| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1fbx_Ah |
d1fbxa_ | A1-A22,A74-A87,A133-A169 | Alpha and beta proteins (a+b) | T-fold | Tetrahydrobiopterin biosynthesis enzymes-like | GTP cyclohydrolase I | GTP cyclohydrolase I |
1o08_Ac |
d1o08a_ | A1014-A1035,A1036-A1046,A1047-A1092 | Alpha and beta proteins (a/b) | HAD-like | HAD-like | beta-Phosphoglucomutase-like | beta-Phosphoglucomutase |
Justification for analogy
The motif in 1fbx: 3-helix bundle uses a N-terminal inserted helix and the two core helices in the T-fold, so this is a hybrid motif. I
kept the loop with the one-turn helix to make the topology up-and-down. Actually, this motif is more like a 4-helix bundle.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 53 | 0.03774 | 3.25737 | 57.54717 | -15.87381 |
| dali | 48 | 0.04167 | 2.96674 | 59.89583 | -17.05572 |
| tm | 54 | 0.05556 | 2.87151 | 60.18519 | -16.19196 |
| fast | 52 | 0.03846 | 3.99119 | 42.30769 | -16.62982 |
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 1fbx_Ah -pslSKEAALVHEALVARGLETpifsglDYANFPkitglskinRIVQFFAQRP------QVQERLTQQILIALQTLLGtn-------- 1o08_Ac tdtaEYHFRAWKALAEEIGING--vdrqFNEQLKg-------vSREDSLQKILdladkkVSAEEFKELAKRKNDNYVKmiqdvspadv
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1fbx_Ah -psLSKEAALVHEALVARGletpifsgldyaNFPKitglskinRIVQFFAQ------rPQVQERLTQQILIALQTLLG--------tn 1o08_Ac tdtAEYHFRAWKALAEEIG--ingvdrqfneQLKG-------vSREDSLQKildladkKVSAEEFKELAKRKNDNYVKmiqdvspadv
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1fbx_Ah ---PSLSKEAALVHEAL-VARGLETP-IFSGLD---YA-NFPKITGLSKINRIVQFFAQ-RP----QV-QERLTQQILIALQTLLG----------TN 1o08_Ac TDT--AEYHFRAWKA-LAE--E-IGIN----GVDRQFNEQLKG-----V--SREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDVSPADV--
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1fbx_Ah PSLS-----KEAALVHEALVARGLETPIFSGLD-------YANFPKITGLS--KINRIVQFFAQRP--QVQERLTQQILIALQTLLGTN----------- 1o08_Ac ----TDTAEYHFRAWKALAEEIGI---------NGVDRQFNEQLKG-----VSREDSLQKILDLADKKVSAEEFKELAKRKNDNYV---KMIQDVSPADV