d1e3pa3d1gpqa_

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1e3p_Ah	d1e3pa3	A3-A57,A116-A151	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	Ribonuclease PH domain 1-like	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4
1gpq_Ac	d1gpqa_	A2-A89,A90-A128	Alpha and beta proteins (a+b)	Inhibitor of vertebrate lysozyme, Ivy	Inhibitor of vertebrate lysozyme, Ivy	Inhibitor of vertebrate lysozyme, Ivy	Inhibitor of vertebrate lysozyme, Ivy

Justification for analogy
The motif in 1e3p: the first two strands come from insertion, and the remaining part comes from the core. 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

1e3p_Ah   -----------------------------------NETHYAEAVIDngafgTRTIRFETGrla--rqaAGSAVAYLD-dDTMVLSATTASKNPNEIQVVATImalnpdhlYDVVAINAASASTQlaglp------
1gpq_Ac   ddltisslakgettkaafnqmvqghklpawvmkggTYTPAQTVTLG-----DETYQVMSAckphdcgsQRIAVMWSEksNQMTGLFSTIDEKTSQEKLTWLNv---ndalSIDGKTVLFAALTGslenhpdgfnf

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

1e3p_Ah   --------------------------------NETHYA-EAVIDNGaFGTRTIRFETGRlarqaAGSAVAYLD-----dDTMVLSATTASknpnEIQVVATIMALNPDH---LYDVVAINAAS--astqlaglp
1gpq_Ac   ddltisslakgettkaafnqmvqghklpawvmKGGTYTpAQTVTLG-DETYQVMSACKP--hdcGSQRIAVMWseksnqMTGLFSTIDEK----TSQEKLTWLNVNDALsidGKTVLFAALTGslenhpdgfnf

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

1e3p_Ah   -----------------------------N---ETHYA-EAVIDNGAFGTRTIRFETGRLARQAAGSAVAYLD-----DDTMVLSATTASKNPNEIQVVATIMALNPDHL--YDVVAINAASA-----------STQLAGLP
1gpq_Ac   DDLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTL-GDETYQVMSACKP--HDCGSQRIAVMWSEKSNQMTGLFSTIDEK----TSQEKLTWLNVNDALSIDGKTVLFAALTGSLENHPDGFNF--------

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

1e3p_Ah   -------------------------------------NETHYAEAVIDNGAFGT-RTIRFETGRLARQAA----------GSAVAYL-DDDTMVLSATTASKNPNEIQVVATIMALNPDHLY---DVVAINAASASTQLAGLP-------------
1gpq_Ac   DDLTISSLAKGETTKAAFNQMVQGHKLPAWVMKGGTYTPAQTVTLG--------DETYQVMS--------ACKPHDCGSQRIAVMWSEKSNQMTGLFSTIDEKTSQEKLTWL----------NVNDALSIDGKTVLFAAL---TGSLENHPDGFNF