d1qo0d_d1hjp_1

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1qo0_Di	d1qo0d_	D87-D102,E2-E13,E108-E130	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	Positive regulator of the amidase operon AmiR	Positive regulator of the amidase operon AmiR
1hjp__c	d1hjp_1	158-172,173-187,188-203	All alpha proteins	RuvA C-terminal domain-like	DNA helicase RuvA subunit, C-terminal domain	DNA helicase RuvA subunit, C-terminal domain	DNA helicase RuvA subunit, C-terminal domain

Justification for analogy
In 1qo0, the motif uses one helix from the flavodoxin core in the first monomer, one helix from the N-terminal extension from the second monomer, and one helix from the flavodoxin core in the second monomer. This is an interface as well as hybrid motif and is analogous to real RuvA C-like left-handed 3-helix bundles.

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

1qo0_Di   eyeSPAVLSQIIELEc----SANSLLGSLRelqpldAHRVLPVLVSARRIseema
1hjp__c   --dAEQEAVAALVALgykpqEASRMVSKIArp--daSSETLIREALRAAL-----

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

1qo0_Di   eYESPaVLSQIIELE----cSANSLLGSLrelqpldaHRVLPVLVSARRISEEMa
1hjp__c   -DAEQ-EAVAALVALgykpqEASRMVSKI------arPDASSETLIREALRAAL-

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

1qo0_Di   -EYE-S-PAVLSQIIE---LECSANSLLGSLRE---LQPLDAHRVLPVLVSARRISEEMA
1hjp__c   D-AEQEAVAALVALGYKPQ---EASRMVSKIARPDA-----SSETLIREALRAAL-----

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

1qo0_Di   EYES--PAVLSQIIELECS-------ANSLLGSLRELQPLDAHRVL-------PVLVSARRISEEMA-
1hjp__c   ----DAEQEAVAALVA---LGYKPQEASRMVSK-------------IARPDASSETLIREALRAA--L