Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_011650794.1 RL_RS05510 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_000009265.1:WP_011650794.1 Length = 474 Score = 648 bits (1672), Expect = 0.0 Identities = 315/460 (68%), Positives = 377/460 (81%) Query: 3 YVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLTPF 62 Y+STRGEAP LGF DALL GLARDGGLY+P+++P F+ ++IRALRGK+Y E+A +L+PF Sbjct: 6 YISTRGEAPSLGFCDALLTGLARDGGLYVPRKWPSFSKKEIRALRGKTYQEIAFTILSPF 65 Query: 63 TGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLARM 122 T GEIP F M+ EAYGTFRH A+ PLVQT N FV+ELFHG TLAFKDVAMQLLAR+ Sbjct: 66 TNGEIPDDTFRAMIDEAYGTFRHPAIAPLVQTGPNSFVMELFHGTTLAFKDVAMQLLARL 125 Query: 123 MDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSSGF 182 MDY L +RGERATIVGATSGDTGGAAI+AF GR+ TDIFILFP+G+VSPVQQRQMT+S Sbjct: 126 MDYALEKRGERATIVGATSGDTGGAAIDAFAGRERTDIFILFPHGKVSPVQQRQMTTSSS 185 Query: 183 SNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALSLG 242 +NVHAL++EGNFDDCQNLVK MFND+ F D + LSGVNSINWARIM Q+VYYFTAA++LG Sbjct: 186 ANVHALAVEGNFDDCQNLVKAMFNDVTFRDKVRLSGVNSINWARIMAQIVYYFTAAVALG 245 Query: 243 APDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGVAQ 302 PDR +SFTVPTGNFGDIFAGY AKRMGLPI++L+IATN+NDIL+RTL++G Y+M+ V Sbjct: 246 GPDRKISFTVPTGNFGDIFAGYCAKRMGLPIDRLVIATNENDILARTLKTGRYDMKAVKA 305 Query: 303 TTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSAGR 362 T+SPSMDIQISSNFERLLFEA+ RDA+ VR M+ LKQS GF I + L AIR +F AGR Sbjct: 306 TSSPSMDIQISSNFERLLFEAYDRDASKVRAAMESLKQSNGFEIGSQALKAIRRDFRAGR 365 Query: 363 STVDETAATIESVLSKDGYLLDPHSAIGVKVAREKASGTAPMVVLATAHPAKFPDAVKAA 422 ++ + A TI ++ GYLLDPHSAIGV VA +K PMV L+TAHPAKFP AVK+A Sbjct: 366 ASEKQVAETIRKTHAETGYLLDPHSAIGVFVAAKKEKPNTPMVTLSTAHPAKFPAAVKSA 425 Query: 423 CGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSR 462 CG++P LP WL DLM R+E F ++ ELK VE ++ H+R Sbjct: 426 CGIDPALPTWLADLMHREERFQIIKPELKAVETFIGKHAR 465 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: 641 Number of extensions: 17 Number of successful extensions: 1 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: 474 Length adjustment: 33 Effective length of query: 430 Effective length of database: 441 Effective search space: 189630 Effective search space used: 189630 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_011650794.1 RL_RS05510 (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.28732.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-90 289.6 0.0 2.3e-90 289.1 0.0 1.1 1 lcl|NCBI__GCF_000009265.1:WP_011650794.1 RL_RS05510 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009265.1:WP_011650794.1 RL_RS05510 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 289.1 0.0 2.3e-90 2.3e-90 15 331 .. 75 425 .. 67 432 .. 0.91 Alignments for each domain: == domain 1 score: 289.1 bits; conditional E-value: 2.3e-90 TIGR00260 15 lvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAt 80 +++ + +fr p++a v+ n +v elfhg tlaFKD+++q +a l+ +ale+ e t+++At lcl|NCBI__GCF_000009265.1:WP_011650794.1 75 FRAMIDEAYGTFRHPAIAPLVQTgPNSFVMELFHGTTLAFKDVAMQLLARLMDYALEKRGEraTIVGAT 143 5567788999********9999999*******************************9877677****** PP TIGR00260 81 sGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke 148 sGdtg aa+ a+ag++ ++++L P+gk+spv + +++t + n++ la++G+FDd+q+lvk++f+d lcl|NCBI__GCF_000009265.1:WP_011650794.1 144 SGDTGGAAIDAFAGRERTDIFILFPHGKVSPVqQRQMTTSSSANVHALAVEGNFDDCQNLVKAMFNDVT 212 *****************************************************************9665 PP TIGR00260 149 ...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpiekl 214 k+ l+ vNsin+ari aq++y+f ++ +lg+ k+ + vp gnfg+i++G+++k+++ lpi+ l lcl|NCBI__GCF_000009265.1:WP_011650794.1 213 frdKVRLSGVNSINWARIMAQIVYYFTAAVALGG-PDRKISFTVPTGNFGDIFAGYCAKRMG-LPIDRL 279 677******************************5.4568**********************9.****** PP TIGR00260 215 aiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale.....larrslgnledlke.... 274 ia++++ di+ r lk+g + k+ k+T s++mdi ++sn+er+l+ a + + +e+lk+ lcl|NCBI__GCF_000009265.1:WP_011650794.1 280 VIATNEN-DILARTLKTGRYDMKAVKATSSPSMDIQISSNFERLLFeaydrDASKVRAAMESLKQsngf 347 ******9.**********99999999******************996322223333444555555**** PP TIGR00260 275 .................svsdeeileaikklaeeegyllephtavavaalkklvekg...vs.atadpa 322 ++s++++ e+i+k +e gyll+ph+a++v + k + + v+ +ta+pa lcl|NCBI__GCF_000009265.1:WP_011650794.1 348 eigsqalkairrdfragRASEKQVAETIRKTHAETGYLLDPHSAIGVFVAAKKEKPNtpmVTlSTAHPA 416 ***********************************************9988888877676337****** PP TIGR00260 323 KFeevveal 331 KF+ +v lcl|NCBI__GCF_000009265.1:WP_011650794.1 417 KFPAAVKSA 425 *****9854 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (474 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 13.92 // [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