| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1cs1_Ah |
d1cs1a_ | A68-A88,A190-A233 | Alpha and beta proteins (a/b) | PLP-dependent transferases | PLP-dependent transferases | Cystathionine synthase-like | Cystathionine gamma-synthase, CGS |
1q8i_Ac |
d1q8ia1 | A39-A60,A61-A109 | Alpha and beta proteins (a/b) | Ribonuclease H-like motif | Ribonuclease H-like | DnaQ-like 3'-5' exonuclease | Exonuclease domain of family B DNA polymerases |
Justification for analogy
The motif in 1cs1: Although each family in the PLP-dependent transferases superfamily has this motif, this is a hybrid, because PLP-dependent
transferases superfamily is homologous to some flavodoxin proteins. So this motif is a hybrid between the Rossmann-like core and the insertions, and
is therefore analogous to ancient folds like ferredoxin.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 55 | 0.07273 | 2.26184 | 65.90909 | -21.76905 |
| dali | 59 | 0.06780 | 3.18354 | 60.16949 | -25.40152 |
| tm | 58 | 0.06897 | 2.34238 | 65.08621 | -24.10769 |
| fast | 54 | 0.05556 | 3.04174 | 61.11111 | -21.09597 |
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 1cs1_Ah -AGAVLTNtGMSAIHLVTTVFl--DLVLHSCTkylnghsdVVAGVVIAKDPDVVTELAWWANNIGVTG------ 1q8i_Ac qESVAFIP-ADQVPRAQHILQgeqGFRLTPLAlkd--fhrQPVYGLYCRAHRQLMNYEKRLREGGVTVyeadvr
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1cs1_Ah -AGAVLTNTgMSAIHLVTTVFL--DLVLHSCTKylngHSDVVAGVVIAKDPDVVTELAWWANNIGVT------g 1q8i_Ac qESVAFIPA-DQVPRAQHILQGeqGFRLTPLAL--kdFHRQPVYGLYCRAHRQLMNYEKRLREGGVTvyeadvr
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1cs1_Ah -AGAVLTNTGMSAIHLVTTVFL--DLVLHSCTKYLN----GHSDVVAGVVIAKDPDVVTELAWWANNIGVTG------ 1q8i_Ac QESVAFIPADQV-PRAQHILQGEQGFRLTPL---ALKDFH---RQPVYGLYCRAHRQLMNYEKRLREGGVTVYEADVR
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1cs1_Ah -AGAVLTNTGMSAIHLVTTVFL----DLVLHSCTKYLNG----HSDVVAGVVIAKDPDVVTELAWWANNIGVTG-------- 1q8i_Ac QESVAFIP-ADQVPRAQHIL--QGEQGFRLTPL------ALKDFHRQPVYGLYCRAHRQLMNYEKRLREGGV--TVYEADVR