d1b05a_d1lc0a2

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1b05_Ah	d1b05a_	A9-A24,A31-A46,A188-A207,A217-A227	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Oligo-peptide binding protein (OPPA)
1lc0_Ac	d1lc0a2	A129-A159,A160-A180,A181-A207,A208-A246	Alpha and beta proteins (a+b)	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Biliverdin reductase	Biliverdin reductase

Justification for analogy
The motif in 1b05: a hybrid motif, because a beta-hairpin is absent in the other duplicate and thus insertion. The motif in 1lc0: although "Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain" is a very variable fold, it is in SCOP a+b class and does not have any resemblance to Rossmann-like structures. 1b05 is in a/b class and is Rossmann-like. So these two motifs are analogs.

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

1b05_Ah   ------------ladkQTLVRNNGsevq-------iegvPESNVSRDLFEg-ngAYKLKNWVVN---------ERIVLERNvinQVTYLPIS----------------------------
1lc0_Ac   meefeflrrevlgkelLKGSLRFTaspleeerfgfpafsGISRLTWLVSLfg--ELSLISATLEerkedqymkMTVQLETQnkgLLSWIEEKgpglkrnryvnfqftsgsleevpsvgvn

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

1b05_Ah   ------------LADKQTLVRNNG----------sEVQIegvPESNVSRDLFegnGAYKLKNWVV---------NERIVLERNVINQVTYLPIS----------------------------
1lc0_Ac   meefeflrrevlGKELLKGSLRFTaspleeerfgfPAFS---GISRLTWLVS-lfGELSLISATLeerkedqymKMTVQLETQNKGLLSWIEEKgpglkrnryvnfqftsgsleevpsvgvn

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

1b05_Ah   -------------LADKQTLVRNNGS---------EVQIEGVPESNVSR--D---LFEGNGAYKLKNWVV---------NERIVLERNVINQVTYLPIS----------------------------
1lc0_Ac   MEEFEFLRREVLGKE-LLKGSLRFTASPLEEERFGFPAF-S-GISRL-TWLVSLF-----GELSLISATLEERKEDQYMKMTVQLETQNKGLLSWIEEKGPGLKRNRYVNFQFTSGSLEEVPSVGVN

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

1b05_Ah   LADKQ-----------------TLVRNNGSEVQIEG------------------VPESNVSRDLFEGNGA--YKLKNWVVN----------ERIVLERNVIN--QVTYLPIS----------------------------
1lc0_Ac   -----MEEFEFLRREVLGKELLKGSLRF--------TASPLEEERFGFPAFSGISRLTWLVSLF------GELSLISATL-EERKEDQYMKMTVQLETQN--KGLLSWIEEKGPGLKRNRYVNFQFTSGSLEEVPSVGVN