Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_012854251.1 TCUR_RS19365 threonine synthase
Query= BRENDA::P9WG59 (360 letters) >NCBI__GCF_000024385.1:WP_012854251.1 Length = 352 Score = 462 bits (1188), Expect = e-135 Identities = 231/351 (65%), Positives = 278/351 (79%), Gaps = 1/351 (0%) Query: 9 HQPWPGVIAAYRDRLPVGDDWTPVTLLEGGTPLIAATNLSKQTGCTIHLKVEGLNPTGSF 68 ++ W G+IA YRDRLPV + VTLLEGGTPL+ A +S+ TGC ++LKVEG NPTGSF Sbjct: 2 NRAWRGLIAEYRDRLPVTEATPVVTLLEGGTPLLPAQRISQLTGCEVYLKVEGANPTGSF 61 Query: 69 KDRGMTMAVTDALAHGQRAVLCASTGNTSASAAAYAARAGITCAVLIPQGKIAMGKLAQA 128 KDRGMT+A++ A G +AV+CASTGNTSASAAAYA RAG+TCAVL+P+GKIAMGKLAQA Sbjct: 62 KDRGMTVAISKAAEEGAKAVICASTGNTSASAAAYAVRAGMTCAVLVPKGKIAMGKLAQA 121 Query: 129 VMHGAKIIQIDGNFDDCLELARKMAADFPTISLVNSVNPVRIEGQKTAAFEIVDVLGTAP 188 ++HGA+++Q+DGNFDDCLELARK+A D+P ++LVNSVN R++GQKTAAFEIVD LG AP Sbjct: 122 LVHGARLLQVDGNFDDCLELARKLAVDYP-VALVNSVNKFRLQGQKTAAFEIVDALGDAP 180 Query: 189 DVHALPVGNAGNITAYWKGYTEYHQLGLIDKLPRMLGTQAAGAAPLVLGEPVSHPETIAT 248 DVH LPVGNAGNI+AYW GYTEY + K PRMLG QA+GAAP V GEPV P+TIAT Sbjct: 181 DVHCLPVGNAGNISAYWMGYTEYAADKVATKTPRMLGFQASGAAPFVKGEPVRSPQTIAT 240 Query: 249 AIRIGSPASWTSAVEAQQQSKGRFLAASDEEILAAYHLVARVEGVFVEPASAASIAGLLK 308 AIRIG+PASW A+ A+ +S G A +D +ILAAY L+AR EGVFVEPASAAS+AG+L+ Sbjct: 241 AIRIGNPASWDLAIAARDESGGAISAVTDRQILAAYRLLAREEGVFVEPASAASVAGVLQ 300 Query: 309 AIDDGWVARGSTVVCTVTGNGLKDPDTALKDMPSVSPVPVDPVAVVEKLGL 359 A + G + G VVCTVTGNGLKDPD A+ P+ V VD A LGL Sbjct: 301 AREQGLIEAGERVVCTVTGNGLKDPDWAISGAPAPITVKVDAHAAASALGL 351 Lambda K H 0.317 0.132 0.392 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: 443 Number of extensions: 14 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: 360 Length of database: 352 Length adjustment: 29 Effective length of query: 331 Effective length of database: 323 Effective search space: 106913 Effective search space used: 106913 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_012854251.1 TCUR_RS19365 (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.10037.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-96 309.1 0.0 2.3e-96 308.9 0.0 1.0 1 lcl|NCBI__GCF_000024385.1:WP_012854251.1 TCUR_RS19365 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024385.1:WP_012854251.1 TCUR_RS19365 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 308.9 0.0 2.3e-96 2.3e-96 1 340 [] 9 326 .. 9 326 .. 0.97 Alignments for each domain: == domain 1 score: 308.9 bits; conditional E-value: 2.3e-96 TIGR00260 1 vvryreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltka 68 + yr l+vt +++v+l eg t+l+ ++++++ g ++y+k ++++Pt++FKDrg ++v+++ka lcl|NCBI__GCF_000024385.1:WP_012854251.1 9 IAEYRDRLPVTeATPVVTLLEGGTPLLPAQRISQLTGC-EVYLKVEGANPTGSFKDRG---MTVAISKA 73 568999*****999******************988888.*******************...******** PP TIGR00260 69 lelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaq 137 +e+g+++v+cA++G+t+a+aa a+a +a++ + vL+Pkgki+ +kl++al+++a++l+++G+FDd++ lcl|NCBI__GCF_000024385.1:WP_012854251.1 74 AEEGAKAVICASTGNTSASAA-AYAVRAGMTCAVLVPKGKIA--MGKLAQALVHGARLLQVDGNFDDCL 139 *********************.********************..************************* PP TIGR00260 138 dlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekk 205 +l ++++ d + +++nsvN +r+++qkt+afeiv++lg ++pd ++pv+ +gn++a+++G+ e+ lcl|NCBI__GCF_000024385.1:WP_012854251.1 140 ELARKLAVDYPVALVNSVN---KFRLQGQKTAAFEIVDALG-DAPDVHCLPVGnAGNISAYWMGYTEYA 204 *******998888888888...99*****************.***********************9987 PP TIGR00260 206 elg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnle 270 p ++l+++a gaa++v+ p ++++T++tA++ignp++++ a ++ +s+g + lcl|NCBI__GCF_000024385.1:WP_012854251.1 205 ADKvatkTP-RMLGFQASGAAPFVKGE-------PVRSPQTIATAIRIGNPASWDLAIAARDESGGAIS 265 766668899.**********9988876.......*********************************** PP TIGR00260 271 dlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdp 339 ++ +d +il a+++la+eeg+++ep++a++va++++ e+g ++ + e+vv+ +tgn+lkdp lcl|NCBI__GCF_000024385.1:WP_012854251.1 266 AV----TDRQILAAYRLLAREEGVFVEPASAASVAGVLQAREQG---LIEAG--ERVVCTVTGNGLKDP 325 **....**************************************...*****..**************9 PP TIGR00260 340 e 340 + lcl|NCBI__GCF_000024385.1:WP_012854251.1 326 D 326 7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (352 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: 7.21 // [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