Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_012407541.1 NPUN_RS03905 threonine synthase
Query= curated2:Q58860 (405 letters) >NCBI__GCF_000020025.1:WP_012407541.1 Length = 436 Score = 278 bits (710), Expect = 3e-79 Identities = 155/404 (38%), Positives = 240/404 (59%), Gaps = 8/404 (1%) Query: 4 RCIKCGKTYDVDEIIYTCE-CGGLLEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVK 62 +C +CG Y++ + CE C G LE+ YDY ++ V+ E ++ +WRY +LPV Sbjct: 22 KCKECGAEYEL-KASNVCELCFGPLEVKYDYSALRLTVTRETIQAGPNSIWRYRPFLPVA 80 Query: 63 DESKIVSLCEGGTPLYRCNNLEKELGIKELYVKNEGAN-PTGSFKDRGMTVGVTRANELG 121 ++ ++ + G TPL R + L + LG+ +LY+KN+ N PT SFKDR ++V ++RA ELG Sbjct: 81 TDN-VIDVGTGMTPLVRSHRLARRLGLNKLYIKNDAVNMPTLSFKDRVVSVALSRARELG 139 Query: 122 VEVVGCASTGNTSASLAAYSARSGKKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDD 181 V CASTGN + S AA +A +G C V +P A GK+ ++ Y ++ VKGN+D Sbjct: 140 FTTVSCASTGNLANSTAAIAAHAGLDCCVFIPADLEA-GKIIGSLIYSPTLMAVKGNYDQ 198 Query: 182 ALDMVKQLAKEKLIYLLN-SINPFRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISA 240 + ++A +N ++ P+ EG KT+ FE+ +QL W++PD V+ P+ + + Sbjct: 199 VNRLCSEVANTHGWGFVNINLRPYYSEGSKTLGFEVAEQLGWELPDHVVAPLASGSLFTK 258 Query: 241 IWKGFKEFEITGII-DELPKMTGIQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIGN 299 I+KGF+EF G++ D+ + +G QA+G PI +AF K +D I P TIA ++ IGN Sbjct: 259 IYKGFQEFIEVGLVEDKKVRFSGAQAEGCSPIAQAF-KEGRDFIKPVKPNTIAKSLAIGN 317 Query: 300 PVNAPKALDAIYSSGGYAEAVTDEEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEGI 359 P + A++ +GG E+V D EI++ KLLA EGIF E A +++A LKKL+E G Sbjct: 318 PADGIYAVELAQKTGGNIESVNDAEIIDGIKLLAETEGIFTETAGGTTVAVLKKLVEAGK 377 Query: 360 IDRDERIVCITTGHGLKDPDAAIRASEEPIKIECDMNVLKRILK 403 ID DE V TG+GLK +A EP+ I+ ++ +R L+ Sbjct: 378 IDPDETTVIYITGNGLKTQEAIQGYVGEPLTIDAKLDSFERALE 421 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: 468 Number of extensions: 28 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: 436 Length adjustment: 32 Effective length of query: 373 Effective length of database: 404 Effective search space: 150692 Effective search space used: 150692 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_012407541.1 NPUN_RS03905 (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.22843.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-105 337.2 0.0 6.6e-105 336.9 0.0 1.1 1 lcl|NCBI__GCF_000020025.1:WP_012407541.1 NPUN_RS03905 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020025.1:WP_012407541.1 NPUN_RS03905 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 336.9 0.0 6.6e-105 6.6e-105 1 340 [] 70 397 .. 70 397 .. 0.99 Alignments for each domain: == domain 1 score: 336.9 bits; conditional E-value: 6.6e-105 TIGR00260 1 vvryreilevtekdlvdlaegstelfrspklaeevgaenlyvkelfhg.PtlaFKDrglqfvavlltka 68 ++ryr +l+v +++d+ +g+t+l+rs++la+++g+++ly+k+++++ Ptl+FKDr+ v+v+l++a lcl|NCBI__GCF_000020025.1:WP_012407541.1 70 IWRYRPFLPVATDNVIDVGTGMTPLVRSHRLARRLGLNKLYIKNDAVNmPTLSFKDRV---VSVALSRA 135 8*********************************************************...******** PP TIGR00260 69 lelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaq 137 +elg +tv cA++G++++++a a+a++a+++++v++P++ ++ ++k++ l++ +++a+kG++D+++ lcl|NCBI__GCF_000020025.1:WP_012407541.1 136 RELGFTTVSCASTGNLANSTA-AIAAHAGLDCCVFIPAD-LE--AGKIIGSLIYSPTLMAVKGNYDQVN 200 *********************.*****************.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_000020025.1:WP_012407541.1 201 RLCSEVA-NTHGWGFVNINLR-PYYSEGSKTLGFEVAEQLGWELPDHVVAPLAsGSLFTKIYKGFQEFI 267 *******.889********88.*******************************8889************ PP TIGR00260 206 elg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnle 270 e+g + +++++++aeg+++i+++f++++d+ + +++T++++++ignp++ +a+ela++++gn+e lcl|NCBI__GCF_000020025.1:WP_012407541.1 268 EVGlvedKKVRFSGAQAEGCSPIAQAFKEGRDFIKPVKPNTIAKSLAIGNPADGIYAVELAQKTGGNIE 336 *****9999************************************************************ PP TIGR00260 271 dlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdp 339 ++ +d+ei++ ik+lae+eg+++e++++++va+lkklve+g ++dp+ e++v ++tgn+lk++ lcl|NCBI__GCF_000020025.1:WP_012407541.1 337 SV----NDAEIIDGIKLLAETEGIFTETAGGTTVAVLKKLVEAG---KIDPD--ETTVIYITGNGLKTQ 396 **....**************************************...*****..*************98 PP TIGR00260 340 e 340 e lcl|NCBI__GCF_000020025.1:WP_012407541.1 397 E 397 7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (436 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: 00:00:00.01 # Mc/sec: 10.59 // [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