d1yua_1

Domain	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP family	Protein
1yua_A1	d1yua_1	A1-A63	Small proteins	Rubredoxin-like	Zinc beta-ribbon	Prokaryotic DNA topoisomerase I, a C-terminal fragment	Prokaryotic DNA topoisomerase I, a C-terminal fragment
1yua_A2	d1yua_2	A64-A122	Small proteins	Rubredoxin-like	Zinc beta-ribbon	Prokaryotic DNA topoisomerase I, a C-terminal fragment	Prokaryotic DNA topoisomerase I, a C-terminal fragment

Alignment-based scores

Aligner	Aligned Length	Sequence Identity	RMSD	GDT-TS	COMPASS
manual	36	0.02778	2.94091	55.55556	-2.90319
dali	37	0.02703	3.01051	52.70270	-2.63637
tm	40	0.02500	3.02451	54.37500	-2.56995
fast	29	0.03448	2.52647	61.20690	-2.63416

In the alignments below, two upper-case letters are aligned, and two lower-case letters are NOT aligned. The superposition files are re-constructed from the corresponding alignments by minimizing the overall RMSD. In a PDB-format superposition file, the first domain is represented by chain S and the second domain is represented by chain A. The coordinates of the first domain are transformed, while the coordinates of the second domain are the same as in the original PDB file.

MANUAL alignment      superposition in PDB format     colored superposition in PyMol

1yua_A1   mngevappkedpvplpeLPCEkSDAYFVLRDGA--AGVFLAANT-fpKSRETRAPLVEElyrfrdr
1yua_A2   -----lpeklryladapQQDP-EGNKTMVRFSRktKQQYVSSEKdgkATGWSAFYVDGKwvegkk-

DALI alignment      superposition in PDB format     colored superposition in PyMol

1yua_A1   mngevappkedpvplpeLPCEKSDAYFVLRDG--aAGVFLAANT-fPKSRETRAPLVEElyrfrdr
1yua_A2   ------lpeklryladaPQQDPEGNKTMVRFSrktKQQYVSSEKdgKATGWSAFYVDGK-wvegkk

TM alignment      superposition in PDB format     colored superposition in PyMol

1yua_A1   ----MNGEVAPPKEDPV--PL-PEL-PCEKSDAYFVLRDGAA-GV-FLAANT---FPKSRETRAPL-VEE-----LYRFRDR
1yua_A2   LPEK------------LRYLAD-APQQDPEGNKT-MVRFSRKTKQQYVSS-EKDGKAT-GWSAFYVDGKWVEGKK-------

FAST alignment      superposition in PDB format     colored superposition in PyMol

1yua_A1   MNGEVAPPKEDPVPLPEL------------PCEKSDAYFVLRDGAA-----GVFLAANTFPKS------RETRAPLVEELYRFRDR-------
1yua_A2   ------------------LPEKLRYLADAPQQDPEGNKTMVRF---SRKTKQQYVSSE-----KDGKATGWSAFYVDG--------KWVEGKK