| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1nf2_Ah |
d1nf2a_ | A99-A127,A128-A153 | Alpha and beta proteins (a/b) | HAD-like | HAD-like | Predicted hydrolases Cof | Hypothetical protein TM0651 |
1ptm_Ah |
d1ptma_ | A146-A202,A258-A289 | Alpha and beta proteins (a/b) | Isocitrate/Isopropylmalate dehydrogenase-like | Isocitrate/Isopropylmalate dehydrogenase-like | PdxA-like | 4-hydroxythreonine-4-phosphate dehydrogenase PdxA |
Justification for analogy
The motif in 1nf2: compare 1nf2 with 1l6r (same family), the inserted subdomain is a circularly permuted ferredoxin in 1l6r. So the motif in 1nf2 is a hybrid.
The motif in 1ptm: occurs at the interface of the two duplicates, hybrid.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 52 | 0.07692 | 2.76900 | 62.50000 | -28.93662 |
| dali | 52 | 0.07692 | 2.45292 | 64.42308 | -31.05108 |
| tm | 54 | 0.09259 | 2.92607 | 63.88889 | -28.21613 |
| fast | 44 | 0.09091 | 2.93184 | 56.81818 | -25.04178 |
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 1nf2_Ah --NVHWQAYIDDVLYSEKd--------------------NEEIKSYARHSN------vDYRVEPN---LSELVSKMG--tTKLLLIDT- 1ptm_Ah akKVVMMLATEELRVALAtthlplrdiadaitpallhevIAILHHDLRTKFgiaepraDAVLAMYhdqGLPVLKYQGfgrGVNITLGLp
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1nf2_Ah --nVHWQAYIDDVLYSEK--------------------DNEEIKSYARHSN------vDYRVEP---NLSELVSKMG--tTKLLLIDT- 1ptm_Ah akkVVMMLATEELRVALAtthlplrdiadaitpallheVIAILHHDLRTKFgiaepraDAVLAMyhdQGLPVLKYQGfgrGVNITLGLp
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1nf2_Ah --NVHWQAYIDDVLYSEK--------------------DNEEIKSYARH-S-N--V--DYRVEP---NLSELVSKM--G-TTKLLLIDT- 1ptm_Ah AKKVVMMLATEELRVALATTHLPLRDIADAITPALLHEVIAILHHDLRTKFGIAEPRADAVLAMYHDQG-LPVLKYQGFGRGVNITLGLP
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1nf2_Ah N---VHWQAYIDDVLYSEKDN-------------------EEIKSYARHSNV------------DYRVEPN---LSELVSKMGTT-----KLLLIDT--- 1ptm_Ah -AKKVVMMLATEELRVAL---ATTHLPLRDIADAITPALLHEVIAILHHD--LRTKFGIAEPRADAVLAMYHDQGLPVLKYQ---GFGRGVNITL--GLP