVWKYAKLLPV 61 LKC ECG EY C G L+V+YDY +I+ + + E S+W+Y LPV Sbjct: 14 LKCKECGHEYDLGAKHVCEDVCFGPLEVVYDYDAIRQRVSRATIEAGPNSIWRYRHFLPV 73 Query: 62 EREPVT-IQEGGTPLYKCDRLAEKIGIKKLYVKHEGMN-PTGSFKDRGMTVGVTKALELG 119 E V + G TPL + RLA ++G+KKL++K++ +N PT SFKDR ++V +T+A ELG Sbjct: 74 TGEDVIDVGTGMTPLVEAKRLARRLGLKKLFIKNDAVNMPTLSFKDRVVSVALTRARELG 133 Query: 120 MNTVACASTGNTSAALAIYGAKAGIPVVVLLPAGKVALGKVAQALMHGAKVLSIRGNFDD 179 +TV+CASTGN + + A A AG+ V +PA A GKV L++ +++++GN+D Sbjct: 134 FSTVSCASTGNLANSTAAIAAHAGLDCCVFIPADLEA-GKVLGTLIYNPTLMAVKGNYDQ 192 Query: 180 ALALVRTLCSQEKIYLLN-SINPYRLEGQKTIGFEIADQLDFKVPDRIVLPVGNAGNITA 238 L + + +N ++ PY EG KT+G+E+A+QL +++PD IV P+ + T Sbjct: 193 VNRLCSEVANTHGWGFVNINLRPYYSEGSKTLGYEVAEQLGWQLPDHIVAPLASGSLFTK 252 Query: 239 IYKGFREFKILGITDSLP-KMTGIQAEGSCPIVKAIKSGAPAITPEENPETVATAIRIGN 297 IYKGFREF +G+ D + +G QAEG PI KA G I PE+ P T+A +I IGN Sbjct: 253 IYKGFREFVDVGLVDDKAVRFSGAQAEGCSPIAKAFHEGRDFIAPEK-PNTIAKSIAIGN 311 Query: 298 PVNATKALSAIRESGGTAESVTDEEILAAQKDLARLEGIGVEPASAASVAGLRKLVDMGV 357 P + A+ R++GG E+V D EI+ K LA EGI E A +VA L+KLV+ G Sbjct: 312 PADGIYAVEIARKTGGNIEAVNDTEIIEGIKLLAETEGIFTETAGGTTVAVLKKLVEAGK 371 Query: 358 IGRDETVVCITTGHLLKDPQTVIDVCEEPTVVDANIDAIREAI 400 I DET V TG+ LK + V EP ++ +++ A+ Sbjct: 372 INPDETTVVYITGNGLKTQEAVQGYIAEPFTIEPKLESFEHAL 414 Lambda K H 0.317 0.135 0.389 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: 468 Number of extensions: 33 Number of successful extensions: 9 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: 405 Length of database: 430 Length adjustment: 32 Effective length of query: 373 Effective length of database: 398 Effective search space: 148454 Effective search space used: 148454 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate Synpcc7942_1782 Synpcc7942_1782 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00260.hmm # target sequence database: /tmp/gapView.3122.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00260 [M=340] Accession: TIGR00260 Description: thrC: threonine synthase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-106 340.1 0.0 8.4e-106 339.9 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1782 Synpcc7942_1782 threonine syntha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1782 Synpcc7942_1782 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 339.9 0.0 8.4e-106 8.4e-106 1 340 [] 64 391 .. 64 391 .. 0.99 Alignments for each domain: == domain 1 score: 339.9 bits; conditional E-value: 8.4e-106 TIGR00260 1 vvryreilevtekdlvdlaegstelfrspklaeevgaenlyvkelfhg.PtlaFKDrglqfvavlltka 68 ++ryr++l+vt +d++d+ +g+t+l+++++la+++g+++l++k+++++ Ptl+FKDr+ v+v+lt+a lcl|FitnessBrowser__SynE:Synpcc7942_1782 64 IWRYRHFLPVTGEDVIDVGTGMTPLVEAKRLARRLGLKKLFIKNDAVNmPTLSFKDRV---VSVALTRA 129 8*********************************************************...******** PP TIGR00260 69 lelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaq 137 +elg tv cA++G++++++a a+a++a+++++v++P++ ++ ++k++ +l++n +++a+kG++D+++ lcl|FitnessBrowser__SynE:Synpcc7942_1782 130 RELGFSTVSCASTGNLANSTA-AIAAHAGLDCCVFIPAD-LE--AGKVLGTLIYNPTLMAVKGNYDQVN 194 *********************.*****************.88..9************************ PP TIGR00260 138 dlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekk 205 +l+ e++ + ++++++N++ p++ e++kt+ +e++eqlg++ pd++v p++ +++f++i+kGf e+ lcl|FitnessBrowser__SynE:Synpcc7942_1782 195 RLCSEVA-NTHGWGFVNINLR-PYYSEGSKTLGYEVAEQLGWQLPDHIVAPLAsGSLFTKIYKGFREFV 261 *******.889********88.*******************************8889************ PP TIGR00260 206 elg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnle 270 +g + +++++++aeg+++i+++f +++d+ e+++T++++++ignp++ +a+e+ar+++gn+e lcl|FitnessBrowser__SynE:Synpcc7942_1782 262 DVGlvddKAVRFSGAQAEGCSPIAKAFHEGRDFIAPEKPNTIAKSIAIGNPADGIYAVEIARKTGGNIE 330 *****9999************************************************************ PP TIGR00260 271 dlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdp 339 ++ +d ei+e ik+lae+eg+++e++++++va+lkklve+g +++p+ e++v+++tgn+lk++ lcl|FitnessBrowser__SynE:Synpcc7942_1782 331 AV----NDTEIIEGIKLLAETEGIFTETAGGTTVAVLKKLVEAG---KINPD--ETTVVYITGNGLKTQ 390 **....**************************************...*****..*************98 PP TIGR00260 340 e 340 e lcl|FitnessBrowser__SynE:Synpcc7942_1782 391 E 391 7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (430 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 12.67 // [ok]
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