Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_009544262.1 CCE_RS06870 threonine synthase
Query= BRENDA::O66740 (352 letters) >NCBI__GCF_000017845.1:WP_009544262.1 Length = 376 Score = 432 bits (1110), Expect = e-126 Identities = 212/351 (60%), Positives = 271/351 (77%), Gaps = 4/351 (1%) Query: 4 WQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFK 63 W G+I+ Y+ YLPV ENTP+VTL EGNTPLI +++ +G K+++KY+GLNPTGSFK Sbjct: 28 WLGLIETYRPYLPVTENTPVVTLLEGNTPLIPVPYISQQVGKGVKVFVKYDGLNPTGSFK 87 Query: 64 DRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQAM 123 DRGMT+AISKA E G +AVICASTGNTSA+AAAYA RAG+RA+V++P G VA+GKL+QA+ Sbjct: 88 DRGMTMAISKAKEDGAKAVICASTGNTSAAAAAYARRAGMRAFVIIPDGYVALGKLAQAL 147 Query: 124 IYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDY 183 +YGA+V+AI G FDDAL +V+++ EN+PV +VNSVNPYR+EGQKTAAFE+ D LG APD+ Sbjct: 148 LYGAEVIAIDGNFDDALTVVKQMAENYPVTLVNSVNPYRLEGQKTAAFEVVDVLGNAPDW 207 Query: 184 HFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATAI 243 IPVGNAGNI+AYW GF Y+ GK KLP+MMG+QA GAAP + G P+ P+T+ATAI Sbjct: 208 LCIPVGNAGNISAYWMGFCQYHSLGKTNKLPKMMGFQAAGAAPFIGGQPVAKPETLATAI 267 Query: 244 KIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKLV 303 +IGNP +W A A S G+ +AV+D EIL AY+L+A+ EGVFCEPASAASVAGL+K+ Sbjct: 268 RIGNPANWDKAWGAKDASQGEFNAVTDEEILDAYRLLAAHEGVFCEPASAASVAGLLKV- 326 Query: 304 REGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEPIT--VPPDFDEVVKVLGF 352 + V C LTGNGLKDPD AI+ + + P+ +V KV+GF Sbjct: 327 -KDRVPTEATVVCVLTGNGLKDPDCAIQHSNNQVKSGIKPELSQVAKVMGF 376 Lambda K H 0.317 0.136 0.400 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: 451 Number of extensions: 15 Number of successful extensions: 2 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: 352 Length of database: 376 Length adjustment: 29 Effective length of query: 323 Effective length of database: 347 Effective search space: 112081 Effective search space used: 112081 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: 49 (23.5 bits)
Align candidate WP_009544262.1 CCE_RS06870 (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.22364.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-108 349.4 0.0 1.3e-108 349.2 0.0 1.0 1 lcl|NCBI__GCF_000017845.1:WP_009544262.1 CCE_RS06870 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017845.1:WP_009544262.1 CCE_RS06870 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 349.2 0.0 1.3e-108 1.3e-108 1 340 [] 32 349 .. 32 349 .. 0.98 Alignments for each domain: == domain 1 score: 349.2 bits; conditional E-value: 1.3e-108 TIGR00260 1 vvryreilevt.ekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltk 67 +++yr +l+vt ++++v+l eg+t+l+ +p ++++vg+ +++vk ++++Pt++FKDrg ++++++k lcl|NCBI__GCF_000017845.1:WP_009544262.1 32 IETYRPYLPVTeNTPVVTLLEGNTPLIPVPYISQQVGKgVKVFVKYDGLNPTGSFKDRG---MTMAISK 97 689********9***********************************************...******* PP TIGR00260 68 alelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDda 136 a+e+g+++v+cA++G+t+aaaa a+a++a+++++v++P+g+++ +kl++al ++a+v+ai+G+FDda lcl|NCBI__GCF_000017845.1:WP_009544262.1 98 AKEDGAKAVICASTGNTSAAAA-AYARRAGMRAFVIIPDGYVA--LGKLAQALLYGAEVIAIDGNFDDA 163 **********************.********************..************************ PP TIGR00260 137 qdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflek 204 +++vk+++e+ + +++nsvN p+r+e+qkt+afe+v+ lg ++pd++++pv+ +gn++a+++Gf+++ lcl|NCBI__GCF_000017845.1:WP_009544262.1 164 LTVVKQMAENYPVTLVNSVN---PYRLEGQKTAAFEVVDVLG-NAPDWLCIPVGnAGNISAYWMGFCQY 228 ********988888888888...*******************.************************** PP TIGR00260 205 kelg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnl 269 ++lg lp ++++++a gaa+++ + p +++eTl+tA++ignp+n+++a+ + s+g++ lcl|NCBI__GCF_000017845.1:WP_009544262.1 229 HSLGktnkLP-KMMGFQAAGAAPFIGGQ-------PVAKPETLATAIRIGNPANWDKAWGAKDASQGEF 289 **********.**********9988777.......9********************************* PP TIGR00260 270 edlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkd 338 +++ +deeil+a+++la++eg+++ep++a++va+l+k + +++ + ++vv++ltgn+lkd lcl|NCBI__GCF_000017845.1:WP_009544262.1 290 NAV----TDEEILDAYRLLAAHEGVFCEPASAASVAGLLKVKD-----RVPTE--ATVVCVLTGNGLKD 347 ***....*********************************987.....78***..************** PP TIGR00260 339 pe 340 p+ lcl|NCBI__GCF_000017845.1:WP_009544262.1 348 PD 349 97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (376 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.45 // [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