d1vk3a3d1w2ia_

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
1w2i_Ah	d1w2ia_	A2-A16,A17-A40,A41-A91	Alpha and beta proteins (a+b)	Ferredoxin-like	Acylphosphatase-like	Acylphosphatase-like	Acylphosphatase

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 1w2i: the last strand does not belong to the ferredoxin core. These two motifs are analogs. In the superposition, the first ferredoxin strand in 1vk3 will be aligned to the first ferredoxin strand in 1w2i. But that is OK, since they are aligned back-to-back, i.e. the helix-packing face in one strand is aligned to the non-helix-packing face in the other strand.

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   kasrPGQVIVIFGGATGrdgagGVLSATSELVAKGNLGAIVHLDrvplrLFGDVvAEVIEe---------------------------------PVYRVMYr
1w2i_Ah   --aiVRAHLKIYGRVQG----vGFRWSMQREARKLGVNGWVRNLp----DGSVE-AVLEGdeervealigwahqgpplarvtrvevkweqpkgeKGFRIVG-

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

1vk3_Ah   kasrpGQVIVIFGGatgrdgaGGVLSATSELVAKGNLGAIVHldRVPLrlfGDVVAEVIE---------------------------------EPVYRVMYr
1w2i_Ah   --aivRAHLKIYGR----vqgVGFRWSMQREARKLGVNGWVR--NLPD---GSVEAVLEGdeervealigwahqgpplarvtrvevkweqpkgEKGFRIVG-

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

1vk3_Ah   KASRPGQVIVIFGGATGRDGAGGV-LSATS-ELVAKGNLGAIVHLDRV-PLRLFGDVVAEVIE---------------------------------EPVYRVMYR
1w2i_Ah   --AIVRAHLKIYGRVQG-V---GFRWS-MQRE-ARKLGVNGWVRN-LPDG-----SVEAVLEGDEERVEALIGWAHQGPPLARVTRVEVKWEQPKGEKGFRIVG-

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

1vk3_Ah   KASRP---GQVIVIFGGATGRDGAGG-----VLSATSELVAKGNLGAIVHLDRVPLRL---FGDVVAEVIEE-----------------------------------PVYRVMYR
1w2i_Ah   -----AIVRAHLKIYGR---------VQGVGFRWSMQREARKLGVNGWVRN-------LPDGSVE-AVLE--GDEERVEALIGWAHQGPPLARVTRVEVKWEQPKGEKGFRIVG-