d1a7j__d1kafa_

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1a7j__h	d1a7j__	203-279	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Phosphoribulokinase/pantothenate kinase	Phosphoribulokinase
1kaf_Ac	d1kafa_	A104-A211	Alpha and beta proteins (a+b)	DNA-binding C-terminal domain of the transcription factor MotA	DNA-binding C-terminal domain of the transcription factor MotA	DNA-binding C-terminal domain of the transcription factor MotA	DNA-binding C-terminal domain of the transcription factor MotA

Justification for analogy
The motif in 1a7j: comparing d1a7j__ and 1uj2 (same SCOP family), three strands and one helix in the motif in 1a7j are absent in 1uj2. So this is a hybrid 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

1a7j__h   --------------------------------------------DI-NFQRVPVvdtsnpfiarwiptadeSVVVIRFRNPRgiDFPYLTSMihGSWMsRA-----NSIVVPGN--KLDLAMQLILTPl
1kaf_Ac   meitsdmeedkdlmlklldkngfvlkkveiyrsnylailekrtnGIrNFEINNN-----------------GNMRIFGYKMMehHIQKFTDI--GMSC-KIakngnVYLDIKRSaeNIEAVITVASEL-

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

1a7j__h   ---------------------------------------------dINFQRVPVvdtsnpfiarwiptadeSVVVIRFRNPRGIDFPYLTSMIhgSWMSR----ANSIVVPGN--KLDLAMQLILTPl
1kaf_Ac   meitsdmeedkdlmlklldkngfvlkkveiyrsnylailekrtngiRNFEINNN-----------------GNMRIFGYKMMEHHIQKFTDIG--MSCKIakngNVYLDIKRSaeNIEAVITVASEL-

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

1a7j__h   -----------------------------------------D----INFQRVPVVDTSNPFIARWIPTADESVVVIRFRNPRGIDFPYLTSMIHGSWMSRA----NSIVVPGN--KLDLAMQLILTPL
1kaf_Ac   MEITSDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINNN-----------------GNMRIFGYKMMEHHIQKFTD-IG-MSCKIAKNGNVYLDIKRSAENIEAVITVASEL-

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

1a7j__h   DI-----------------------------------------------NFQRVPVVDTSNPFIARWIPTADES--VVVIRFRNPRGID---FPYLTSMIHGSWMSRAN-------SIVVPGN---KLDLAMQLILTPL
1kaf_Ac   --MEITSDMEEDKDLMLKLLDKNGFVLKKVEIYRSNYLAILEKRTNGIRNFEINN-------------------NGNMRIFGYKMM---EHHIQKFTDI--GMSCK---IAKNGNVYLDIKR-SAENIEAVITVASEL-