d1efdn_d1r0va3

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1efd_Nh	d1efdn_	N174-N241	Alpha and beta proteins (a/b)	Chelatase-like	"Helical backbone" metal receptor	Periplasmic ferric siderophore binding protein FhuD	Periplasmic ferric siderophore binding protein FhuD
1r0v_Ac	d1r0va3	A140-A214	Alpha and beta proteins (a+b)	MutS N-terminal domain-like	tRNA-intron endonuclease N-terminal domain-like	tRNA-intron endonuclease N-terminal domain-like	Dimeric tRNA splicing endonuclease, domains 1 and 3

Justification for analogy
Comparing the two duplicates in 1efd, the motif results from some deletions in the Rossmann-like structure. Strictly speaking, this is not a hybrid motif. However, since d1r0va3 (and its homolog d1w7aa4) is drastically different than Rossmann structures, the motif in 1efd and the motif in 1r0v are analogs.

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

1efd_Nh   -----ARPLLLTTLIDpRHMLVFGpnslfqeildeygipnawqgetnfwGSTAVSIDRLAAYKd-vDVLCFDhd-------------
1r0v_Ac   geqkeELPEIAGVLSD-EYVITKQteifsry-----------fygsekgDLVTLSLIESLYLLdlgKLNLLNadreelvkrarever

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

1efd_Nh   -----ARPLLLTTLIDpRHMLVFGpnslfqeildeygipnaWQGE-------TNFWgSTAVSIDRLAAY-KDVDVLCFD-------------hd
1r0v_Ac   geqkeELPEIAGVLSD-EYVITKQ-----------------TEIFsryfygsEKGD-LVTLSLIESLYLlDLGKLNLLNadreelvkrarever

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

1efd_Nh   -----ARPLLLTTLIDPRHMLVF-GPNSLFQEILDEYGIPNAWQ---G--ETNFWGSTAVSIDRL-AAY-KDVDVLCFD---------------HD
1r0v_Ac   GEQKEELPEIAGVLSD-EYVITKQTE----------------IFSRYFYGSEKG-DLVTLSLIESLY-LLDLGKLNLLNADREELVKRAREVER--

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

1efd_Nh   ARP--------LLLTTLIDPRHMLVFGPNSLFQEILDEYGIPNAWQ----------GETNFWGSTAVSIDRLAA-YKDVDVLCFDHD----------------
1r0v_Ac   ---GEQKEELPEIAGVLSD-EYVITK--------------------QTEIFSRYFYGSEKG-DLVTLSLIESLYLLDLGKLNLL---NADREELVKRAREVER