d1vk3a3d1lbu_2

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1vk3_Ah	d1vk3a3	A167-A186,A239-A267,A306-A325	Alpha and beta proteins (a+b)	PurM C-terminal domain-like	PurM C-terminal domain-like	PurM C-terminal domain-like	Phosphoribosylformylglycinamidine synthase II, domains 2 and 4
1lbu__h	d1lbu_2	157-166,167-189,190-213	Alpha and beta proteins (a+b)	Hedgehog/DD-peptidase	Hedgehog/DD-peptidase	Muramoyl-pentapeptide carboxypeptidase	Zn2+ DD-carboxypeptidase C-terminal catalytic domain

Justification for analogy
The motif in 1vk3: if 1vk3 is considered to be an elaborated ferredoxin, one helix and two strands in the motif are insertions. Hybrid motif. The motif in 1lbu: comparing with 1vhh, which lacks the last strand in the motif, this hedgehog/DD-peptidase fold has a circularly permuted ferredoxin core. So the motif in 1lbu is a hybrid with the last strand being insertion.

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

1vk3_Ah   kasRPGQVIVIFGgatgrdgagGVLSATSELVAKGNL-GAIVHldrvplrlfgdvVAEVIE--EPVYRVmyr--
1lbu__h   ---GHAADLGAGS---------QGFCALAQAARNHGFtEILGPgy-----pghndHTHVAGgdGRFWSApscgi

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

1vk3_Ah   kasrpGQVIVIFGGatgrdgagGVLSATSELVakgnlGAIVH-----LDRVplrlfgdvVAEVIEEPVYRVMYR---
1lbu__h   ----gHAADLGAGS----qgfcALAQAARNHG----fTEILGpgypgHNDH--------THVAGGDGRFWSAPScgi

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

1vk3_Ah   KASRPGQVIV-IFGGAT-GRDGAGG-VLSATSELVAKGNLGAIVHLD----RVPLRLFGDVVAEVIEEPVYRVMY----R
1lbu__h   ---GH-AADLGAGSQGFC------ALAQ-AARNH-G---FTEILGPGYPGHN-------DHTHVAGGDGRFWSAPSCGI-

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

1vk3_Ah   KASRPG---QVIVIFGGATGRDGA-GGVLSATSELVAKGNL-GAIVHLDRVPLRLFGDV--------VAEVIE--EPVYRVMYR----
1lbu__h   ------GHAADLGAG---------SQGFCALAQA-ARNHGFTEILG-------------PGYPGHNDHTHVAGGDGRFWSAP--SCGI