d1smta_d1b7ta4

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1smt_Ai	d1smta_	A28-A59,A101-A121,B28-B59,B101-B120	All alpha proteins	DNA/RNA-binding 3-helical bundle	"Winged helix" DNA-binding domain	ArsR-like transcriptional regulators	SmtB repressor
1b7t_Ac	d1b7ta4	A323-A364,A371-A402,A410-453,A591-A624	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Motor proteins	Myosin S1, motor domain

Justification for analogy
The motif in 1smt: it comes from a dimer interface, so it is an interface motif. As long as the DALI hits are not DNA/RNA-binding 3-helix bundle, they can be used as analogs to the interface 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

1smt_Ai   -----------------------iAPEVAQSLAEFFAVLAdpnrlrllsllarse--------------qlqdhHIVALYQNALDHlqec-iapeVAQSLAEFFAVLADpnrlrllsllarse--------------------qlqdHHIVALYQNAldhlqe-----
1b7t_Ac   ddveefklcdeafdilgftkeekqSMFKCTASILHMGEMKfk-------------qaesdgtaeaekvaflcgiNAGDLLKALLKPk---vtkgqNMNQVVNSVGALAKslydrmfnwlvrrvnktldtkakrnitgwleknkdpinENVVALLGASkeplvaelfka

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

1smt_Ai   -----------------------iAPEVAQSLAEFFAVLaDPNR--LRLLsllarseqlqdhHIVALYQNALDHLQECiapeVAQSLAEFFAVLADpnRLRLLSLL----------------------arseqlqdHHIVALYQnalDHLQ-------e
1b7t_Ac   ddveefklcdeafdilgftkeekqSMFKCTASILHMGEM-KFKQaeSDGTaeaekvaflcgiNAGDLLKALLKPKVTK--gqNMNQVVNSVGALAK--SLYDRMFNwlvrrvnktldtkakrnitgwleknkdpinENVVALLG--aSKEPlvaelfka

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

1smt_Ai   ---------------------I--APEVAQSLAEFFAVLADPN-RLRLLSLL--ARSEQLQ---D---HHIVALYQNA-LDH-LQECIAPEVAQSLAEFFAVLAD-PNRLRLLS---------------------------LLARSEQLQDHHIVALY--QNAL---------DHLQE
1b7t_Ac   DDVEEFKLCDEAFDILGFTKEEKQSMFKCTASILHMGEM-KFKQAESDG--TAE-----AEKVAFLCGINAGDLLKALLKPKVTKG----QNMNQVVNSVGALAKSLYDRMFNWLVRRVNKTLDTKAKRNITGWLEKNKDP-------INENVVAL-LGASK-EPLVAELFKA-----

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

1smt_Ai   IAP-------------------EVAQSLAEFFAVLADPNRLRLLSLLARSEQLQDHHIVAL-----------------------YQNALDHLQECIA------------PEVAQSLAEFFAVLADPNRLRLLSLLARSEQLQDHHIVALYQNALDHLQE-----------------------------------------
1b7t_Ac   ---DDVEEFKLCDEAFDILGFTKEEKQSMFKCTASIL--HMGEM-----------------KFKQAESDGTAEAEKVAFLCGINAGDLLKALLK---PKVTKGQNMNQVVNSVGALAKSLYDRM--FNWLVRRVNKTL---------------------DTKAKRNITGWLEKNKDPINENVVALLGASKEPLVAELFKA