d1efdn_d1r0va3

Motif
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SCOPidRangeSCOP ClassSCOP FoldSCOP SuperfamilySCOP FamilyProtein
1efd_Nh
d1efdn_N174-N241Alpha and beta proteins (a/b)Chelatase-like"Helical backbone" metal receptorPeriplasmic ferric siderophore binding protein FhuDPeriplasmic ferric siderophore binding protein FhuD
1r0v_Ac
d1r0va3A140-A214Alpha and beta proteins (a+b)MutS N-terminal domain-liketRNA-intron endonuclease N-terminal domain-liketRNA-intron endonuclease N-terminal domain-likeDimeric 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.


Alignment-based scores
AlignerAligned LengthSequence IdentityRMSDGDT-TSCOMPASS
manual380.105262.6875464.47368-12.39450
dali470.085112.8539060.10638-12.02067
tm470.085112.4825864.89362-11.43141
fast400.100002.3857362.50000-11.32607

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