Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate AO353_04350 AO353_04350 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >FitnessBrowser__pseudo3_N2E3:AO353_04350 Length = 469 Score = 515 bits (1326), Expect = e-150 Identities = 266/462 (57%), Positives = 324/462 (70%), 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 IP ADF++++ E YG F H AV PL Q ++NE+VLELFHGPTLAFKD A+QLL Sbjct: 61 PFVSGSIPDADFKKILEETYGVFSHSAVAPLRQLNSNEWVLELFHGPTLAFKDFALQLLG 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 R++DYVL +RGER IVGATSGDTG AAIE +N DIFIL P+ RVS VQ+RQMT+ Sbjct: 121 RLLDYVLEKRGERVVIVGATSGDTGSAAIEGCKHCENVDIFILHPHNRVSEVQRRQMTTI 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 N+H ++IEGNFDDCQ +VK F D F L VNSINWARIM Q+VYYF AAL Sbjct: 181 FGENIHNIAIEGNFDDCQEMVKASFADQSFLKGTRLVAVNSINWARIMAQIVYYFHAALQ 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LG P R+VSF+VPTGNFGDIFAGY+A+ MGLPI QLI+ATN NDIL R + Y + Sbjct: 241 LGGPARSVSFSVPTGNFGDIFAGYLARNMGLPINQLIVATNRNDILHRFMSGNQYVKETL 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 T SPSMDI +SSNFERLLF+ HGR+ AA+ GLM KQ GGF++ ++ + R F + Sbjct: 301 HATLSPSMDIMVSSNFERLLFDLHGRNGAAIAGLMDTFKQGGGFSVEQERWTEARKLFDS 360 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVARE-KASGTAPMVVLATAHPAKFPDAV 419 +T TI V + G LLDPH+AIGVK ARE + S PMV+L TAHP KFP+AV Sbjct: 361 LAVDDAQTCETIAEVFEQTGELLDPHTAIGVKAARECRRSLDIPMVILGTAHPVKFPEAV 420 Query: 420 -KAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHH 460 KA G +LPA L DL +R E TVL N+LK V+ +V H Sbjct: 421 EKAGVGKALELPAHLSDLFERDERCTVLPNDLKAVQAFVSQH 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: 563 Number of extensions: 18 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 AO353_04350 AO353_04350 (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.27631.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-85 272.1 0.0 4.4e-85 271.8 0.0 1.1 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_04350 AO353_04350 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_04350 AO353_04350 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 271.8 0.0 4.4e-85 4.4e-85 10 337 .. 67 430 .. 58 433 .. 0.92 Alignments for each domain: == domain 1 score: 271.8 bits; conditional E-value: 4.4e-85 TIGR00260 10 vtekdlvdlaegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelg 72 ++++d +++ e + +f ++a +++ + n +v+elfhgPtlaFKD++lq ++ ll ++le+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_04350 67 IPDADFKKILEETYGVFSHSAVAplRQLNS-NEWVLELFHGPTLAFKDFALQLLGRLLDYVLEKR 130 448899999999999999998887788888.99*****************************998 PP TIGR00260 73 ne..tvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFD 134 e ++++AtsGdtg+aa+e+ + +nv++++L P+ ++s v +++t en++ +ai+G+FD lcl|FitnessBrowser__pseudo3_N2E3:AO353_04350 131 GErvVIVGATSGDTGSAAIEGCKHCENVDIFILHPHNRVSEVqRRQMTTIFGENIHNIAIEGNFD 195 777899************************************99********************* PP TIGR00260 135 daqdlvkeifedke...klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfga 196 d+q++vk+ f d+ + l++vNsin+ari aq++y+f ++ qlg+ + v ++vp gnfg+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_04350 196 DCQEMVKASFADQSflkGTRLVAVNSINWARIMAQIVYYFHAALQLGGPA-RSVSFSVPTGNFGD 259 **********977779899****************************655.57************ PP TIGR00260 197 ilkGflekkelglpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnverale. 260 i++G+l+ +++ lpi+ l +a++ + di++rf+ + + ++ + +Tls++mdi +sn+er+l+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_04350 260 IFAGYLARNMG-LPINQLIVATNRN-DILHRFMSGNQYVKETLHATLSPSMDIMVSSNFERLLFd 322 ****9999999.******9999998.******877777777777*******************99 PP TIGR00260 261 larrslgnledlke.........................svsdeeileaikklaeeegyllepht 300 l r+++ + l +v d+++ e+i ++ e+ g ll+pht lcl|FitnessBrowser__pseudo3_N2E3:AO353_04350 323 LHGRNGAAIAGLMDtfkqgggfsveqerwtearklfdslAVDDAQTCETIAEVFEQTGELLDPHT 387 999999999988669999*********************************************** PP TIGR00260 301 avavaalkklvekg...vs..atadpaKFeevve.altgnklk 337 a++v+a ++ + + +ta+p KF+e+ve a g+ l+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_04350 388 AIGVKAARECRRSLdipMVilGTAHPVKFPEAVEkAGVGKALE 430 ******998887666652257************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.60 // [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