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