d1d5ya1

DomainSCOPidRangeSCOP ClassSCOP FoldSCOP SuperfamilySCOP familyProtein
1d5y_A1d1d5ya1A3-A56All alpha proteinsDNA/RNA-binding 3-helical bundleHomeodomain-likeAraC type transcriptional activatorRob transcription factor, N-terminal domain
1d5y_A2d1d5ya2A57-A121All alpha proteinsDNA/RNA-binding 3-helical bundleHomeodomain-likeAraC type transcriptional activatorRob transcription factor, N-terminal domain

Alignment-based scores

AlignerAligned LengthSequence IdentityRMSDGDT-TSCOMPASS
manual480.166671.8123873.4375022.46096
tm480.166671.7811574.4791729.86550
fast460.152171.7766474.4565226.68947

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