| 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 |
1d1r_Ac |
d1d1ra_ | A29-A111 | Alpha and beta proteins (a+b) | eIF1-like | eIF1-like | eIF1-like | YciH |
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 eIF1-like fold is drastically different than Rossmann structures, the motif in 1efd and the motif in 1d1r are analogs.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 40 | 0.15000 | 3.81339 | 48.75000 | -17.74097 |
| dali | 45 | 0.04444 | 3.53332 | 53.33333 | -23.89151 |
| tm | 55 | 0.05455 | 4.04133 | 48.18182 | -19.70456 |
| fast | 40 | 0.07500 | 3.18074 | 54.37500 | -20.92965 |
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 -arPLLLTTLIDp-----RHMLVFGpnslfqeildeygipna--wqgetnfwGSTAVSIDRLAAY------KDVDVLCFDHD- 1d1r_Ac kgdGVVRIQRQTsgrkgkGVCLITGvdlddaeltklaaelkkkcgcggavkdGVIEIQGDKRDLLkslleaKGMKVKLAGGLe
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1efd_Nh -ARPLLLTTLID-----PRHMLVF---gpnslfqeildeygipnawqgETNFWGSTAVSID---rlAAYK--DVDVLCFDHD- 1d1r_Ac kGDGVVRIQRQTsgrkgKGVCLITgvdlddaeltklaaelkkkcgcggAVKDGVIEIQGDKrdllkSLLEakGMKVKLAGGLe
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1efd_Nh --ARPLLLTTLI--DP--RHMLVFGPNSLFQEILDEYGIPN----AW-QG----------ETNF--WGSTAV-SIDRL-AAYK---DVDVLCFDHD 1d1r_Ac KGDGVVRIQRQTSGRKGK-GVCLIT--------G----VDLDDAELTKLAAELKKKCGCGGAVKDGVIEIQGDKRDLLKSLLEAKGMKVKLAGGLE
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1efd_Nh AR---PLLLTTLIDPR--------HMLVFGPNSLFQEILDEYGIPNAWQG------------------------ETNFWGSTAVS----IDRLAAYK---DVDVLCFDHD- 1d1r_Ac --KGDGVVRIQRQ---TSGRKGKGVCLIT---------------------GVDLDDAELTKLAAELKKKCGCGGAVKD-GVIEIQGDKRDLLKSLL-EAKGMKVKLAGGLE