| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1ert__h |
d1ert__ | 1-61 | Alpha and beta proteins (a/b) | Thioredoxin fold | Thioredoxin-like | Thioltransferase | Thioredoxin |
1jr3_Dc |
d1jr3d2 | D17-D117 | Alpha and beta proteins (a/b) | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | Extended AAA-ATPase domain | delta subunit of DNA polymerase III, N-domain |
Justification for analogy
The motif in 1ert: comparing d1ert__ and d1h75a_ (same family, different protein), one strand and one helix are insertion. hybrid.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 53 | 0.03774 | 1.77527 | 75.94340 | -18.88124 |
| dali | 57 | 0.03509 | 2.23924 | 70.17544 | -19.69574 |
| tm | 57 | 0.03509 | 1.82493 | 76.75439 | -21.30420 |
| fast | 53 | 0.03774 | 3.01278 | 56.60377 | -26.12939 |
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 1ert__h --MVKQIE------SKTAFQEALDAAG--------------------------------dKLVVVDFSAt--wCGPCKMIKPFFHSLSekYSNVIFLEVDvdd 1jr3_Dc lrAAYLLLgndpllLQESQDAVRQVAAaqgfeehhtfsidpntdwnaifslcqamslfasRQTLLLLLPengpNAAINEQLLTLTGLL--HDDLLLIVRGnkl
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1ert__h --MVKQI------eSKTAFQEALDAAG--------------------------------dKLVVVDFSA--TWCGPCKMIKPFFHSLSekYSNVIFLEVDVDD 1jr3_Dc lrAAYLLlgndpllLQESQDAVRQVAAaqgfeehhtfsidpntdwnaifslcqamslfasRQTLLLLLPenGPNAAINEQLLTLTGLL--HDDLLLIVRGNKL
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1ert__h --MVKQIE------SKTAFQEALDAAG--DK------------------------------LVVVDFSA--TWCGPCKMIKPFFHSLSEKYSNVIFLEVDVDD-- 1jr3_Dc LRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLL--HDDLLLIVRG--NKL
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1ert__h M---VKQIES------KTAFQEALDAAGDK------LVVVDFSATWCGPCKMIKPFFHSLSEKYSN-VIFLEVDVDD-------------------------------- 1jr3_Dc -LRAAYLLLGNDPLLLQESQDAVRQVA---AAQGFEEHHTFSIDPNTD--WNAIFSLCQAMSLFASRQTLLLLLP--ENGPNAAINEQLLTLTGLLHDDLLLIVRGNKL