Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate YP_428315.1 Rru_A3233 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_000013085.1:YP_428315.1 Length = 470 Score = 483 bits (1243), Expect = e-141 Identities = 252/465 (54%), Positives = 318/465 (68%), Gaps = 4/465 (0%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 M+YVSTRG+APVL F D LLAGLA DGGLY+PQ +P F+ + IR +R +Y E+A+ V+ Sbjct: 1 MRYVSTRGQAPVLSFDDVLLAGLASDGGLYVPQTWPSFSEDDIRDMRALTYQELAVRVMG 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 PF G + + +V +AY F H AV PLVQ A+++V+ELFHGPTLAFKD A+Q++ Sbjct: 61 PFMGAAVTDDELTEVVEQAYAGFSHPAVAPLVQIGAHDWVMELFHGPTLAFKDYALQVVG 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 + D +L +RG R T+VGATSGDTG AAIEA R+ D+ IL P GRVS VQ+RQMT+ Sbjct: 121 GLFDLILTRRGSRITVVGATSGDTGSAAIEACRDREAVDVIILLPKGRVSEVQRRQMTTV 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 SNVHA+ +EG FDDCQ LVK +FND F ++L+ VNSINWARIM Q VYYF AAL Sbjct: 181 TSSNVHAIEVEGTFDDCQALVKALFNDPAFRSEVNLAAVNSINWARIMAQTVYYFWAALQ 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LGAPDR++ F+VPTGNFG++ AGY AKRMGLPI++L++ +N NDIL+R LE+G + RGV Sbjct: 241 LGAPDRSLGFSVPTGNFGNVLAGYCAKRMGLPIDRLVVGSNSNDILTRFLETGTMQSRGV 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 QT SPSMDIQ+SSNFERLLFE RD+A V LM +GG+T+ + F Sbjct: 301 VQTHSPSMDIQVSSNFERLLFEVVDRDSAEVERLMAQFALTGGYTLDSALHQELLGLFRG 360 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVARE---KASGTAPMVVLATAHPAKFPD 417 R D T I + + G +LDPHS IGV RE + +GT PMV LATAHPAKF D Sbjct: 361 FRVDNDATLRAIAELYAATGMILDPHSVIGVIAGREAGHRDTGT-PMVALATAHPAKFAD 419 Query: 418 AVKAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSR 462 V+ A G P LP L DL+ R E + N+ + V+ VR SR Sbjct: 420 VVEQATGQRPALPGALSDLLTRPERRAEVANDPEAVKALVRSLSR 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: 534 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: 470 Length adjustment: 33 Effective length of query: 430 Effective length of database: 437 Effective search space: 187910 Effective search space used: 187910 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 YP_428315.1 Rru_A3233 (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.5700.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-88 283.4 0.0 2e-88 282.7 0.0 1.2 1 lcl|NCBI__GCF_000013085.1:YP_428315.1 Rru_A3233 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013085.1:YP_428315.1 Rru_A3233 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 282.7 0.0 2e-88 2e-88 11 335 .. 68 428 .. 60 432 .. 0.92 Alignments for each domain: == domain 1 score: 282.7 bits; conditional E-value: 2e-88 TIGR00260 11 tekdlvdlaegstelfrspklaeevga.enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcA 79 t+ +l ++ e+ ++ f p++a v++ +v elfhgPtlaFKD +lq v+ l+ +l + tv++A lcl|NCBI__GCF_000013085.1:YP_428315.1 68 TDDELTEVVEQAYAGFSHPAVAPLVQIgAHDWVMELFHGPTLAFKDYALQVVGGLFDLILTRRGSriTVVGA 139 47788999999*********996666665889*************************9988766557***** PP TIGR00260 80 tsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke.. 148 tsGdtg+aa+ea + ++ v+v++L+Pkg++s v +++t+ +n++ ++++G+FDd+q+lvk++f+d lcl|NCBI__GCF_000013085.1:YP_428315.1 140 TSGDTGSAAIEACRDREAVDVIILLPKGRVSEVqRRQMTTVTSSNVHAIEVEGTFDDCQALVKALFNDPAfr 211 *********************************99*******************************965567 PP TIGR00260 149 .klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaae 219 +++l +vNsin+ari aq +y+f ++ qlg + ++vp gnfg++l+G+++k+++ lpi+ l + ++ lcl|NCBI__GCF_000013085.1:YP_428315.1 212 sEVNLAAVNSINWARIMAQTVYYFWAALQLG-APDRSLGFSVPTGNFGNVLAGYCAKRMG-LPIDRLVVGSN 281 7*******************88888888999.3445699********************9.*********** PP TIGR00260 220 gaadivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke................ 274 ++ di++rfl++g ++ + ++T s++mdi +sn+er+l+ ++ r +++e l + lcl|NCBI__GCF_000013085.1:YP_428315.1 282 SN-DILTRFLETGTMQSRGVVQTHSPSMDIQVSSNFERLLFeVVDRDSAEVERLMAqfaltggytldsalhq 352 *8.**********99999999*******************99************88**************** PP TIGR00260 275 .........svsdeeileaikklaeeegyllephtavavaalkklvekgvs......atadpaKFeevveal 331 +v ++++l+ai +l++ g++l+ph+ ++v a ++ +++ ata+paKF++vve lcl|NCBI__GCF_000013085.1:YP_428315.1 353 ellglfrgfRVDNDATLRAIAELYAATGMILDPHSVIGVIAGREAGHRDTGtpmvalATAHPAKFADVVEQA 424 ***************************************999988877733345678*************99 PP TIGR00260 332 tgnk 335 tg+ lcl|NCBI__GCF_000013085.1:YP_428315.1 425 TGQR 428 9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (470 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 12.71 // [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