Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_085636009.1 MGEO_RS06980 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_002115805.1:WP_085636009.1 Length = 462 Score = 517 bits (1331), Expect = e-151 Identities = 262/458 (57%), Positives = 327/458 (71%), Gaps = 1/458 (0%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 M+Y+STRG+AP LGF D +L+GLARDGGLY+P+ P +A IRA+ G SY E+A V+ Sbjct: 1 MQYISTRGKAPALGFEDTMLSGLARDGGLYVPETIPTLSAGDIRAMHGLSYEEIAFRVMR 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 PF G F ++ +AY F HDA PLVQ F+LELFHGPTLAFKD AMQL+ Sbjct: 61 PFVGDAFTDEVFADLIAKAYAGFGHDARAPLVQLGNGHFLLELFHGPTLAFKDFAMQLIG 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 +M L++ G+R TIVGATSGDTG AAIEAF G D D+FIL+P+GRVS VQ+RQMT+ Sbjct: 121 QMFQEALSRSGKRVTIVGATSGDTGSAAIEAFRGLDAVDVFILYPHGRVSEVQRRQMTTP 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 SNVHAL+++G FDDCQ +K MFN EF DA+ L+GVNSINW R++ QVVYYF++A+S Sbjct: 181 VESNVHALALDGTFDDCQARLKDMFNHFEFRDAVKLAGVNSINWGRVLAQVVYYFSSAVS 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LGAPDR VSFTVPTGNFGDIFAGY+AKRMGLPI++L++ATN NDIL R L +G Y V Sbjct: 241 LGAPDRTVSFTVPTGNFGDIFAGYIAKRMGLPIDRLVVATNQNDILHRCLTTGGYVTDSV 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 + SPSMDIQ+SSNFER LF+A+ RD AV LM LK +GGF +S+ + +R + + Sbjct: 301 TPSISPSMDIQVSSNFERALFDAYNRDGNAVSQLMDELK-AGGFHVSQGAMEVLRDHYDS 359 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAREKASGTAPMVVLATAHPAKFPDAVK 420 GR + DET + I G LL PHSAIGVKVA ++ PM+ LATAHPAKFPDAV+ Sbjct: 360 GRVSEDETLSMITHAHRHMGELLCPHSAIGVKVAEDQRDPATPMITLATAHPAKFPDAVE 419 Query: 421 AACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVR 458 A GV P LP + DL R E T + N+L +E ++ Sbjct: 420 QASGVRPPLPERMADLFDRAERVTRVANDLDQLEALIK 457 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: 603 Number of extensions: 22 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: 463 Length of database: 462 Length adjustment: 33 Effective length of query: 430 Effective length of database: 429 Effective search space: 184470 Effective search space used: 184470 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_085636009.1 MGEO_RS06980 (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.1059370.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-84 269.3 0.0 3.2e-84 268.9 0.0 1.1 1 NCBI__GCF_002115805.1:WP_085636009.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002115805.1:WP_085636009.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 268.9 0.0 3.2e-84 3.2e-84 15 334 .. 72 424 .. 60 430 .. 0.90 Alignments for each domain: == domain 1 score: 268.9 bits; conditional E-value: 3.2e-84 TIGR00260 15 lvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdt 84 +dl+++ ++ f ++ a v++ + +++elfhgPtlaFKD+++q +++++++al + + t+++AtsGdt NCBI__GCF_002115805.1:WP_085636009.1 72 FADLIAKAYAGFGHDARAPLVQLgNGHFLLELFHGPTLAFKDFAMQLIGQMFQEALSRSGKrvTIVGATSGDT 144 5788899999998888887777666889**************************998766556********** PP TIGR00260 85 gaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klkln 153 g+aa+ea++g v+v++LyP+g++s v +++t + +n++ la +G+FDd+q+ +k++f++ e ++kl NCBI__GCF_002115805.1:WP_085636009.1 145 GSAAIEAFRGLDAVDVFILYPHGRVSEVqRRQMTTPVESNVHALALDGTFDDCQARLKDMFNHFEfrdAVKLA 217 ****************************99*******************************9655677***** PP TIGR00260 154 svNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivr 226 vNsin++r++aq++y+f+ + lg v + vp gnfg+i++G+ +k+++ lpi+ l +a++++ di++ NCBI__GCF_002115805.1:WP_085636009.1 218 GVNSINWGRVLAQVVYYFSSAVSLG-APDRTVSFTVPTGNFGDIFAGYIAKRMG-LPIDRLVVATNQN-DILH 287 *************************.4444699**************9999999.************8.**** PP TIGR00260 227 rflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke........................ 274 r l +g ++ + +s++mdi +sn+eral+ + +r ++ + +l NCBI__GCF_002115805.1:WP_085636009.1 288 RCLTTGGYVTDSVTPSISPSMDIQVSSNFERALFdAYNRDGNAVSQLMDelkaggfhvsqgamevlrdhydsg 360 ******7777777789*****************95555555555555446777******************** PP TIGR00260 275 svsdeeileaikklaeeegyllephtavavaalkklvekg....vsatadpaKFeevvealtgn 334 +vs++e+l+ i + ++ g ll ph+a++v++ +++ + + ata+paKF+++ve +g NCBI__GCF_002115805.1:WP_085636009.1 361 RVSEDETLSMITHAHRHMGELLCPHSAIGVKVAEDQRDPAtpmiTLATAHPAKFPDAVEQASGV 424 **************************************99775444************988886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (462 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 28.26 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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