d1qo0d_d1hjp_1

Motif
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SCOPidRangeSCOP ClassSCOP FoldSCOP SuperfamilySCOP FamilyProtein
1qo0_Di
d1qo0d_D87-D102,E2-E13,E108-E130Alpha and beta proteins (a/b)Flavodoxin-likeCheY-likePositive regulator of the amidase operon AmiRPositive regulator of the amidase operon AmiR
1hjp__c
d1hjp_1158-172,173-187,188-203All alpha proteinsRuvA C-terminal domain-likeDNA helicase RuvA subunit, C-terminal domainDNA helicase RuvA subunit, C-terminal domainDNA 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.


Alignment-based scores
AlignerAligned LengthSequence IdentityRMSDGDT-TSCOMPASS
manual360.055562.8171361.80556-15.47998
dali390.025642.9502459.61538-17.23074
tm370.135143.2250857.43243-23.62371
fast290.034482.0200268.10345-13.17284

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