| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1lci__h |
d1lci__ | 83-99,20-41,52-74 | Multi-domain proteins (alpha and beta) | Acetyl-CoA synthetase-like | Acetyl-CoA synthetase-like | Acetyl-CoA synthetase-like | Luciferase |
1lla__c |
d1lla_1 | 30-68,69-84,85-109 | All alpha proteins | Hemocyanin, N-terminal domain | Hemocyanin, N-terminal domain | Hemocyanin, N-terminal domain | Hemocyanin, N-terminal domain |
Justification for analogy
The motif in 1lci: the first helix is a N-terminal extension, the second one is present in the other duplicate, the third one is a
Rossmann helix. So this is a hybrid motif, but needs circular permutation to make it into a common topology.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 45 | 0.11111 | 2.81404 | 63.33333 | -16.48281 |
| dali | 50 | 0.10000 | 3.87803 | 57.50000 | -17.10608 |
| tm | 36 | 0.02778 | 3.36059 | 59.72222 | -30.42445 |
| fast | 43 | 0.11628 | 3.74353 | 48.25581 | -17.33204 |
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 1lci__h --------------------enSLQFFMPVLGALFIG---gTAGEQLHKAMKRYAlvpgtiatYAEYFEMSVRLAEAMKryglnt--- 1lla__c hsdrlknvgklqpgaifscfhpDHLEEARHLYEVFWEagdfNDFIEIAKEARTFV--------NEGLFAFAAEVAVLHRddckglyvp
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1lci__h --------------------ENSLQFFMPVLGALFIG---gTAGEQLHKAMKRYAlvpgtiatYAEYFEMSVRLAEAMKRYG---lnt 1lla__c hsdrlknvgklqpgaifscfHPDHLEEARHLYEVFWEagdfNDFIEIAKEARTFV--------NEGLFAFAAEVAVLHRDDCkglyvp
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1lci__h --ENSLQFFMPVLGALFIGGTAGEQLHKAMKR--YALV-PGTIATYAEYFEMSVRLAEAMKRYGL--N-------------------------------------T 1lla__c HS------------DRL-----K--NVGK-LQPGAIFSCFH---PDHLEEARHLYEVFWEA--GDFNDFIEIAKEARTFVNEGLFAFAAEVAVLHRDDCKGLYVP-
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1lci__h EN----------------------SLQFFMPVLGALFIGGTAG---EQLHKAMKRYALVPGTIATY---AEYFEMSVRLAEAMKRYGLNT--------- 1lla__c --HSDRLKNVGKLQPGAIFSCFHPDHLEEARHLYEVFWE----AGDFNDFIEIAKEART-------FVNEGLFAFAAEVAVLHR------DDCKGLYVP