Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_085769774.1 B1812_RS00100 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_002117405.1:WP_085769774.1 Length = 471 Score = 498 bits (1282), Expect = e-145 Identities = 255/466 (54%), Positives = 329/466 (70%), Gaps = 5/466 (1%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 M Y+STRG AP L F + +L GLA DGGLY+P+ YP ++I A G+ Y E A ++ Sbjct: 1 MDYISTRGRAPELPFDEVVLTGLAADGGLYVPRRYPTVDHKEIAAFAGRPYAETAETLIA 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 PFT G +P + R AY TF H AV PL Q N FVLELFHGPTLAFKD+AMQLL Sbjct: 61 PFTEG-LPRDLLHQAARGAYATFSHAAVAPLTQIGDNLFVLELFHGPTLAFKDLAMQLLG 119 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 R+MD +L RG RATIVGATSGDTG AAIEAF GR N D+FIL+P+GRVS VQ+RQMT+ Sbjct: 120 RLMDALLETRGLRATIVGATSGDTGAAAIEAFRGRANVDVFILYPDGRVSDVQRRQMTTV 179 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 +NVHA++++G+FDD Q L+KG+F D F + L+GVNSINWAR++ Q+VYYFT+A++ Sbjct: 180 ADANVHAIALDGSFDDAQTLLKGLFRDESFRRGVGLAGVNSINWARVVAQMVYYFTSAVT 239 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LG+P R +SF VPTGNFGD+ AGYVAKRMGLP+E+LI+ATN+NDIL+R L +G YE RGV Sbjct: 240 LGSPHRKISFAVPTGNFGDVLAGYVAKRMGLPVERLIVATNENDILARALATGRYEPRGV 299 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 T SPSMDIQ+SSNFERLLF+A GRD+ +V + L + G F I L A+R +F A Sbjct: 300 TPTQSPSMDIQLSSNFERLLFDAIGRDSGSVVQAFEALDRDGAFEIPPGALRAVREDFDA 359 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAR---EKASGTAPMVVLATAHPAKFPD 417 ET A I GY++DPH+A GV+ AR EK+ GT P+V L+TAHPAKFPD Sbjct: 360 LAVNEAETQAEIARTYRDSGYVIDPHTATGVRAARAQLEKSPGT-PVVALSTAHPAKFPD 418 Query: 418 AVKAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSRA 463 A++ A G+ + P L +++ KE + + + V+ ++ H+RA Sbjct: 419 AIERAIGLRIEPPPRLAPVLEGKERIARMKRDSETVKRFILEHARA 464 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: 575 Number of extensions: 19 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: 471 Length adjustment: 33 Effective length of query: 430 Effective length of database: 438 Effective search space: 188340 Effective search space used: 188340 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_085769774.1 B1812_RS00100 (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.12193.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-90 289.9 0.0 1.8e-90 289.5 0.0 1.0 1 lcl|NCBI__GCF_002117405.1:WP_085769774.1 B1812_RS00100 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002117405.1:WP_085769774.1 B1812_RS00100 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 289.5 0.0 1.8e-90 1.8e-90 18 331 .. 74 423 .. 61 429 .. 0.91 Alignments for each domain: == domain 1 score: 289.5 bits; conditional E-value: 1.8e-90 TIGR00260 18 laegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsG 82 a g +++f ++a ++g nl+v+elfhgPtlaFKD+++q ++ l+ ++le t+++AtsG lcl|NCBI__GCF_002117405.1:WP_085769774.1 74 AARGAYATFSHAAVAplTQIGD-NLFVLELFHGPTLAFKDLAMQLLGRLMDALLETRGLraTIVGATSG 141 4567788887777665566666.******************************99764345******** PP TIGR00260 83 dtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke.. 148 dtgaaa+ea++g+anv+v++LyP+g++s v +++t+ + n++ +a +G FDdaq+l+k +f d+ lcl|NCBI__GCF_002117405.1:WP_085769774.1 142 DTGAAAIEAFRGRANVDVFILYPDGRVSDVqRRQMTTVADANVHAIALDGSFDDAQTLLKGLFRDESfr 210 ******************************99*******************************976668 PP TIGR00260 149 .klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklai 216 ++l vNsin+ar+ aq++y+f + lg k+ ++vp gnfg++l+G+++k+++ lp+e l + lcl|NCBI__GCF_002117405.1:WP_085769774.1 211 rGVGLAGVNSINWARVVAQMVYYFTSAVTLG-SPHRKISFAVPTGNFGDVLAGYVAKRMG-LPVERLIV 277 89****************************9.78889******************99999.******** PP TIGR00260 217 aaegaadivrrflksgdlepkedkeTlstAmdignpsnverale..larrslgnledlke......... 274 a++++ di+ r l +g ep+ T s++mdi +sn+er+l+ + r s+ +++ ++ lcl|NCBI__GCF_002117405.1:WP_085769774.1 278 ATNEN-DILARALATGRYEPRGVTPTQSPSMDIQLSSNFERLLFdaIGRDSGSVVQAFEAldrdgafei 345 ****9.**********99999999*******************99666777777888877999****** PP TIGR00260 275 ...............svsdeeileaikklaeeegyllephtavavaalkklvekg....vs..atadpa 322 +v+++e+ +i + ++ gy+++phta++v+a + ++ek+ v +ta+pa lcl|NCBI__GCF_002117405.1:WP_085769774.1 346 ppgalravredfdalAVNEAETQAEIARTYRDSGYVIDPHTATGVRAARAQLEKSpgtpVValSTAHPA 414 *******************************************************87662268****** PP TIGR00260 323 KFeevveal 331 KF++++e+ lcl|NCBI__GCF_002117405.1:WP_085769774.1 415 KFPDAIERA 423 ****99843 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (471 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: 9.39 // [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