Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_020562611.1 A3OW_RS0106470 threonine synthase
Query= BRENDA::O66740 (352 letters) >NCBI__GCF_000372865.1:WP_020562611.1 Length = 364 Score = 407 bits (1045), Expect = e-118 Identities = 195/354 (55%), Positives = 267/354 (75%), Gaps = 7/354 (1%) Query: 4 WQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFK 63 + G+I++Y+ LPV +T I++L EGNTPLI N+ R G + I++K+EGLNPTGSFK Sbjct: 7 YTGLIERYRDRLPVSASTRIISLNEGNTPLIRLQNIPRLTGKEVDIHVKFEGLNPTGSFK 66 Query: 64 DRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQAM 123 DRGMT+A++KAVE G RA+ICASTGNTSASAAAYAARAG++A+V++P+G +A+GKL+Q + Sbjct: 67 DRGMTMAVTKAVEEGSRAIICASTGNTSASAAAYAARAGIKAFVIIPEGKIALGKLAQTL 126 Query: 124 IYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDY 183 +Y A ++ I+G FD + +V++I ++ PV IVNS+NP+RI+GQKTA+FEI D LG+APDY Sbjct: 127 MYDATIIQIRGNFDQGMTLVKEIADHAPVTIVNSINPFRIDGQKTASFEIIDALGDAPDY 186 Query: 184 HFIPVGNAGNITAYWKGFKIYYEEGK-----ITKLPRMMGWQAEGAAPIVKGYPIKNPQT 238 H +PVGNAGNITAYWKG+K Y + + K P M G+QA GAAP + G+PI++P+T Sbjct: 187 HCLPVGNAGNITAYWKGYKEYSTDSETHQAVTRKRPVMCGYQAAGAAPFLAGHPIEHPET 246 Query: 239 IATAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAG 298 +ATAI+IGNP SW A A +ESGG D +D EIL A K+++ EG+FCEPASA S+AG Sbjct: 247 VATAIRIGNPQSWDYAWAAQKESGGWFDKFTDEEILAAQKMLSQYEGIFCEPASATSLAG 306 Query: 299 LIKLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVC--EEPITVPPDFDEVVKVL 350 +K +R G G + CTLTG GLKDPDTAI+ C +P+T+ + + V + + Sbjct: 307 ALKDIRSGKIPEGSRIVCTLTGVGLKDPDTAIRQCAATQPLTIEAELNAVKRAI 360 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: 454 Number of extensions: 21 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: 364 Length adjustment: 29 Effective length of query: 323 Effective length of database: 335 Effective search space: 108205 Effective search space used: 108205 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_020562611.1 A3OW_RS0106470 (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.25696.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-96 309.1 0.0 2.2e-96 308.9 0.0 1.0 1 lcl|NCBI__GCF_000372865.1:WP_020562611.1 A3OW_RS0106470 threonine synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000372865.1:WP_020562611.1 A3OW_RS0106470 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 308.9 0.0 2.2e-96 2.2e-96 1 340 [] 11 335 .. 11 335 .. 0.97 Alignments for each domain: == domain 1 score: 308.9 bits; conditional E-value: 2.2e-96 TIGR00260 1 vvryreilevt.ekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltk 67 ++ryr l+v+ +++++l+eg+t+l+r +++++ g+ +++vk ++++Pt++FKDrg +++++tk lcl|NCBI__GCF_000372865.1:WP_020562611.1 11 IERYRDRLPVSaSTRIISLNEGNTPLIRLQNIPRLTGKeVDIHVKFEGLNPTGSFKDRG---MTMAVTK 76 78*******************************99999899******************...******* PP TIGR00260 68 alelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDda 136 a e+g +++cA++G+t+a+aa a+a++a++k++v++P+gki+ +kl+++l++ a++++i+G+FD+ lcl|NCBI__GCF_000372865.1:WP_020562611.1 77 AVEEGSRAIICASTGNTSASAA-AYAARAGIKAFVIIPEGKIA--LGKLAQTLMYDATIIQIRGNFDQG 142 **********************.********************..************************ PP TIGR00260 137 qdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflek 204 +lvkei+++ + + +ns+N p+ri +qkt+ fei+++lg ++pd ++pv+ +gn++a++kG++e+ lcl|NCBI__GCF_000372865.1:WP_020562611.1 143 MTLVKEIADHAPVTIVNSIN---PFRIDGQKTASFEIIDALG-DAPDYHCLPVGnAGNITAYWKGYKEY 207 ********998877777777...*******************.************************** PP TIGR00260 205 kelg.........lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarr 264 + +p + + +a gaa+++ p+e++eT++tA++ignp ++++a+++ ++ lcl|NCBI__GCF_000372865.1:WP_020562611.1 208 STDSethqavtrkRP-VMCGYQAAGAAPFLAGH-------PIEHPETVATAIRIGNPQSWDYAWAAQKE 268 999899999999999.99999****98888777.......***************************** PP TIGR00260 265 slgnledlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtg 333 s+g +++ +deeil a+k l + eg+++ep++a+++a+ +k + +g +++++ +++v+ ltg lcl|NCBI__GCF_000372865.1:WP_020562611.1 269 SGGWFDKF----TDEEILAAQKMLSQYEGIFCEPASATSLAGALKDIRSG---KIPEG--SRIVCTLTG 328 ********....**************************************...*****..********* PP TIGR00260 334 nklkdpe 340 +lkdp+ lcl|NCBI__GCF_000372865.1:WP_020562611.1 329 VGLKDPD 335 *****97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (364 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.84 // [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