Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_018231340.1 THITHI_RS0101705 threonine synthase
Query= BRENDA::O66740 (352 letters) >NCBI__GCF_000378965.1:WP_018231340.1 Length = 379 Score = 393 bits (1010), Expect = e-114 Identities = 198/370 (53%), Positives = 264/370 (71%), Gaps = 22/370 (5%) Query: 3 RWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTGSF 62 R+ G+I +Y+ LPV ++T I++L EGNTPLI +N+ R +G + IY+KYEGLNPTGSF Sbjct: 6 RYTGLIDRYRDRLPVHDDTRIISLGEGNTPLIRLNNIPRIVGREVDIYVKYEGLNPTGSF 65 Query: 63 KDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLSQA 122 KDRGMT+A++KAVE G +A+ICASTGNTSA+AAAYAARAG+ A+V++P G +A+GKL+QA Sbjct: 66 KDRGMTMAVTKAVEEGSKAIICASTGNTSAAAAAYAARAGIAAFVIIPDGKIAMGKLAQA 125 Query: 123 MIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEAPD 182 M++G+ V+ I+G FDD + +V+++ PV IVNS+NPYR++GQKTAAFEI + LG APD Sbjct: 126 MMHGSVVIQIKGNFDDGMRLVKEVASEAPVTIVNSINPYRLQGQKTAAFEITEELGRAPD 185 Query: 183 YHFIPVGNAGNITAYWKGFKIY--------------------YEEGKIT-KLPRMMGWQA 221 YH +PVGNAGNITA+W G+ Y Y G I P+M+G+QA Sbjct: 186 YHCLPVGNAGNITAHWIGYCEYSSASGDHVTEACTFCKGHCAYAGGAIVGNRPKMVGYQA 245 Query: 222 EGAAPIVKGYPIKNPQTIATAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIA 281 G+AP ++G + NP T+ATAI+IG+P SW SA K +ESGG D +D+EIL A KL+A Sbjct: 246 AGSAPFMRGEMVDNPDTVATAIRIGHPQSWDSAWKVKEESGGWFDECTDAEILAAQKLLA 305 Query: 282 STEGVFCEPASAASVAGLIKLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVCEEP-ITVP 340 EGVFCEPASAAS+AG ++ V+ G + CTLTG+GLKDPDTAI P I V Sbjct: 306 EKEGVFCEPASAASLAGALRDVQNDRIPEGSSIVCTLTGHGLKDPDTAIAQSTRPLINVE 365 Query: 341 PDFDEVVKVL 350 D+V + + Sbjct: 366 ATLDQVKRAI 375 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: 422 Number of extensions: 19 Number of successful extensions: 3 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: 379 Length adjustment: 30 Effective length of query: 322 Effective length of database: 349 Effective search space: 112378 Effective search space used: 112378 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_018231340.1 THITHI_RS0101705 (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.28440.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-94 303.4 0.0 2.1e-94 302.4 0.0 1.4 1 lcl|NCBI__GCF_000378965.1:WP_018231340.1 THITHI_RS0101705 threonine synth Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000378965.1:WP_018231340.1 THITHI_RS0101705 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 302.4 0.0 2.1e-94 2.1e-94 1 340 [] 11 351 .. 11 351 .. 0.97 Alignments for each domain: == domain 1 score: 302.4 bits; conditional E-value: 2.1e-94 TIGR00260 1 vvryreilevt.ekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltk 67 + ryr l+v ++++++l eg+t+l+r +++++ vg ++yvk ++++Pt++FKDrg +++++tk lcl|NCBI__GCF_000378965.1:WP_018231340.1 11 IDRYRDRLPVHdDTRIISLGEGNTPLIRLNNIPRIVGReVDIYVKYEGLNPTGSFKDRG---MTMAVTK 76 579**********************************999*******************...******* PP TIGR00260 68 alelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDda 136 a e+g ++++cA++G+t+aaaa a+a++a++ ++v++P+gki+ +kl++a++++ v++ikG+FDd lcl|NCBI__GCF_000378965.1:WP_018231340.1 77 AVEEGSKAIICASTGNTSAAAA-AYAARAGIAAFVIIPDGKIA--MGKLAQAMMHGSVVIQIKGNFDDG 142 **********************.********************..************************ PP TIGR00260 137 qdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflek 204 +lvke++++ + + +ns+N p+r+++qkt+afei e+lg ++pd ++pv+ +gn++a + G++e+ lcl|NCBI__GCF_000378965.1:WP_018231340.1 143 MRLVKEVASEAPVTIVNSIN---PYRLQGQKTAAFEITEELG-RAPDYHCLPVGnAGNITAHWIGYCEY 207 ********887766666666...*******************.9************************* PP TIGR00260 205 kelg.........................lpieklaiaaegaadivrrflksgdlepkedkeTlstAmd 248 ++ +p ++ + +a g+a+++r +++T++tA++ lcl|NCBI__GCF_000378965.1:WP_018231340.1 208 SSASgdhvteactfckghcayaggaivgnRP-KMVGYQAAGSAPFMRGE-------MVDNPDTVATAIR 268 999889**********************99*.**********9999887.......67889******** PP TIGR00260 249 ignpsnveralelarrslgnledlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsa 317 ig+p +++ a+++ ++s+g +++ +d+eil a+k+lae+eg+++ep++a+++a+ ++ v+++ lcl|NCBI__GCF_000378965.1:WP_018231340.1 269 IGHPQSWDSAWKVKEESGGWFDEC----TDAEILAAQKLLAEKEGVFCEPASAASLAGALRDVQND--- 330 ***********************9....**************************************... PP TIGR00260 318 tadpaKFeevvealtgnklkdpe 340 +++++ + +v+ ltg++lkdp+ lcl|NCBI__GCF_000378965.1:WP_018231340.1 331 RIPEG--SSIVCTLTGHGLKDPD 351 *****..**************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (379 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 3.91 // [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