Date post: | 21-Dec-2015 |
Category: |
Documents |
View: | 220 times |
Download: | 0 times |
Evaluating alignments using motif detection
• Let’s evaluate alignments by searching for motifs
• If alignment X reveals more functional motifs than Y using technique Z then X is better than Y w.r.t. Z
• Motifs could be functional sites in proteins or functional regions in non-coding DNA
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.
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.
Phylogenetic motifs
• PMs are short sequence fragments that conserve the overall familial phylogeny
• Are they functional?
• How do we detect them?
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Functional PMsPAl=blueMUSCLE=redBoth=green
(a)=enolase, (b)ammonia channel,(c)=tri-isomerase, (d)=permease,(e)=cytochrome