Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_036258646.1 DL86_RS04035 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_000746085.1:WP_036258646.1 Length = 472 Score = 547 bits (1410), Expect = e-160 Identities = 275/460 (59%), Positives = 337/460 (73%), Gaps = 2/460 (0%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 MKY+STRGEAP + F++ L+AGLA DGGLYLP+ YP+F I G+SY +VA A++ Sbjct: 1 MKYISTRGEAPPVSFTETLIAGLAPDGGLYLPESYPEFGHGAIADFAGQSYADVAQAIVA 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 PF GEI M+ AY +FRH AV PLVQ DAN F LELFHG TLAFKD+AMQLLA Sbjct: 61 PFVAGEIEPPILRGMIDAAYASFRHPAVAPLVQIDANLFALELFHGRTLAFKDIAMQLLA 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 R++D+VL RG+RATIVGATSGDTG AAIEAF G D+FIL+P+GRVS VQ+RQMT+ Sbjct: 121 RLIDHVLQARGQRATIVGATSGDTGAAAIEAFRGLAQVDVFILYPHGRVSEVQRRQMTTV 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 N+HA+++EG FDD Q +K +FN + L LSGVNSINW RI+ Q VYYFT+A++ Sbjct: 181 EGDNIHAIALEGTFDDAQACIKALFNHANLREELKLSGVNSINWVRILAQTVYYFTSAVA 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LG P+R +S+ VPTGNFGDIFAG++AKRMGLPIE+L+IATN NDIL+R L SGAY + GV Sbjct: 241 LGGPNRKISYVVPTGNFGDIFAGWIAKRMGLPIERLVIATNSNDILARALASGAYGVTGV 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 T SPSMDIQ+SSNFERLLFEAHGR+A A+R LM L+QSGGFTI PL AIR+EF A Sbjct: 301 HATQSPSMDIQVSSNFERLLFEAHGRNAGALRTLMARLRQSGGFTIEPAPLKAIRAEFDA 360 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAR--EKASGTAPMVVLATAHPAKFPDA 418 ET I + GYL DPH+A+G+ AR + +G P+VVL TAHPAKFPDA Sbjct: 361 FSVNETETTQEIARAWREAGYLADPHTAVGINAARRAQAQNGKTPLVVLGTAHPAKFPDA 420 Query: 419 VKAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVR 458 + A G P LPA L L +KE FT+L N+ K +E ++R Sbjct: 421 IALATGQRPPLPAHLAGLFDKKEHFTILPNDQKEIERFIR 460 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: 602 Number of extensions: 19 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: 472 Length adjustment: 33 Effective length of query: 430 Effective length of database: 439 Effective search space: 188770 Effective search space used: 188770 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_036258646.1 DL86_RS04035 (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.3198.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-87 280.2 0.0 1.6e-87 279.7 0.0 1.0 1 lcl|NCBI__GCF_000746085.1:WP_036258646.1 DL86_RS04035 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000746085.1:WP_036258646.1 DL86_RS04035 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 279.7 0.0 1.6e-87 1.6e-87 21 335 .. 78 428 .. 68 432 .. 0.92 Alignments for each domain: == domain 1 score: 279.7 bits; conditional E-value: 1.6e-87 TIGR00260 21 gstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtga 86 ++ fr p++a v++ nl+ +elfhg tlaFKD+++q +a l+ ++l++ + t+++AtsGdtga lcl|NCBI__GCF_000746085.1:WP_036258646.1 78 AAYASFRHPAVAPLVQIdANLFALELFHGRTLAFKDIAMQLLARLIDHVLQARGQraTIVGATSGDTGA 146 578999*****98888888******************************99765556************ PP TIGR00260 87 aaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeife...dkeklk 151 aa+ea++g a v+v++LyP+g++s v +++t+ n++ +a +G+FDdaq+ +k++f+ +e+lk lcl|NCBI__GCF_000746085.1:WP_036258646.1 147 AAIEAFRGLAQVDVFILYPHGRVSEVqRRQMTTVEGDNIHAIALEGTFDDAQACIKALFNhanLREELK 215 **************************99*******************************9554555*** PP TIGR00260 152 lnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaeg 220 l+ vNsin+ ri+aq +y+f + +lg + k+ +vp gnfg+i++G+ +k+++ lpie l ia+++ lcl|NCBI__GCF_000746085.1:WP_036258646.1 216 LSGVNSINWVRILAQTVYYFTSAVALG-GPNRKISYVVPTGNFGDIFAGWIAKRMG-LPIERLVIATNS 282 ****************99999999999.56679****************9999999.************ PP TIGR00260 221 aadivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke.............. 274 + di+ r l sg +T s++mdi +sn+er+l+ + r+ g l l + lcl|NCBI__GCF_000746085.1:WP_036258646.1 283 N-DILARALASGAYGVTGVHATQSPSMDIQVSSNFERLLFeAHGRNAGALRTLMArlrqsggftiepap 350 9.**********66666666*******************9888899999999988************** PP TIGR00260 275 ...........svsdeeileaikklaeeegyllephtavavaalkklvekg.....vs.atadpaKFee 326 sv++ e++++i ++ +e gyl++phtav+++a ++ +++ v +ta+paKF++ lcl|NCBI__GCF_000746085.1:WP_036258646.1 351 lkairaefdafSVNETETTQEIARAWREAGYLADPHTAVGINAARRAQAQNgktplVVlGTAHPAKFPD 419 *******************************************9998777766554227********** PP TIGR00260 327 vvealtgnk 335 +++ tg+ lcl|NCBI__GCF_000746085.1:WP_036258646.1 420 AIALATGQR 428 ***999986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (472 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: 00:00:00.03 # Mc/sec: 4.84 // [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