Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_041457108.1 AVA_RS25115 threonine synthase
Query= curated2:Q58860 (405 letters) >NCBI__GCF_000204075.1:WP_041457108.1 Length = 434 Score = 284 bits (727), Expect = 3e-81 Identities = 158/404 (39%), Positives = 242/404 (59%), Gaps = 8/404 (1%) Query: 4 RCIKCGKTYDVDEIIYTCE-CGGLLEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVK 62 +C +CG Y++ + + CE C G LE+ YDY ++ V+ EK++ +WRY +LPV Sbjct: 20 KCKECGAEYEL-KATHVCEYCFGPLEVKYDYNALRLSVTREKIQAGPNSIWRYRPFLPVT 78 Query: 63 DESKIVSLCEGGTPLYRCNNLEKELGIKELYVKNEGAN-PTGSFKDRGMTVGVTRANELG 121 ++ ++ + G TPL R + L + LG+ +LY+KN+ N PT SFKDR ++V ++RA ELG Sbjct: 79 TDN-VIDVGTGMTPLVRSHRLARRLGLNKLYIKNDAVNMPTLSFKDRVVSVALSRARELG 137 Query: 122 VEVVGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDD 181 V CASTGN + S AA +A +G C V +P A GK+ ++ Y ++ VKGN+D Sbjct: 138 FTTVSCASTGNLANSTAAIAAHAGLDCCVFIPADLEA-GKILGSLIYSPTLMAVKGNYDQ 196 Query: 182 ALDMVKQLAKEKLIYLLN-SINPFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISA 240 + ++A +N ++ P+ EG KT+ FE+ +QL W++PD V+ P+ + + Sbjct: 197 VNRLCSEVANTHGWGFVNINLRPYYSEGSKTLGFEVAEQLGWELPDHVVAPLASGSLFTK 256 Query: 241 IWKGFKEFEITGIID-ELPKMTGIQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIGN 299 I+KGF+EF G+++ + + +G QA+G PI +AF K +D I P TIA +I IGN Sbjct: 257 IYKGFQEFVEVGLVEGKKVRFSGAQAEGCSPIAQAF-KEDRDFIKPVKPNTIAKSIAIGN 315 Query: 300 PVNAPKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEGI 359 P + A+D +GG E+V D EI+E KLLA EGIF E A +++A LKKL+E G Sbjct: 316 PADGVYAVDIAKKTGGNIESVNDAEIIEGIKLLAETEGIFTETAGGTTVAVLKKLVEAGK 375 Query: 360 IDRDERIVCITTGHGLKDPDAAIRASEEPIKIECDMNVLKRILK 403 ID DE V TG+GLK +A EP+ I+ ++ +R L+ Sbjct: 376 IDPDETTVVYITGNGLKTQEAVQGYVGEPLTIDAKLDSFERALE 419 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: 471 Number of extensions: 33 Number of successful extensions: 7 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: 434 Length adjustment: 32 Effective length of query: 373 Effective length of database: 402 Effective search space: 149946 Effective search space used: 149946 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_041457108.1 AVA_RS25115 (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.25135.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-106 341.2 0.0 4.3e-106 340.9 0.0 1.1 1 lcl|NCBI__GCF_000204075.1:WP_041457108.1 AVA_RS25115 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204075.1:WP_041457108.1 AVA_RS25115 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 340.9 0.0 4.3e-106 4.3e-106 1 340 [] 68 395 .. 68 395 .. 0.99 Alignments for each domain: == domain 1 score: 340.9 bits; conditional E-value: 4.3e-106 TIGR00260 1 vvryreilevtekdlvdlaegstelfrspklaeevgaenlyvkelfhg.PtlaFKDrglqfvavlltka 68 ++ryr +l+vt +++d+ +g+t+l+rs++la+++g+++ly+k+++++ Ptl+FKDr+ v+v+l++a lcl|NCBI__GCF_000204075.1:WP_041457108.1 68 IWRYRPFLPVTTDNVIDVGTGMTPLVRSHRLARRLGLNKLYIKNDAVNmPTLSFKDRV---VSVALSRA 133 8*********************************************************...******** PP TIGR00260 69 lelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaq 137 +elg +tv cA++G++++++a a+a++a+++++v++P++ ++ ++k++ l++ +++a+kG++D+++ lcl|NCBI__GCF_000204075.1:WP_041457108.1 134 RELGFTTVSCASTGNLANSTA-AIAAHAGLDCCVFIPAD-LE--AGKILGSLIYSPTLMAVKGNYDQVN 198 *********************.*****************.88..9************************ PP TIGR00260 138 dlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekk 205 +l+ e++ + ++++++N++ p++ e++kt+ fe++eqlg+e pd+vv p++ +++f++i+kGf+e+ lcl|NCBI__GCF_000204075.1:WP_041457108.1 199 RLCSEVA-NTHGWGFVNINLR-PYYSEGSKTLGFEVAEQLGWELPDHVVAPLAsGSLFTKIYKGFQEFV 265 *******.889********88.*******************************8889************ PP TIGR00260 206 elg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnle 270 e+g + +++++++aeg+++i+++f++++d+ + +++T++++++ignp++ +a+++a++++gn+e lcl|NCBI__GCF_000204075.1:WP_041457108.1 266 EVGlvegKKVRFSGAQAEGCSPIAQAFKEDRDFIKPVKPNTIAKSIAIGNPADGVYAVDIAKKTGGNIE 334 ****99999************************************************************ PP TIGR00260 271 dlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdp 339 ++ +d+ei+e ik+lae+eg+++e++++++va+lkklve+g ++dp+ e++v+++tgn+lk++ lcl|NCBI__GCF_000204075.1:WP_041457108.1 335 SV----NDAEIIEGIKLLAETEGIFTETAGGTTVAVLKKLVEAG---KIDPD--ETTVVYITGNGLKTQ 394 **....**************************************...*****..*************98 PP TIGR00260 340 e 340 e lcl|NCBI__GCF_000204075.1:WP_041457108.1 395 E 395 7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (434 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 8.32 // [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