LociOiling Lv 1
The protein in this puzzle matches PDB 5DJW, as shown below in the Jpred alignment results.
The Foldit protein has a couple of gaps in its sequence. In the puzzle, these gaps are marked by light blue connectors that look a little like cutpoints. I'm calling them "uncut points". Unlike a cutpoint, they can't be closed, and don't affect whether the score is valid.
If you look at the details for 5DJW, the gaps correspond to "missing residues", which were part of the sequence, but then weren't found in the electron density results.
Assuming the crystallographers were close to begin with, the segments on either side of the uncut points should stay near where they start. Left to their own devices, the uncut points seem to want to close up, much like cutpoints.
>5djw_A mol:protein length:697 Alpha-glucosidase II
Length = 697
Score = 1213 bits (3139), Expect = 0.0
Identities = 588/612 (96%), Positives = 588/612 (96%), Gaps = 24/612 (3%)
Query: 1 SLTDGKANASLTVPEGTSIYGGGEVTGSLLRNGKTIKLWNTDSGAYGVDKGTRLYQSHPW 60
SLTDGKANASLTVPEGTSIYGGGEVTGSLLRNGKTIKLWNTDSGAYGVDKGTRLYQSHPW
Sbjct: 46 SLTDGKANASLTVPEGTSIYGGGEVTGSLLRNGKTIKLWNTDSGAYGVDKGTRLYQSHPW 105
Query: 61 MMGVRKDGTAFGILFDTTWKAELSSTDEKIELKSEGIPFRVFIIDRESPQAVIRGLSELT 120
MMGVRKDGTAFGILFDTTWKAELSSTDEKIELKSEGIPFRVFIIDRESPQAVIRGLSELT
Sbjct: 106 MMGVRKDGTAFGILFDTTWKAELSSTDEKIELKSEGIPFRVFIIDRESPQAVIRGLSELT 165
Query: 121 GTMPMIPRWALGYQQCRFSYSPDSRVIEIADTFRLKRIPCDVIWMDIDYMDGYRIFTFNP 180
GTMPMIPRWALGYQQCRFSYSPDSRVIEIADTFRLKRIPCDVIWMDIDYMDGYRIFTFNP
Sbjct: 166 GTMPMIPRWALGYQQCRFSYSPDSRVIEIADTFRLKRIPCDVIWMDIDYMDGYRIFTFNP 225
Query: 181 KSFPNPKAVNRDLHIRGFHSAWMIDPGAKVDPNYFVYKSGTENDVWVKTADGKNFHGDAW 240
KSFPNPKAVNRDLHIRGFHSAWMIDPGAKVDPNYFVYKSGTENDVWVKTADGKNFHGDAW
Sbjct: 226 KSFPNPKAVNRDLHIRGFHSAWMIDPGAKVDPNYFVYKSGTENDVWVKTADGKNFHGDAW 285
Query: 241 PGAAAFPDFTSPKVNKWWRNLYKDFLAQGVDGVWNDVNEPQINDTPNKTMPED------- 293
PGAAAFPDFTSPKVNKWWRNLYKDFLAQGVDGVWNDVNEPQINDTPNKTMPED
Sbjct: 286 PGAAAFPDFTSPKVNKWWRNLYKDFLAQGVDGVWNDVNEPQINDTPNKTMPEDNLHRGGG 345
Query: 294 ---------YHNVYGFLMVKASREGILDARPEKRPFILTRSNFLGGQRYAATWTGDNGSC 344
YHNVYGFLMVKASREGILDARPEKRPFILTRSNFLGGQRYAATWTGDNGSC
Sbjct: 346 KLPAGTHLQYHNVYGFLMVKASREGILDARPEKRPFILTRSNFLGGQRYAATWTGDNGSC 405
Query: 345 WDHLKMSVPMSLTLGLSGQPFSGADIGGFLFNADADLFGNWIGFGAFYPFARGHACAGTN 404
WDHLKMSVPMSLTLGLSGQPFSGADIGGFLFNADADLFGNWIGFGAFYPFARGHACAGTN
Sbjct: 406 WDHLKMSVPMSLTLGLSGQPFSGADIGGFLFNADADLFGNWIGFGAFYPFARGHACAGTN 465
Query: 405 NKEPWVFGQKVEDASRIALERRYILLPYFYTLLHEASTNGMPIMRPVFFSDPKDLSLRAE 464
NKEPWVFGQKVEDASRIALERRYILLPYFYTLLHEASTNGMPIMRPVFFSDPKDLSLRAE
Sbjct: 466 NKEPWVFGQKVEDASRIALERRYILLPYFYTLLHEASTNGMPIMRPVFFSDPKDLSLRAE 525
Query: 465 EEAFLVGDNLLIIPAFANQPALPKGIWKEL--------DKYQAKMKIRGGAIIPTGKIIQ 516
EEAFLVGDNLLIIPAFANQPALPKGIWKEL DKYQAKMKIRGGAIIPTGKIIQ
Sbjct: 526 EEAFLVGDNLLIIPAFANQPALPKGIWKELSLVEGDQNDKYQAKMKIRGGAIIPTGKIIQ 585
Query: 517 NTTENSLDPLTLLVCLDEQGKASGNMYWDAGDGWSYKKGDYSLLQFVAERNGDKVTVKLT 576
NTTENSLDPLTLLVCLDEQGKASGNMYWDAGDGWSYKKGDYSLLQFVAERNGDKVTVKLT
Sbjct: 586 NTTENSLDPLTLLVCLDEQGKASGNMYWDAGDGWSYKKGDYSLLQFVAERNGDKVTVKLT 645
Query: 577 KKTGKYNTENKD 588
KKTGKYNTENKD
Sbjct: 646 KKTGKYNTENKD 657