d1qd1b1d1n62c2

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1qd1_Bh	d1qd1b1	B2083-B2180	Alpha and beta proteins (a+b)	Ferredoxin-like	Formiminotransferase domain of formiminotransferase-cyclodeaminase.	Formiminotransferase domain of formiminotransferase-cyclodeaminase.	Formiminotransferase domain of formiminotransferase-cyclodeaminase.
1n62_Cc	d1n62c2	C1-C61	Alpha and beta proteins (a+b)	FAD-binding domain	FAD-binding domain	CO dehydrogenase flavoprotein N-terminal domain-like	Carbon monoxide (CO) dehydrogenase flavoprotein, N-terminal domain

Justification for analogy
The motif in 1qd1: uses the last strand in ferredoxin and the C-terminal extensions, hybrid. Compare the two duplicates. The motif in 1n62: stand-along, core 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

1qd1_Bh   prmgalDVCPFIpvrgvtmdeCVRCAQAFGQRLAeelgvPVYLYGeaartagrqSLPALRAGEyealpeklkqaewapdfgpsafvpswgATVAGARK-----
1n62_Cc   mipgsfDYHRPK---------SIADAVALLTKLGe----DARPLA---------GGHSLIPIMktrla--------------------tpEHLVDLRDigdlv

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

1qd1_Bh   prmgALDVCPFIpvrgvtmdeCVRCAQAFGQRLAeelgVPVYLYgeaartagrQSLPALRAGEYEAlpeklkqaewapdfgpsafvpswgATVAGARK-----
1n62_Cc   mipgSFDYHRPK---------SIADAVALLTKLG----EDARPL---------AGGHSLIPIMKTR--------------------latpEHLVDLRDigdlv

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

1qd1_Bh   -PRMGALDVCPFIPVRGVTMDECVRCAQAFGQRLAEELGVPVYLYGEAARTAGRQSLPALRAGEYEALPEKLKQAEWAPDFGPSAFVPSWGA-TVAGARK-----
1n62_Cc   MIPGSFD-YHRPK---------SIADAVALLTKLG----EDARPL---------AGGHSLIPIMKTRL--A-------------------TPEHLVDLRDIGDLV

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

1qd1_Bh   PRMGALD-------VCPFIPVRGVTMDEC-VRCAQAFGQRLAEELGV--PVYLYGEAARTAGRQSLPALRAGEYEALPEKLKQAEWAPDFGPSAFVPSWGA----------TVAGARK------
1n62_Cc   -------MIPGSFDYHRPK----------SIADAVALLTKL------GEDARPL---------AGGHSLIP------------------------------IMKTRLATPEHLVDLR-DIGDLV