Note the missing loops in 1TFH_B. 

This benchmark case is special.  Because the alignments below align only the residues visible in the
electron densities, you cannot see that there is a stretch of 5 residues missing in BOTH bound and unbound
structures 1JPS_H and 1JPT_H. 

NOTE THAT IN THE ALIGNMENTS BELOW, GAPS MOST LIKELY INDICATE
RESIDUES MISSING IN THE ELECTRON DENSITY. 


Alignment: 1JPS_H against 1JPT_H
Query=
(213 letters)

>1JPT_H
Length = 212

Score = 430 bits (1106), Expect = e-126
Identities = 212/213 (99%), Positives = 212/213 (99%), Gaps = 1/213 (0%)

Query: 1 EVQLVESGGGLVQPGGSLRLSCAASGFNIKEYYMHWVRQAPGKGLEWVGLIDPEQGNTIY 60
EVQLVESGGGLVQPGGSLRLSCAASGFNIKEYYMHWVRQAPGKGLEWVGLIDPEQGNTIY
Sbjct: 1 EVQLVESGGGLVQPGGSLRLSCAASGFNIKEYYMHWVRQAPGKGLEWVGLIDPEQGNTIY 60

Query: 61 DPKFQDRATISADNSKNTAYLQMNSLRAEDTAVYYCARDTAAYFDYWGQGTLVTVSSAST 120
DPKFQDRATISADNSKNTAYLQMNSLRAEDTAVYYCARDTAAYFDYWGQGTLVTVSSAST
Sbjct: 61 DPKFQDRATISADNSKNTAYLQMNSLRAEDTAVYYCARDTAAYFDYWGQGTLVTVSSAST 120

Query: 121 KGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSS 180
KGPSVFPLAP SGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSS
Sbjct: 121 KGPSVFPLAP-SGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSS 179

Query: 181 VVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 213
VVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP
Sbjct: 180 VVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 212


Alignment: 1JPS_L against 1JPT_L
Query=
(213 letters)

>1JPT_L
Length = 213

Score = 431 bits (1107), Expect = e-126
Identities = 213/213 (100%), Positives = 213/213 (100%)

Query: 1 DIQMTQSPSSLSASVGDRVTITCRASRDIKSYLNWYQQKPGKAPKVLIYYATSLAEGVPS 60
DIQMTQSPSSLSASVGDRVTITCRASRDIKSYLNWYQQKPGKAPKVLIYYATSLAEGVPS
Sbjct: 1 DIQMTQSPSSLSASVGDRVTITCRASRDIKSYLNWYQQKPGKAPKVLIYYATSLAEGVPS 60

Query: 61 RFSGSGSGTDYTLTISSLQPEDFATYYCLQHGESPWTFGQGTKVEIKRTVAAPSVFIFPP 120
RFSGSGSGTDYTLTISSLQPEDFATYYCLQHGESPWTFGQGTKVEIKRTVAAPSVFIFPP
Sbjct: 61 RFSGSGSGTDYTLTISSLQPEDFATYYCLQHGESPWTFGQGTKVEIKRTVAAPSVFIFPP 120

Query: 121 SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT 180
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
Sbjct: 121 SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT 180

Query: 181 LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE
Sbjct: 181 LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213


Alignment: 1JPS_T against 1TFH_B
Query=
(200 letters)

>1TFH_B
Length = 182

Score = 352 bits (902), Expect = e-102
Identities = 182/199 (91%), Positives = 182/199 (91%), Gaps = 17/199 (8%)

Query: 1 NTVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIV 60
NTVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIV
Sbjct: 1 NTVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIV 60

Query: 61 KDVKQTYLARVFSYPAGNVEPLYENSPEFTPYLETNLGQPTIQSFEQVGTKVNVTVEDER 120
KDVKQTYLARVFSYPAGNVEPLYENSPEFTPYLETNLGQPTIQS TKVNVTVEDER
Sbjct: 61 KDVKQTYLARVFSYPAGNVEPLYENSPEFTPYLETNLGQPTIQS-----TKVNVTVEDER 115

Query: 121 TLVRRNNTFLSLRDVFGKDLIYTLYYWKSSSSGKKTAKTNTNEFLIDVDKGENYCFSVQA 180
TLV NTFLSLRDVFGKDLIYTLYY GKKTAKTNTNEFLIDVDKG CFSVQA
Sbjct: 116 TLV---NTFLSLRDVFGKDLIYTLYY------GKKTAKTNTNEFLIDVDKG---CFSVQA 163

Query: 181 VIPSRTVNRKSTDSPVECM 199
VIPSRTVNRKSTDSPVECM
Sbjct: 164 VIPSRTVNRKSTDSPVECM 182