| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1ukf_Ah |
d1ukfa_ | A166-A268 | Alpha and beta proteins (a+b) | Cysteine proteinases | Cysteine proteinases | Avirulence protein Avrpph3 | Avirulence protein Avrpph3 |
1gsa__c |
d1gsa_2 | 123-206 | Alpha and beta proteins (a+b) | ATP-grasp | Glutathione synthetase ATP-binding domain-like | ATP-binding domain of peptide synthetases | Prokaryotic glutathione synthetase, C-domain |
Justification for analogy
The motif in 1ukf: compare d1qmya_ and 1ukf, the two helices in the reverse-ferredoxin motif in 1ukf are absent in d1qmya_. So this is a hybrid motif.
This cysteine proteinase superfamily is very diverged in structures.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 60 | 0.03333 | 3.24065 | 60.00000 | -1.00482 |
| dali | 56 | 0.05357 | 2.67146 | 62.50000 | -0.91272 |
| tm | 65 | 0.06154 | 3.45032 | 59.61538 | -1.42108 |
| fast | 49 | 0.06122 | 3.43507 | 52.55102 | -1.16334 |
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 1ukf_Ah --------gfslrrEPKTVHasggsaqLGQTVAHDVAQSgRKHLLSLRFanvqGHAIACSCegsqFKlfdpnlgefqssrsaapQLIKGLIDHYNSlnydVACVNEFRVSV---- 1gsa__c neklftawfsdltpETLVTR-------NKAQLKAFWEKH-SDIILKPLDgmggASIFRVKE----GD-----------------PNLGVIAETLTEh--gTRYCMAQNYLPaikd
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1ukf_Ah --------gfslrREPKTVHasggsaqLGQTVAHDVAQsgRKHLLSLRFanvqGHAIACSCegsQFKLfdpnlgefqssrsaapQLIKGLIdhynslnydvACVNEFRVSV---- 1gsa__c neklftawfsdltPETLVTR-------NKAQLKAFWEK-hSDIILKPLDgmggASIFRVKE---GDPN---------------lGVIAETL-----tehgtRYCMAQNYLPaikd
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1ukf_Ah -----------GFSLRREPKTVHASGGSAQLGQTVAHDVAQSGRKHLLSLRFANVQ---GHAIACSCEGSQFKLFDPNLGEFQSSRSAAPQLIKGL-IDHYNSLNYDVACVNEFRVSV---- 1gsa__c NEKLFTAWFSD---LTPETLVT-R------NKAQLKAFWEK-HSDIILKPL---DGMGGASIFRVKE----GD---------PN-------LG-VIAETLTEH---GTRYCMAQNYLPAIKD
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1ukf_Ah GFSLRRE---------------PKTVHASGGSAQL--GQTVAHDVAQSGR---KHLLSLRFANVQG------HAIACSCEGSQFKLFDPNLGEFQSSR---SAAPQLIKGLIDHYNSLNYDVA--CVNEFRVSV---- 1gsa__c -------NEKLFTAWFSDLTPETLVT---------RNKAQLKAFWE----KHSDIILKPL------DGMGGASIFRVK--------------------EGDPNLGVIAETLTEHG--------TRYCMAQNYLPAIKD