protein functional site prediction
DESCRIPTION
Protein Functional Site Prediction. The identification of protein regions responsible for stability and function is an especially important post-genomic problem - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/1.jpg)
Protein Functional Site Prediction
• The identification of protein regions responsible for stability and function is an especially important post-genomic problem
• With the explosion of genomic data from recent sequencing efforts, protein functional site prediction from only sequence is an increasingly important bioinformatic endeavor.
![Page 2: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/2.jpg)
What is a “Functional Site”?
• Defining what constitutes a “functional site” is not trivial
• Residues that include and cluster around known functionality are clear candidates for functional sites
• We define a functional site as catalytic residues, binding sites, and regions that clustering around them.
![Page 3: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/3.jpg)
Protein
![Page 4: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/4.jpg)
Protein + Ligand
![Page 5: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/5.jpg)
Functional Sites (FS)
![Page 6: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/6.jpg)
Regions that Cluster Around FS
![Page 7: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/7.jpg)
Phylogenetic motifs
• PMs are short sequence fragments that conserve the overall familial phylogeny
• Are they functional?
• How do we detect them?
![Page 8: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/8.jpg)
Phylogenetic motifs
• PMs are short sequence fragments that conserve the overall familial phylogeny
• Are they functional?• How do we detect them? • First we design a simple heuristic to find
them• Then we see if the detected sites are
functional
![Page 9: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/9.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Whole Tree
![Page 10: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/10.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Whole Tree
![Page 11: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/11.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Windowed Tree Whole Tree
![Page 12: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/12.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 6
Windowed Tree Whole Tree
![Page 13: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/13.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 8
Windowed Tree Whole Tree
![Page 14: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/14.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 4
Windowed Tree Whole Tree
![Page 15: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/15.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 6
Windowed Tree Whole Tree
![Page 16: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/16.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 8
Windowed Tree Whole Tree
![Page 17: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/17.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 6
Windowed Tree Whole Tree
![Page 18: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/18.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 6
Windowed Tree Whole Tree
![Page 19: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/19.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 0
Windowed Tree Whole Tree
![Page 20: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/20.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 6
Windowed Tree Whole Tree
![Page 21: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/21.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 6
Windowed Tree Whole Tree
![Page 22: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/22.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 8
Windowed Tree Whole Tree
![Page 23: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/23.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 0
Windowed Tree Whole Tree
![Page 24: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/24.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 6
Windowed Tree Whole Tree
![Page 25: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/25.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 6
Windowed Tree Whole Tree
![Page 26: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/26.jpg)
Scan for Similar Trees
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Partition Metric Score: 6
Windowed Tree Whole Tree
![Page 27: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/27.jpg)
Phylogenetic Motif Identification
• Compare all windowed trees with whole tree and keep track of the partition metric scores
• Normalize all partition metric scores by calculating z-scores
• Call these normalized scores Phylogenetic Similarity Z-scores (PSZ)
• Set a PSZ threshold for identifying windows that represent phylogenetic motifs
![Page 28: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/28.jpg)
Set PSZ Threshold
![Page 29: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/29.jpg)
Regions of PMs
![Page 30: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/30.jpg)
Map PMs to the Structure
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
![Page 31: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/31.jpg)
Map PMs to the Structure
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Set PSZ Threshold
![Page 32: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/32.jpg)
Map PMs to the Structure
Map
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Set PSZ Threshold
![Page 33: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/33.jpg)
Map PMs to the Structure
Map
2DBL DVVMTQIPLSLPVNL GDQASIS CRSSQSLIHSNGNTYLH WYLQKPGQS PKLLMYKVSNRF 1NCA DIVMTQSPKFMSTSV GDRVTIT CKASQ----- DVSTAVV WYQQKPGQS PKLLIYWASTRH 2JEL DVLMTQTPLSLPVSL GDQASIS CRSSQSIVHGNGNTYLE WYLQKPGQS PKLLIYKISNRF 2IGF DVLMTQTPLSLPVSL GDQASIS CRSNQTILLSDGDTYLE WYLQKPGQS PKLLIYKVSNRF 3HFM DIVLTQSPATLSVTP GNSVSLS CRASQS ----- IGNNLH WYQQKSHES PRLLIKYASQSI 3HFL DIVLTQSPAIMSASP GEKVTMT CSASSS ------ VNYMY WYQQKSGTS PKRWIYDT SKLA 1NGP QAVV TQES-ALTTSP GETVTLT CRSSTG --AVTTSNYAN WVQEKPDHLFTG LIGGTNNRA 2DBL YGVPDRFSGS GSGTDFTLKISRVEA EDLGIYFCS QSSHVPPTFGGGTKLEIK -RADAAPT 1NCA IGVPDRFAGSGSGTDYTLTISSVQA EDLALYYCQQHYSPPWTFGGGTKLEIK -RADAAPT 2JEL SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPYTFGGGTKLEIK -RADAAPT 2IGF SGVPDRFSGS GSGTDFTLKISRVEA EDLGVYYCFQGSHVPPTFGGGTKLEIK -RADAAPT 3HFM SGIPSRFSGS GSGTDFTLSINSVET EDFGMYFCQQSNSWPYTFGGGTKLEIK -RADAAPT 3HFL SGVPVRFSGS GSGTSYSLTISSMET EDAATYYCQQWGRNP-TFGGGTKLEIK -RADAAPT 1NGP PGVPARFSGS LIGDKAA LTITGAQT EDEAIYFCALWYSNHWV FGGGTKL TVLGQPKSSPS 2DBL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR ---QIQLVQSGPELKKPGETVKI 1NCA MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECQI QLVQSGPELKKPGETVKI 2JEL MSSTLTLTKDEYERHNSYTCEATHKTS DSPIVKSFNR N--QVQLAQSGPELVRPGVSVKI 2IGF MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECEV QLVESGGDLVKPGGSLK L 3HFM MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECDV QLQESGPSLVKPSQTLS L 3HFL MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR NECXV QLQQSGAELMKPGASVKI 1NGP ASSYLTLTARAWERHSSYSCQVTHEGHT--VEKSLSR---QVQLQQPGAELVKPGASVK L
Set PSZ Threshold
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PMs in Various Structures
![Page 35: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/35.jpg)
PMs and Traditional Motifs
![Page 36: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/36.jpg)
TIM
Phylogenetic Similarity False Positive Expectation
![Page 37: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/37.jpg)
TIM
Phylogenetic Similarity False Positive Expectation
![Page 38: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/38.jpg)
TIM
Phylogenetic Similarity False Positive Expectation
![Page 39: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/39.jpg)
TIM
Phylogenetic Similarity False Positive Expectation
![Page 40: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/40.jpg)
Cytochrome P450
Phylogenetic Similarity False Positive Expectation
![Page 41: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/41.jpg)
Cytochrome P450
Phylogenetic Similarity False Positive Expectation
![Page 42: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/42.jpg)
Enolase
Phylogenetic Similarity False Positive Expectation
![Page 43: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/43.jpg)
Glycerol Kinase
Phylogenetic Similarity False Positive Expectation
![Page 44: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/44.jpg)
Glycerol Kinase
Phylogenetic Similarity False Positive Expectation
![Page 45: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/45.jpg)
Myoglobin
Phylogenetic Similarity False Positive Expectation
![Page 46: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/46.jpg)
Myoglobin
Phylogenetic Similarity False Positive Expectation
![Page 47: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/47.jpg)
Evaluating alignments
• For a given alignment compute the PMs
• Determine the number of functional PMs
• Those identifying more functional PMs will be classified as better alignments
![Page 48: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/48.jpg)
Protein datasets
![Page 49: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/49.jpg)
Running time
![Page 50: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/50.jpg)
Functional PMsPAl=blueMUSCLE=redBoth=green
(a)=enolase, (b)ammonia channel,(c)=tri-isomerase, (d)=permease,(e)=cytochrome
![Page 51: Protein Functional Site Prediction](https://reader030.vdocuments.us/reader030/viewer/2022032805/5681315b550346895d97d0cd/html5/thumbnails/51.jpg)