Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_078429991.1 BK574_RS21135 threonine synthase
Query= BRENDA::O66740 (352 letters) >NCBI__GCF_002019605.1:WP_078429991.1 Length = 354 Score = 428 bits (1101), Expect = e-125 Identities = 214/341 (62%), Positives = 271/341 (79%), Gaps = 4/341 (1%) Query: 1 MNRWQGIIKQYKKYLPVDENTPIVTLYEGNTPLIEADNLARAIGFKGKIYLKYEGLNPTG 60 M++W+G++++YK++LPV+ENTP+++L EGNTPLI +NL++ G +Y+K EG NPTG Sbjct: 1 MSQWKGLLEEYKQFLPVNENTPMLSLREGNTPLIPLENLSKEWGVD--VYVKVEGANPTG 58 Query: 61 SFKDRGMTLAISKAVEAGKRAVICASTGNTSASAAAYAARAGLRAYVLLPKGAVAIGKLS 120 SFKDRGM +A++KA E G + +ICASTGNTSA+AAAY ARAGLR V++P+G +A+GKL+ Sbjct: 59 SFKDRGMVMAVAKAKEEGSKTIICASTGNTSAAAAAYGARAGLRCIVVIPEGKIALGKLA 118 Query: 121 QAMIYGAKVLAIQGTFDDALNIVRKIGENFPVEIVNSVNPYRIEGQKTAAFEICDTLGEA 180 QA++YGA+VL I+G FD+AL+IVRKI E P+ +VNSVNPYRIEGQKTAAFEICD LG+A Sbjct: 119 QAVMYGAEVLEIKGNFDNALDIVRKISEQEPITLVNSVNPYRIEGQKTAAFEICDALGQA 178 Query: 181 PDYHFIPVGNAGNITAYWKGFKIYYEEGKITKLPRMMGWQAEGAAPIVKGYPIKNPQTIA 240 PD IPVGNAGNITAYWKGFK Y E K T LP+M G+QA G+A IV+ I++P+TIA Sbjct: 179 PDVLAIPVGNAGNITAYWKGFK-EYNEAKQTGLPQMRGFQAWGSAAIVRNEVIESPETIA 237 Query: 241 TAIKIGNPYSWKSALKAAQESGGKIDAVSDSEILYAYKLIASTEGVFCEPASAASVAGLI 300 TAI+IGNP SWK A+ A ES G ID+V+D EIL AY+L+AS EGVF EPAS AS+AGLI Sbjct: 238 TAIRIGNPASWKQAVAARDESNGHIDSVTDEEILAAYQLLASREGVFAEPASCASIAGLI 297 Query: 301 KLVREGFFKGGEVVTCTLTGNGLKDPDTAIKVCE-EPITVP 340 K + G K G V C LTGNGLKDP TA+ E +PI +P Sbjct: 298 KQINTGEIKKGAKVVCVLTGNGLKDPTTAMDTVEVKPIVLP 338 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: 466 Number of extensions: 16 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: 354 Length adjustment: 29 Effective length of query: 323 Effective length of database: 325 Effective search space: 104975 Effective search space used: 104975 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_078429991.1 BK574_RS21135 (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.5196.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-109 351.6 0.1 2.6e-109 351.4 0.1 1.0 1 lcl|NCBI__GCF_002019605.1:WP_078429991.1 BK574_RS21135 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078429991.1 BK574_RS21135 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 351.4 0.1 2.6e-109 2.6e-109 3 339 .. 10 323 .. 8 324 .. 0.97 Alignments for each domain: == domain 1 score: 351.4 bits; conditional E-value: 2.6e-109 TIGR00260 3 ryreilevt.ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltkale 70 y+++l+v+ ++++++l eg+t+l+ ++l++e g+ ++yvk ++++Pt++FKDrg + ++++ka+e lcl|NCBI__GCF_002019605.1:WP_078429991.1 10 EYKQFLPVNeNTPMLSLREGNTPLIPLENLSKEWGV-DVYVKVEGANPTGSFKDRG---MVMAVAKAKE 74 799******99*************************.*******************...********** PP TIGR00260 71 lgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDdaqdl 139 +g +t++cA++G+t+aaaa a+ ++a+++++v++P+gki+ +kl++a++++a+vl+ikG+FD+a+d+ lcl|NCBI__GCF_002019605.1:WP_078429991.1 75 EGSKTIICASTGNTSAAAA-AYGARAGLRCIVVIPEGKIA--LGKLAQAVMYGAEVLEIKGNFDNALDI 140 *******************.********************..*************************** PP TIGR00260 140 vkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflekkel 207 v++i e+++++++nsvN p+rie+qkt+afei+++lg ++pd +++pv+ +gn++a++kGf+e++e+ lcl|NCBI__GCF_002019605.1:WP_078429991.1 141 VRKISEQEPITLVNSVN---PYRIEGQKTAAFEICDALG-QAPDVLAIPVGnAGNITAYWKGFKEYNEA 205 ************99999...*******************.***********************987655 PP TIGR00260 208 g...lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnledlk 273 lp ++++++a g+a ivr+ +e++eT++tA++ignp+++++a+++ +s+g+++++ lcl|NCBI__GCF_002019605.1:WP_078429991.1 206 KqtgLP-QMRGFQAWGSAAIVRNE-------VIESPETIATAIRIGNPASWKQAVAARDESNGHIDSV- 265 4444**.**************998.......899**********************************. PP TIGR00260 274 esvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkdp 339 +deeil a+++la +eg+++ep++++++a+l+k+++ g +++++ ++vv++ltgn+lkdp lcl|NCBI__GCF_002019605.1:WP_078429991.1 266 ---TDEEILAAYQLLASREGVFAEPASCASIAGLIKQINTG---EIKKG--AKVVCVLTGNGLKDP 323 ...**************************************...*****..*************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (354 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: 11.98 // [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