d1d5ya1

Domain	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP family	Protein
1d5y_A1	d1d5ya1	A3-A56	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	AraC type transcriptional activator	Rob transcription factor, N-terminal domain
1d5y_A2	d1d5ya2	A57-A121	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	AraC type transcriptional activator	Rob transcription factor, N-terminal domain

Alignment-based scores

Aligner	Aligned Length	Sequence Identity	RMSD	GDT-TS	COMPASS
manual	48	0.16667	1.81238	73.43750	22.46096
tm	48	0.16667	1.78115	74.47917	29.86550
fast	46	0.15217	1.77664	74.45652	26.68947

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

1d5y_A1   qaGIIRDLLIWLEGHldqpLSLDNVAA-KAGY-SKWHLQRMFKDVTGHAIGAYIRA---------------
1d5y_A2   --RRLSKSAVALRLT----ARPILDIAlQYRFdSQQTFTRAFKKQFAQTPALYRRSpewsafgirpplrlg

TM alignment      superposition in PDB format     colored superposition in PyMol

1d5y_A1   QAGIIRDLLIWLEGHLDQPLSLDNVAAK-AGY-SKWHLQRMFKDVTGHAIGAYIRA---------------
1d5y_A2   --RRLSKSAVALRLT---ARP-ILDIALQYRFDSQQTFTRAFKKQFAQTPALYRRSPEWSAFGIRPPLRLG

FAST alignment      superposition in PDB format     colored superposition in PyMol

1d5y_A1   QAG-IIRDLLIWLEGHLDQPL-SLDNVAA-KAGYS-KWHLQRMFKDVTGHAIGAYIRA---------------
1d5y_A2   ---RRLSKSAVALRLT-----ARPILDIALQYRFDSQQTFTRAFKKQFAQTPALYRRSPEWSAFGIRPPLRLG