d1hrda1d1rp3a3

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1hrd_Ah	d1hrda1	A195-A226,A369-A424	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Aminoacid dehydrogenase-like, C-terminal domain	Glutamate dehydrogenase
1rp3_Ac	d1rp3a3	A1-A36,A37-A87	All alpha proteins	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma2 domain of RNA polymerase sigma factors	Sigma factor sigma-28 (FliA)

Justification for analogy
The motif in 1hrd: first helix is from the Rossmann core, the other two helices are from C-terminal extension. So this is a hybrid motif.

In the alignments below, two upper-case letters are aligned, while two lower-case letters are NOT aligned. The two sequences in an alignment are NOT continuous in most cases (see their ranges). The superpositions 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.

MANUAL alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1hrd_Ah   ----karsfggslVRPEATGYGSVYYVEAVMKHend--SKAVN-AGGVLVSGFEMSQnserlswTAEEVDSKLHQVMTDIHDGSAaaaeryglgy
1rp3_Ac   mknpysnqiereeLILKYLPLVKAIATNIKKHLpedvdIRDLIsYGVIGLIKAVDNLstenpkrAEAYIKLRIKGAIYDYLRSLDfg--------

DALI alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1hrd_Ah   kARSF-ggslvRPEATGYGSVYYVEAVMKHEND----------sKAVNA-GGVLVSGFEmsqnserlsWTAEEVDSKLHQVMTDIHDGSAAAAERYglgy
1rp3_Ac   -MKNPysnqieREELILKYLPLVKAIATNIKKHlpedvdirdliSYGVIgLIKAVDNLS--------tENPKRAEAYIKLRIKGAIYDYLRSLDFG----

TM alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1hrd_Ah   --------KAR-SFGGSLVRPEATGYGSVYYVEAVM-----KHENDSKAVNA-GGVLVSGFEMSQNSERLS----WTAEEVDSKLHQVMTDIHDGSAAAAERYGLGY
1rp3_Ac   MKNPYSNQIERE--ELILKYLPLVKAIATNIKKHLPEDVDI-----R-DLISYGVIGLIKAVDNL----STENPKRAEAYIKLRIKGAIYDYLRSLDF--G------

FAST alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1hrd_Ah   KARSFGGSLV-------RPEATGYGSVYYVEAVMKHENDSKA-------------------VNAGGVLVSGFEMSQNSERLSW---TAEEVDSKLHQVMTDIHDGSAAAAERYGLGY---
1rp3_Ac   ----------MKNPYSNQIEREELILKYLPLVKAIAT-----NIKKHLPEDVDIRDLISYGVIGLIKAVDNL-----------STENPKRAEAYIKLRIKGAIYDYLRSL-------DFG