Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate PP_1471 PP_1471 Threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >FitnessBrowser__Putida:PP_1471 Length = 469 Score = 503 bits (1294), Expect = e-147 Identities = 260/462 (56%), Positives = 322/462 (69%), Gaps = 2/462 (0%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 M+Y+STRG+AP L F D LLAGLA DGGLY+P+ P+FT E+I + G Y E+A V+ Sbjct: 1 MRYISTRGQAPALNFEDVLLAGLASDGGLYVPENLPRFTQEEIASWAGLPYHELAFRVMR 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 PF G I ADF++++ E YG F H AV PL Q ++NE+VLELFHGPTLAFKD A+QLL Sbjct: 61 PFVEGSIADADFKKILEETYGEFAHAAVAPLRQLNSNEWVLELFHGPTLAFKDFALQLLG 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 R++D+VLA+R ER I+GATSGDTG AAIE DN DIFIL P+ RVS VQ+RQMT+ Sbjct: 121 RLLDHVLAKRNERVVIIGATSGDTGSAAIEGCRRCDNVDIFILHPHQRVSEVQRRQMTTI 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 N+H ++IEGNFDDCQ +VK F D F L VNSINWARIM Q+VYYF AAL Sbjct: 181 FGDNIHNIAIEGNFDDCQEMVKASFADQSFLKGTRLVAVNSINWARIMAQIVYYFHAALQ 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LG P R+V+F+VPTGNFGDIFAGY+A+ MGLP+ QLI+ATN NDIL R + Y + Sbjct: 241 LGGPARSVAFSVPTGNFGDIFAGYLARNMGLPVSQLIVATNRNDILHRFMSGNQYVKETL 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 T SPSMDI +SSNFERLLF+ HGR+ A+ LM KQ GGF++ + + R F + Sbjct: 301 HATLSPSMDIMVSSNFERLLFDLHGRNGGAIAELMANFKQGGGFSVEQDRWTEARKLFDS 360 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVARE-KASGTAPMVVLATAHPAKFPDAV 419 + ++T TI V + G +LDPH+AIGVK ARE + S PMVVL TAHP KFP+AV Sbjct: 361 LAVSDEQTCETIAEVFAATGEVLDPHTAIGVKAARECRRSLDTPMVVLGTAHPVKFPEAV 420 Query: 420 -KAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHH 460 KA G +LPA L DL R+E TVL N+LK V+ +V H Sbjct: 421 EKAGVGKALELPAHLSDLFSREERCTVLANDLKAVQGFVSQH 462 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: 569 Number of extensions: 20 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: 469 Length adjustment: 33 Effective length of query: 430 Effective length of database: 436 Effective search space: 187480 Effective search space used: 187480 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 PP_1471 PP_1471 (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.11625.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-86 276.6 0.0 1.9e-86 276.3 0.0 1.1 1 lcl|FitnessBrowser__Putida:PP_1471 PP_1471 Threonine synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_1471 PP_1471 Threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 276.3 0.0 1.9e-86 1.9e-86 12 337 .. 69 430 .. 58 433 .. 0.91 Alignments for each domain: == domain 1 score: 276.3 bits; conditional E-value: 1.9e-86 TIGR00260 12 ekdlvdlaegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsG 82 ++d +++ e + f+ ++a +++ + n +v+elfhgPtlaFKD++lq ++ ll ++l + ne ++++AtsG lcl|FitnessBrowser__Putida:PP_1471 69 DADFKKILEETYGEFAHAAVAplRQLNS-NEWVLELFHGPTLAFKDFALQLLGRLLDHVLAKRNErvVIIGATSG 142 7888888888888888887776688888.99*******************************9999999****** PP TIGR00260 83 dtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klkln 153 dtg+aa+e+ ++ nv++++L P+ ++s v +++t n++ +ai+G+FDd+q++vk+ f d+ + l+ lcl|FitnessBrowser__Putida:PP_1471 143 DTGSAAIEGCRRCDNVDIFILHPHQRVSEVqRRQMTTIFGDNIHNIAIEGNFDDCQEMVKASFADQSflkGTRLV 217 ******************************99*******************************977779899*** PP TIGR00260 154 svNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrf 228 +vNsin+ari aq++y+f ++ qlg+ + v+++vp gnfg+i++G+l+ +++ lp+ l +a++ + di++rf lcl|FitnessBrowser__Putida:PP_1471 218 AVNSINWARIMAQIVYYFHAALQLGGPA-RSVAFSVPTGNFGDIFAGYLARNMG-LPVSQLIVATNRN-DILHRF 289 *************************655.57****************9999999.**99999999998.****** PP TIGR00260 229 lksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke.........................svs 277 + + + ++ + +Tls++mdi +sn+er+l+ l r++g + +l + +vs lcl|FitnessBrowser__Putida:PP_1471 290 MSGNQYVKETLHATLSPSMDIMVSSNFERLLFdLHGRNGGAIAELMAnfkqgggfsveqdrwtearklfdslAVS 364 877777777777*******************999***********88**************************** PP TIGR00260 278 deeileaikklaeeegyllephtavavaalkklvekg.....vsatadpaKFeevve.altgnklk 337 de++ e+i ++ + g +l+phta++v+a ++ + v +ta+p KF+e+ve a g+ l+ lcl|FitnessBrowser__Putida:PP_1471 365 DEQTCETIAEVFAATGEVLDPHTAIGVKAARECRRSLdtpmvVLGTAHPVKFPEAVEkAGVGKALE 430 *****************************987766544455334************9777777665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (469 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 11.83 // [ok]
This GapMind analysis is from Apr 09 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