Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_015799239.1 AFER_RS09545 threonine synthase
Query= curated2:Q58860 (405 letters) >NCBI__GCF_000023265.1:WP_015799239.1 Length = 414 Score = 286 bits (731), Expect = 1e-81 Identities = 150/381 (39%), Positives = 235/381 (61%), Gaps = 8/381 (2%) Query: 5 CIKCGKTYDVDEIIYTCE-CGGLLEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVKD 63 C +CG+TY + + CE C G LE+ YDYE+I +V+ E+++ +WRY E LP++ Sbjct: 10 CRECGRTYPISPT-HVCEFCFGPLEVAYDYEQIAARVTRERIQSGPPTLWRYGELLPIER 68 Query: 64 ESKIVSLCEGGTPLYRCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRANELGVE 123 + + L G TPL L ELG+ ELY+KN+ NPTGSFKDR + V +++A E G+ Sbjct: 69 DEARIDLGAGFTPLVPAPRLAAELGLGELYLKNDTVNPTGSFKDRVVAVALSKAREFGMR 128 Query: 124 VVGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDAL 183 V CASTGN + S+AA++AR+G + V +P + LA A+ YGA ++ + G +DD Sbjct: 129 VASCASTGNLANSVAAHAARAGMEAYVFIPANLERVKVLATAV-YGANIVAIDGTYDDVN 187 Query: 184 DMVKQLAKEKLIYLLNSIN--PFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISAI 241 + ++ E+ + ++N PF EG KT+ FE+ +QL W+ PD V+VPV + ++ I Sbjct: 188 RLCAEIVSERGDWGFANVNLRPFYSEGSKTLGFEVVEQLGWRYPDHVVVPVASGSQLTRI 247 Query: 242 WKGFKEFEITGIIDELP--KMTGIQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIGN 299 +GF+E + G++ E P +++G QA G P+ +AF + + ++ P T+A ++ IGN Sbjct: 248 HRGFEELALAGLMPEPPSVRVSGAQAQGCSPVAQAF-EAGRSLVRPVRPSTVAKSLAIGN 306 Query: 300 PVNAPKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEGI 359 P + A+D ++GG AV+D+EI+EA L+AR EGIFVE A ++A L KL +GI Sbjct: 307 PADGSYAVDVARATGGAIGAVSDDEILEAIALVARTEGIFVETAGGVTVATLAKLASQGI 366 Query: 360 IDRDERIVCITTGHGLKDPDA 380 + DE +V +G+GLK +A Sbjct: 367 VRPDETVVAYLSGNGLKTVEA 387 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: 413 Number of extensions: 20 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: 414 Length adjustment: 31 Effective length of query: 374 Effective length of database: 383 Effective search space: 143242 Effective search space used: 143242 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_015799239.1 AFER_RS09545 (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.37861.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-93 298.3 0.0 4.4e-93 298.1 0.0 1.0 1 NCBI__GCF_000023265.1:WP_015799239.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000023265.1:WP_015799239.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 298.1 0.0 4.4e-93 4.4e-93 2 340 .] 58 386 .. 57 386 .. 0.98 Alignments for each domain: == domain 1 score: 298.1 bits; conditional E-value: 4.4e-93 TIGR00260 2 vryreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgn 73 +ry e+l++ ++ +dl +g+t+l+ +p+la+e+g+ +ly+k++ ++Pt++FKDr+ vav+l+ka+e g+ NCBI__GCF_000023265.1:WP_015799239.1 58 WRYGELLPIErDEARIDLGAGFTPLVPAPRLAAELGLGELYLKNDTVNPTGSFKDRV---VAVALSKAREFGM 127 9*********9999*******************************************...************* PP TIGR00260 74 etvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifed 146 + cA++G++++++a a+a++a+++++v++P+ ++ k++ + +++a+++ai+G++Dd+++l++ei+++ NCBI__GCF_000023265.1:WP_015799239.1 128 RVASCASTGNLANSVA-AHAARAGMEAYVFIPAN-LE--RVKVLATAVYGANIVAIDGTYDDVNRLCAEIVSE 196 ****************.****************9.89..99******************************** PP TIGR00260 147 keklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekkelg.....lpiek 213 + +++ +vN++ p++ e++kt+ fe+veqlg++ pd+vvvpv+ ++ ++ i++Gf e+ +g ++ NCBI__GCF_000023265.1:WP_015799239.1 197 RGDWGFANVNLR-PFYSEGSKTLGFEVVEQLGWRYPDHVVVPVAsGSQLTRIHRGFEELALAGlmpepPSVRV 268 **********88.*******************************7789***************98876669** PP TIGR00260 214 laiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnledlkesvsdeeileaik 286 ++++a+g+++++++f ++ l+ +++T++++++ignp++ +a+++ar ++g + ++ sd+eileai NCBI__GCF_000023265.1:WP_015799239.1 269 SGAQAQGCSPVAQAFEAGRSLVRPVRPSTVAKSLAIGNPADGSYAVDVARATGGAIGAV----SDDEILEAIA 337 ***************9999****************************************....********** PP TIGR00260 287 klaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdpe 340 ++a++eg+++e++++v+va l kl+ +g + p+ e+vv++l+gn+lk+ e NCBI__GCF_000023265.1:WP_015799239.1 338 LVARTEGIFVETAGGVTVATLAKLASQG---IVRPD--ETVVAYLSGNGLKTVE 386 ****************************...*****..************9865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (414 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 17.82 // [ok]
This GapMind analysis is from Jul 25 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