Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_017599310.1 D471_RS0114685 threonine synthase
Query= curated2:Q58860 (405 letters) >NCBI__GCF_000341125.1:WP_017599310.1 Length = 419 Score = 246 bits (627), Expect = 1e-69 Identities = 141/394 (35%), Positives = 223/394 (56%), Gaps = 17/394 (4%) Query: 5 CIKCGKTYDVDEIIYTCE-CGGLLEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVKD 63 C +CG+ YD+ + CE C G LE+ YD+ V+ + +WRY LPV Sbjct: 22 CRECGERYDLTPR-FACEFCFGPLEVAYDF----GAVTRADIESGPNNIWRYRSLLPVPT 76 Query: 64 E-SKIVSLCEGGTPLYRCNNLEKELGIKELYVKNEGANPTGSFKDRGMTVGVTRANELGV 122 +++ ++ G TPL R + L ELG+ L+VK++ NPT SFKDR + + V A G Sbjct: 77 NVAELPNMNPGLTPLVRADRLAAELGLDSLHVKDDSGNPTHSFKDRVVAIAVEAARTFGF 136 Query: 123 EVVGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDA 182 + C+STGN + ++ A +AR+G + V +P G + GK+ A YG KV+ + GN+DD Sbjct: 137 TTLSCSSTGNLAGAVGAAAARAGFESCVFIPAG-LEEGKVVMAAVYGGKVVAIDGNYDDV 195 Query: 183 LDMVKQL----AKEKLIYLLNSINPFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNI 238 +L A E ++ ++ P+ EG KT+A+EI +QL W++P+++++P+ + + Sbjct: 196 NRFCSELIGDPAGEGWGFVNVNLRPYYGEGSKTLAYEIAEQLGWRLPEQIVIPIASGSQL 255 Query: 239 SAIWKGFKEFEITGIIDELP-KMTGIQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRI 297 + I KGF+E G++ + P ++ G QA G P+ +A+ + D+I P+TIA ++ I Sbjct: 256 TKIDKGFQELIKLGLVQDRPYRIFGAQATGCSPVAKAW-EAGHDVIQPVKPDTIAKSLAI 314 Query: 298 GNPVNAPKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEE 357 GNP + P LD +GG E V+D E+V++ LLAR EGIF E A + L+KL+ E Sbjct: 315 GNPADGPYVLDIAQRTGGSVEHVSDAEVVDSINLLARTEGIFAETAGGVTTGVLRKLVRE 374 Query: 358 GIIDRDERIVCITTGHGLKD---PDAAIRASEEP 388 G +D V + TG GLK DA + A+ P Sbjct: 375 GRLDPKAETVVLNTGDGLKTLNAVDAGVTATIAP 408 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: 474 Number of extensions: 22 Number of successful extensions: 5 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: 419 Length adjustment: 31 Effective length of query: 374 Effective length of database: 388 Effective search space: 145112 Effective search space used: 145112 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_017599310.1 D471_RS0114685 (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.26852.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-85 272.2 0.0 3.8e-85 272.0 0.0 1.0 1 lcl|NCBI__GCF_000341125.1:WP_017599310.1 D471_RS0114685 threonine synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000341125.1:WP_017599310.1 D471_RS0114685 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 272.0 0.0 3.8e-85 3.8e-85 1 338 [. 65 394 .. 65 396 .. 0.96 Alignments for each domain: == domain 1 score: 272.0 bits; conditional E-value: 3.8e-85 TIGR00260 1 vvryreilevt..ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltk 67 ++ryr++l+v+ ++l +++ g t+l+r+++la+e+g+ l+vk+++ +Pt +FKDr+ va ++++ lcl|NCBI__GCF_000341125.1:WP_017599310.1 65 IWRYRSLLPVPtnVAELPNMNPGLTPLVRADRLAAELGLDSLHVKDDSGNPTHSFKDRV---VAIAVEA 130 8*********96556666778889***********************************...******* PP TIGR00260 68 alelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDda 136 a+ g +t+ c+++G+++ a+ a a++a+ + +v++P+g ++ ++k+v a +++ kv+ai+G++Dd+ lcl|NCBI__GCF_000341125.1:WP_017599310.1 131 ARTFGFTTLSCSSTGNLAGAVG-AAAARAGFESCVFIPAG-LE--EGKVVMAAVYGGKVVAIDGNYDDV 195 *********************9.*****************.88..************************ PP TIGR00260 137 qdlvkeife..dkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGfl 202 ++ + e+++ e +++++vN++ p++ e++kt+a+ei+eqlg++ p+++v+p++ ++ +++i kGf+ lcl|NCBI__GCF_000341125.1:WP_017599310.1 196 NRFCSELIGdpAGEGWGFVNVNLR-PYYGEGSKTLAYEIAEQLGWRLPEQIVIPIAsGSQLTKIDKGFQ 263 ********955566********88.*******************************7789********* PP TIGR00260 203 ekkelg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslg 267 e+ +lg +p + +++a+g+++++++ + d+ + +++T++++++ignp++ +++l++a+r++g lcl|NCBI__GCF_000341125.1:WP_017599310.1 264 ELIKLGlvqdRPYRIFGAQATGCSPVAKAWEAGHDVIQPVKPDTIAKSLAIGNPADGPYVLDIAQRTGG 332 **********9*******************7777*********************************** PP TIGR00260 268 nledlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnkl 336 +e++ sd+e+++ i++la++eg+++e++++v+ +l+klv +g ++dp+ +e+v+ tg +l lcl|NCBI__GCF_000341125.1:WP_017599310.1 333 SVEHV----SDAEVVDSINLLARTEGIFAETAGGVTTGVLRKLVREG---RLDPK--AETVVLNTGDGL 392 *****....**************************************...*****..999999999999 PP TIGR00260 337 kd 338 k+ lcl|NCBI__GCF_000341125.1:WP_017599310.1 393 KT 394 87 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (419 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: 00:00:00.01 # Mc/sec: 10.70 // [ok]
This GapMind analysis is from Apr 10 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