| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1htj_Fh |
d1htjf_ | F320-F352,F441-F487 | All alpha proteins | Regulator of G-protein signaling, RGS | Regulator of G-protein signaling, RGS | Regulator of G-protein signaling, RGS | Pdz-RhoGEF RGS-like domain |
1nhu_Ac |
d1nhua_ | A386-A477,A478-A563 | Multi-domain proteins (alpha and beta) | DNA/RNA polymerases | DNA/RNA polymerases | RNA-dependent RNA-polymerase | Viral RNA polymerase |
Justification for analogy
From the 1htj paper, the last three helices (helix 10-12) are an integral extension of the RGS fold with many hydrophobic interactions.
These three helices are absent in other RGS, so they are insertions. The 4-helix motif is a hybrid, using 2 helices from the RGS core and
2 helices from the insertion.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 65 | 0.15385 | 3.26925 | 55.76923 | -3.87278 |
| dali | 69 | 0.10145 | 3.63008 | 52.53623 | -3.89189 |
| tm | 68 | 0.10294 | 2.93833 | 56.25000 | -4.45816 |
| fast | 59 | 0.13559 | 3.36772 | 53.81356 | -3.27757 |
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 1htj_Fh ------------------------------------RPAHLGVFLRYIFSQA-----------------DPSPLLFYLCAEVYqqa-------------------gdplrERQVAEKQLAALGDILSAYaADRSAPMDFALNTYMShagirl--------------------------- 1nhu_Ac rdpttplaraawetarhtpvnswlgniimyaptlwaRMILMTHFFSILLAQEqlekaldcqiygacysiEPLDLPQIIERLHGlsafslhsyspgeinrvasclrklgvpPLRVWRHRARSVRARLLSQ-GGRAATCGKYLFNWAVktklkltpipaasqldlsgwfvagysggdiyhs
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1htj_Fh ------------------------------------RPAHLGVFLRYIFSQADPS--------------PLLFyLCAEVYQQA------------------------GDPLReRQVAEKQLAALGDILsayaadRSAP-MDFALNTYMshaGIRL--------------------------------- 1nhu_Ac rdpttplaraawetarhtpvnswlgniimyaptlwaRMILMTHFFSILLAQEQLEkaldcqiygacysiEPLD-LPQIIERLHglsafslhsyspgeinrvasclrkLGVPP-LRVWRHRARSVRARL-----lSQGGrAATCGKYLF---NWAVktklkltpipaasqldlsgwfvagysggdiyhs
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1htj_Fh ----------------------------------R--PAHLGVFLRYIFS--Q-AD---------------PSPLLFYLCAEVYQQA-------------GDP--------LRERQVAEKQLAALGDILSAYAADR--SAPMDFALNTYMSHAGIRL--------------------------------- 1nhu_Ac RDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSIL-LAQEQLEKALDCQIYGACYSIEPLDLPQIIERLHGLSAFSLHSYSPGEINRVASCLRKLGVP-PL-RVWRHRARSVRARLLSQG--GRAA-TCGKYLFN--W----AVKTKLKLTPIPAASQLDLSGWFVAGYSGGDIYHS
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1htj_Fh RP--------------------------------------AHLGVFLRYIFSQADPSPLLF-----------------YLCAEVYQQAGDPLRE------------------------------RQVAEKQLAALGDILSAYAADRSAPMDFALNTYMSHAGIRL---------------------------------- 1nhu_Ac --RDPTTPLARAAWETARHTPVNSWLGNIIMYAPTLWARMILMTHFFSILLAQEQLE----KALDCQIYGACYSIEPLDLPQIIERL-------HGLSAFSLHSYSPGEINRVASCLRKLGVPPLRVWRHRARSVRARLLSQ-GGRAATCGKYLFNWA-------VKTKLKLTPIPAASQLDLSGWFVAGYSGGDIYHS