Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_101443628.1 BD749_RS05135 threonine synthase
Query= curated2:Q58860 (405 letters) >NCBI__GCF_002846395.1:WP_101443628.1 Length = 400 Score = 234 bits (596), Expect = 4e-66 Identities = 136/378 (35%), Positives = 209/378 (55%), Gaps = 11/378 (2%) Query: 5 CIKCGKTYDVDE--IIYTCECGGLLEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVK 62 C CG Y E + C C L Y + + +K E L RE +WRYLE LPV Sbjct: 17 CSNCGALYSPFEKQTVSAC-CQMPLLAGYAPDVLPEK---EALLTREGTMWRYLEMLPVL 72 Query: 63 DESKIVSLCEGGTPLYRCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRANELGV 122 + IVSL EG TP+ + NL ++ ++ L +K+EG NPTGSFK RG+++ +++A E GV Sbjct: 73 HKENIVSLGEGYTPILQLANLARKYELRSLLLKDEGQNPTGSFKARGLSMAISKAKEHGV 132 Query: 123 EVVGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDA 182 E + GN ++AAY A++G + V++P + + +YGA+V+QV G +D Sbjct: 133 EGCIIPTAGNAGVAMAAYCAKAGMRATVVMPRHTPKAFR-DECYWYGAEVVQVDGLINDC 191 Query: 183 LDMVKQL-AKEKLIYLLNSINPFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISAI 241 VK+L +L+ + P+RLEG+KT+ +EI +Q NWQ+PD ++ P G + I Sbjct: 192 AAKVKELNTAGELLDVSTLKEPYRLEGKKTMGYEIAEQGNWQLPDVILYPAGGGTGLIGI 251 Query: 242 WKGFKEFEITGIIDE---LPKMTGIQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIG 298 WK F+E + G + E LP+M +QA+ +P+VE F R + Y TIA + + Sbjct: 252 WKAFREMKKIGWLPEDAKLPRMVAVQAENCRPLVETFYGRQANAQNYMGKPTIANGLAVP 311 Query: 299 NPVNAPKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEG 358 P+ L + SGG A +++++E++ K L EG+FV P A+ +KLL+ G Sbjct: 312 RPLGEQLMLQTLQESGGTAISISEQEMITGLKELGSSEGLFVAPEGAAVWMAARKLLDTG 371 Query: 359 IIDRDERIVCITTGHGLK 376 I DE I+ + TG G K Sbjct: 372 FIQYDEEILLLNTGSGQK 389 Lambda K H 0.317 0.137 0.395 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: 442 Number of extensions: 19 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: 405 Length of database: 400 Length adjustment: 31 Effective length of query: 374 Effective length of database: 369 Effective search space: 138006 Effective search space used: 138006 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 WP_101443628.1 BD749_RS05135 (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.1142866.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-54 171.8 0.0 1.3e-54 171.6 0.0 1.0 1 NCBI__GCF_002846395.1:WP_101443628.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002846395.1:WP_101443628.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 171.6 0.0 1.3e-54 1.3e-54 1 337 [. 62 389 .. 62 392 .. 0.95 Alignments for each domain: == domain 1 score: 171.6 bits; conditional E-value: 1.3e-54 TIGR00260 1 vvryreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelg 72 ++ry e+l+v ++++v+l eg t+ ++ +la++ +++ l +k+++ +Pt++FK rg ++++++ka+e+g NCBI__GCF_002846395.1:WP_101443628.1 62 MWRYLEMLPVLhKENIVSLGEGYTPILQLANLARKYELRSLLLKDEGQNPTGSFKARG---LSMAISKAKEHG 131 69*********9**********************************************...************ PP TIGR00260 73 netvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeife 145 +e + t G+ g a+a a+ +ka++++ v++P+ + k ++a+v++++G d+ + vke+ NCBI__GCF_002846395.1:WP_101443628.1 132 VEGCIIPTAGNAGVAMA-AYCAKAGMRATVVMPRH-TP--KAFRDECYWYGAEVVQVDGLINDCAAKVKELNT 200 *****************.****************9.44..3333456789*********************** PP TIGR00260 146 dkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekkelg.......lp 210 e l ++ p+r+e++kt+ +ei+eq +++ pd + p + + + i+k+f e+k+ g lp NCBI__GCF_002846395.1:WP_101443628.1 201 AGELLDVSTLK--EPYRLEGKKTMGYEIAEQGNWQLPDVILYPAGgGTGLIGIWKAFREMKKIGwlpedakLP 271 ********999..9*******************************7667889********************* PP TIGR00260 211 ieklaiaaegaadivrrflksg.dlepkedkeTlstAmdignpsnveralelarrslgnledlkesvsdeeil 282 ++ a++ae++ + v+ f ++ + +++ k T+++ +++ +p + +l+ ++s+g + ++ s++e++ NCBI__GCF_002846395.1:WP_101443628.1 272 -RMVAVQAENCRPLVETFYGRQaNAQNYMGKPTIANGLAVPRPLGEQLMLQTLQESGGTAISI----SEQEMI 339 .*****************9998899999999****************************9999....****** PP TIGR00260 283 eaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklk 337 k+l +eg+++ p +a+ a +kl++ g ++++ ee+ + tg ++k NCBI__GCF_002846395.1:WP_101443628.1 340 TGLKELGSSEGLFVAPEGAAVWMAARKLLDTG---FIQYD--EEILLLNTGSGQK 389 ******************************99...99999..9988888887776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (400 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 17.70 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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