Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_010529190.1 ON01_RS01240 threonine synthase
Query= BRENDA::O66740 (352 letters) >NCBI__GCF_000224785.1:WP_010529190.1 Length = 353 Score = 413 bits (1062), Expect = e-120 Identities = 207/340 (60%), Positives = 262/340 (77%), Gaps = 4/340 (1%) Query: 4 WQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSFK 63 WQG+I+ Y+ LPV + TP ++L EGNT LI L+ +G + +Y K EG NPTGSFK Sbjct: 3 WQGLIRHYQSNLPVTDRTPEISLQEGNTSLIHFSTLSEQLGIE--LYGKVEGANPTGSFK 60 Query: 64 DRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQAM 123 DRGM LA++KA+E G AVICASTGNTSASAAAYAARAG+RA +++PKG +A+GKL+QA+ Sbjct: 61 DRGMALAVAKAIEEGSNAVICASTGNTSASAAAYAARAGIRAIIVIPKGKIALGKLAQAV 120 Query: 124 IYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPDY 183 +YGA ++ I G FDDAL IVRKI E PV +VNSVNPYR+EGQKTAAFE+CD LG APD Sbjct: 121 MYGADIVEIDGNFDDALKIVRKISETAPVTLVNSVNPYRLEGQKTAAFEVCDVLGSAPDI 180 Query: 184 HFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIATAI 243 IPVGNAGNI+AYWKGFK Y+E K T LP+M G++AEGAA IV ++NP+TIATAI Sbjct: 181 LAIPVGNAGNISAYWKGFKEYHEM-KQTGLPQMFGFEAEGAAAIVGNEVVQNPETIATAI 239 Query: 244 KIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLIKLV 303 +IGNP SWK A++A ESGGKI +V+D+EI +A KL+A+ EGVF EP S AS+AG+I+ Sbjct: 240 RIGNPASWKLAVQARDESGGKIGSVTDTEIAHAQKLLATQEGVFAEPGSCASIAGIIQQR 299 Query: 304 REGFFKGGEVVTCTLTGNGLKDPDTAI-KVCEEPITVPPD 342 ++ G V LTGNGLKDP TAI ++ ++P+T+P D Sbjct: 300 KQNTITEGSKVAAVLTGNGLKDPQTAIDQIDQDPVTLPND 339 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: 453 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 352 Length of database: 353 Length adjustment: 29 Effective length of query: 323 Effective length of database: 324 Effective search space: 104652 Effective search space used: 104652 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_010529190.1 ON01_RS01240 (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.296022.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.3e-99 317.3 0.7 7.3e-99 317.1 0.7 1.0 1 NCBI__GCF_000224785.1:WP_010529190.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000224785.1:WP_010529190.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 317.1 0.7 7.3e-99 7.3e-99 2 339 .. 8 322 .. 7 323 .. 0.97 Alignments for each domain: == domain 1 score: 317.1 bits; conditional E-value: 7.3e-99 TIGR00260 2 vryreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgn 73 y++ l+vt ++ ++l+eg+t+l+++ +l+e++g+ +ly k ++++Pt++FKDrg +a +++ka e+g NCBI__GCF_000224785.1:WP_010529190.1 8 RHYQSNLPVTdRTPEISLQEGNTSLIHFSTLSEQLGI-ELYGKVEGANPTGSFKDRG---MALAVAKAIEEGS 76 579999****999************************.*******************...************* PP TIGR00260 74 etvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdlvkeifed 146 ++v+cA++G+t+a+aa a+a++a++++++++Pkgki+ +kl++a++++a +++i+G+FDda+++v++i e NCBI__GCF_000224785.1:WP_010529190.1 77 NAVICASTGNTSASAA-AYAARAGIRAIIVIPKGKIA--LGKLAQAVMYGADIVEIDGNFDDALKIVRKISET 146 ****************.********************..********************************99 PP TIGR00260 147 keklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekkelg...lpiekla 215 + +++nsvN p+r+e+qkt+afe+++ lg +pd +++pv+ +gn++a++kGf+e++e+ lp ++ + NCBI__GCF_000224785.1:WP_010529190.1 147 APVTLVNSVN---PYRLEGQKTAAFEVCDVLG-SAPDILAIPVGnAGNISAYWKGFKEYHEMKqtgLP-QMFG 214 9999998888...*******************.9**********************9987665555**.**** PP TIGR00260 216 iaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnledlkesvsdeeileaikkl 288 ++aegaa iv + +++eT++tA++ignp++++ a+++ +s+g++ ++ +d ei +a+k+l NCBI__GCF_000224785.1:WP_010529190.1 215 FEAEGAAAIVGNE-------VVQNPETIATAIRIGNPASWKLAVQARDESGGKIGSV----TDTEIAHAQKLL 276 ******9999988.......7899*********************************....************ PP TIGR00260 289 aeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdp 339 a +eg+++ep +++++a+++++ +++ t+ ++ ++v ++ltgn+lkdp NCBI__GCF_000224785.1:WP_010529190.1 277 ATQEGVFAEPGSCASIAGIIQQRKQN---TITEG--SKVAAVLTGNGLKDP 322 **************************...*****..99999********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (353 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: 00:00:00.00 # Mc/sec: 21.51 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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