Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_068462681.1 APY04_RS11275 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_001541235.1:WP_068462681.1 Length = 468 Score = 536 bits (1381), Expect = e-157 Identities = 278/464 (59%), Positives = 333/464 (71%), Gaps = 2/464 (0%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 M Y+STRGEAP+LGF D +LAGLARDGGLY+P+ +P + E+I + G + +VA V+ Sbjct: 1 MNYISTRGEAPLLGFEDVVLAGLARDGGLYVPETWPTLSPEKIASFAGMPFADVAAEVIA 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 PFTGG I + M +AY F H AV PLVQ N FVLELFHGPTLAFKDVAMQLLA Sbjct: 61 PFTGGAITRDELRAMAADAYSGFGHSAVTPLVQIGPNRFVLELFHGPTLAFKDVAMQLLA 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 R+M+ VLA RG+RATIVGATSGDTGGAAIEAF G + D+ ILFP GRVS VQ+R MT+ Sbjct: 121 RLMERVLAARGQRATIVGATSGDTGGAAIEAFRGSPHVDVAILFPEGRVSDVQRRMMTTP 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 NVHA+S+ GNFDDCQ+LVK MFND F D +SL+GVNSINWARI QV YYF A + Sbjct: 181 TEGNVHAISVRGNFDDCQSLVKAMFNDHGFRDRISLAGVNSINWARIAAQVTYYFVAGAA 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LGAP R VSF VPTGNFGDIFAGYVAKRMGLPIE+L+IA+N NDIL RTL++GAY+MRGV Sbjct: 241 LGAPFRPVSFVVPTGNFGDIFAGYVAKRMGLPIEKLVIASNVNDILPRTLDNGAYQMRGV 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 T+SPSMDIQISSNFER LFEA GRDA +R M L+++GGF + A+R EF A Sbjct: 301 VATSSPSMDIQISSNFERYLFEASGRDAPFIRAKMSALRETGGFDLGPVK-DAMRREFGA 359 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVA-REKASGTAPMVVLATAHPAKFPDAV 419 ++ + A I + GY+ DPH+A + A R G AP VVL+TAHPAKFPDA+ Sbjct: 360 SAASEQDVAEAIMRTRAATGYVADPHTACAIVAAERVLGEGGAPQVVLSTAHPAKFPDAM 419 Query: 420 KAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSRA 463 + G P LP L LM KE FT + N++ E +V +RA Sbjct: 420 EDITGERPGLPPRLSTLMTDKERFTTIDNDIAAAEAHVEALTRA 463 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: 629 Number of extensions: 27 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: 468 Length adjustment: 33 Effective length of query: 430 Effective length of database: 435 Effective search space: 187050 Effective search space used: 187050 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_068462681.1 APY04_RS11275 (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.23787.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-85 271.7 0.0 6e-85 271.3 0.0 1.1 1 lcl|NCBI__GCF_001541235.1:WP_068462681.1 APY04_RS11275 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001541235.1:WP_068462681.1 APY04_RS11275 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 271.3 0.0 6e-85 6e-85 16 334 .. 73 425 .. 65 430 .. 0.88 Alignments for each domain: == domain 1 score: 271.3 bits; conditional E-value: 6e-85 TIGR00260 16 vdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAts 81 ++a+ ++ f +++ v++ n +v+elfhgPtlaFKD+++q +a l++++l + + t+++Ats lcl|NCBI__GCF_001541235.1:WP_068462681.1 73 RAMAADAYSGFGHSAVTPLVQIgPNRFVLELFHGPTLAFKDVAMQLLARLMERVLAARGQraTIVGATS 141 56667777778888888666666799***************************876544445******* PP TIGR00260 82 GdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalae.nakvlaikGdFDdaqdlvkeifedke. 148 Gdtg aa+ea++g + v+v +L P+g++s v+ +++t++ e n++ ++++G+FDd+q lvk++f+d+ lcl|NCBI__GCF_001541235.1:WP_068462681.1 142 GDTGGAAIEAFRGSPHVDVAILFPEGRVSDVQRRMMTTPTEgNVHAISVRGNFDDCQSLVKAMFNDHGf 210 *******************************999888876538*********************96555 PP TIGR00260 149 ..klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpiekla 215 + l vNsin+ari+aq+ty+f + ++lg v ++vp gnfg+i++G+++k+++ lpiekl lcl|NCBI__GCF_001541235.1:WP_068462681.1 211 rdRISLAGVNSINWARIAAQVTYYFVAGAALG-APFRPVSFVVPTGNFGDIFAGYVAKRMG-LPIEKLV 277 779*****************************.66678******************99999.******* PP TIGR00260 216 iaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnledlke.......... 274 ia++ + di++r l +g + + ++T s++mdi ++sn+er l+ a ++ + k lcl|NCBI__GCF_001541235.1:WP_068462681.1 278 IASNVN-DILPRTLDNGAYQMRGVVATSSPSMDIQISSNFERYLFEASGRDAPFIRAKMsalretggfd 345 ***998.**********66666666*****************99944443333332222455569**** PP TIGR00260 275 ...............svsdeeileaikklaeeegyllephtavavaalkklvekg...vs..atadpaK 323 ++s++++ eai++ + gy+++phta a+ a ++ + +g + +ta+paK lcl|NCBI__GCF_001541235.1:WP_068462681.1 346 lgpvkdamrrefgasAASEQDVAEAIMRTRAATGYVADPHTACAIVAAERVLGEGgapQVvlSTAHPAK 414 **************999************************************998873367******* PP TIGR00260 324 Feevvealtgn 334 F+++ e +tg+ lcl|NCBI__GCF_001541235.1:WP_068462681.1 415 FPDAMEDITGE 425 *********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (468 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: 9.09 // [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