d1vk3a3d1lbu_2

Motif
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SCOPidRangeSCOP ClassSCOP FoldSCOP SuperfamilySCOP FamilyProtein
1vk3_Ah
d1vk3a3A167-A186,A239-A267,A306-A325Alpha and beta proteins (a+b)PurM C-terminal domain-likePurM C-terminal domain-likePurM C-terminal domain-likePhosphoribosylformylglycinamidine synthase II, domains 2 and 4
1lbu__h
d1lbu_2157-166,167-189,190-213Alpha and beta proteins (a+b)Hedgehog/DD-peptidaseHedgehog/DD-peptidaseMuramoyl-pentapeptide carboxypeptidaseZn2+ 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.


Alignment-based scores
AlignerAligned LengthSequence IdentityRMSDGDT-TSCOMPASS
manual420.047622.9772458.92857-14.04313
dali430.069773.0703358.72093-23.66165
tm460.065222.9058960.86957-24.53976
fast380.052632.7815163.81579-18.63780

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