Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_090443022.1 BLS63_RS09065 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_900100495.1:WP_090443022.1 Length = 469 Score = 506 bits (1302), Expect = e-148 Identities = 263/463 (56%), Positives = 323/463 (69%), Gaps = 4/463 (0%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 M+Y+STRG+AP L F D LLAGLA DGGLY+P+ P+FT E+I + G Y E+A V+ Sbjct: 1 MRYISTRGQAPALNFEDVLLAGLASDGGLYVPENLPRFTVEEIASWAGLPYHELAFRVMR 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 PF G IP ADF+R++ E YG F H AV PL Q + NE+VLELFHGPTLAFKD A+QLL Sbjct: 61 PFVTGSIPDADFKRILEETYGVFAHSAVAPLRQLNGNEWVLELFHGPTLAFKDFALQLLG 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 R++DYVLA+R ER I+GATSGDTG AAIE DN DIFIL P+ RVS VQ+RQMT+ Sbjct: 121 RLLDYVLAKRNERVVIMGATSGDTGSAAIEGCKSCDNVDIFILHPHNRVSEVQRRQMTTI 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 N+H ++IEGNFDDCQ +VK F D F L VNSINWARIM Q+VYYF AA+ Sbjct: 181 LGDNIHNIAIEGNFDDCQEMVKDSFADQSFLKGTRLVAVNSINWARIMAQIVYYFHAAIQ 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LG P R+++F+VPTGNFGDIFAGY+A+ MGLPI QLI+ATN NDIL R + Y + Sbjct: 241 LGGPARSIAFSVPTGNFGDIFAGYLARNMGLPINQLIVATNRNDILHRFMSGNQYVKDTL 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 T SPSMDI +SSNFERLLF+ HGR+ AA+ LM KQ GGF++ E + R F + Sbjct: 301 HPTLSPSMDIMVSSNFERLLFDLHGRNGAAIAELMATFKQGGGFSVEEDRWTEARKLFDS 360 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVARE-KASGTAPMVVLATAHPAKFPDAV 419 T TI V ++ G LLDPH+AIGV+ ARE + S PMV+L TAHP KFP+AV Sbjct: 361 LAVDDQATCETIADVFAECGELLDPHTAIGVRAARECRRSLATPMVILGTAHPVKFPEAV 420 Query: 420 KAACGV--EPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHH 460 + A GV P LPA L DL +R+E +VL N+LK V+ +V H Sbjct: 421 EQA-GVTQAPALPAHLADLFEREERCSVLANDLKTVQGFVSQH 462 Lambda K H 0.320 0.135 0.389 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: 586 Number of extensions: 23 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: 463 Length of database: 469 Length adjustment: 33 Effective length of query: 430 Effective length of database: 436 Effective search space: 187480 Effective search space used: 187480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 bits)
Align candidate WP_090443022.1 BLS63_RS09065 (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.10644.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-84 269.1 0.0 3.6e-84 268.8 0.0 1.1 1 lcl|NCBI__GCF_900100495.1:WP_090443022.1 BLS63_RS09065 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900100495.1:WP_090443022.1 BLS63_RS09065 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 268.8 0.0 3.6e-84 3.6e-84 10 329 .. 67 421 .. 58 428 .. 0.93 Alignments for each domain: == domain 1 score: 268.8 bits; conditional E-value: 3.6e-84 TIGR00260 10 vtekdlvdlaegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne.. 74 ++++d + + e + +f+ ++a +++ + n +v+elfhgPtlaFKD++lq ++ ll ++l + ne lcl|NCBI__GCF_900100495.1:WP_090443022.1 67 IPDADFKRILEETYGVFAHSAVAplRQLNG-NEWVLELFHGPTLAFKDFALQLLGRLLDYVLAKRNErv 134 457888999999999999998887799999.99*******************************99999 PP TIGR00260 75 tvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvke 142 ++++AtsGdtg+aa+e+ + nv++++L P+ ++s v +++t l n++ +ai+G+FDd+q++vk+ lcl|NCBI__GCF_900100495.1:WP_090443022.1 135 VIMGATSGDTGSAAIEGCKSCDNVDIFILHPHNRVSEVqRRQMTTILGDNIHNIAIEGNFDDCQEMVKD 203 99************************************99***************************** PP TIGR00260 143 ifedke...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelg 208 f d+ + l++vNsin+ari aq++y+f ++ qlg+ + ++++vp gnfg+i++G+l+ +++ lcl|NCBI__GCF_900100495.1:WP_090443022.1 204 SFADQSflkGTRLVAVNSINWARIMAQIVYYFHAAIQLGGPA-RSIAFSVPTGNFGDIFAGYLARNMG- 270 **977779899****************************655.57****************9999999. PP TIGR00260 209 lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke.. 274 lpi+ l +a++ + di++rf+ + + ++ + Tls++mdi +sn+er+l+ l r+++ + +l + lcl|NCBI__GCF_900100495.1:WP_090443022.1 271 LPINQLIVATNRN-DILHRFMSGNQYVKDTLHPTLSPSMDIMVSSNFERLLFdLHGRNGAAIAELMAtf 338 ******9999998.******888877777777*******************99999*********88** PP TIGR00260 275 .......................svsdeeileaikklaeeegyllephtavavaalkklvekg...vs. 316 +v d+++ e+i + +e g ll+phta++v+a ++ + + lcl|NCBI__GCF_900100495.1:WP_090443022.1 339 kqgggfsveedrwtearklfdslAVDDQATCETIADVFAECGELLDPHTAIGVRAARECRRSLatpMVi 407 *******************************************************98776655444225 PP TIGR00260 317 .atadpaKFeevve 329 +ta+p KF+e+ve lcl|NCBI__GCF_900100495.1:WP_090443022.1 408 lGTAHPVKFPEAVE 421 8***********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (469 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: 12.34 // [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