| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1ac5__h |
d1ac5__ | 373-446 | Alpha and beta proteins (a/b) | alpha/beta-Hydrolases | alpha/beta-Hydrolases | Serine carboxypeptidase-like | Serine carboxypeptidase II |
1vk0_Ah |
d1vk0a_ | A1-A206 | Alpha and beta proteins (a/b) | Ribonuclease H-like motif | Ribonuclease H-like | DnaQ-like 3'-5' exonuclease | Hypothetical protein AT5G06450 |
Justification for analogy
The motif in 1ac5: 2nd and 3rd helices are insertion, other elements belong to the Rossmann core. hybrid motif;
The motif in 1vk0: 1st strand and 1st helix are insertion, other elements belong to the RNaseH core. hybrid motif;
Basically, insertion in RNaseH is aligned to core elements in Rossmann, and insertion in Rossmann is aligned to core elements in RNaseH.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 55 | 0.10909 | 3.14261 | 59.09091 | -24.75561 |
| dali | 66 | 0.10606 | 4.14872 | 45.07576 | -25.11515 |
| tm | 62 | 0.11290 | 2.83739 | 64.11290 | -26.07432 |
| fast | 60 | 0.11667 | 3.97250 | 49.58333 | -27.32647 |
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 1ac5__h ---------------IEIVLFNGDKdlicNNKGVLDTIDNLkwggikgfsDDAVSFDWIHKSKst--ddsEEFSGYVKYDRNLTFVSVYNa------------------------------------------------------------------------------------------------------------------- 1vk0_Ah sasfdgpkfkmtdgsYVQTKTIDVGss-tDISPYLSLIREDsil---ngnRAVIFDVYWDVGF--tktsgWSLSSVKLSTRNLCLFLRLPkpfhdnlkdlyrffaskfvtfvgvqieedldllrenhglvirnainvgklaaeargtlvleflgtrelahrvlwsdlgqldsieakwekagpeeqleaaaiegwlivnvwdqlsde
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1ac5__h ---------------IEIVLFNGDKDLiCNNKGVLDTIDNL--KWGGikgfsDDAVSFDWIHKSKsTDDSEEFSGYVKYDRNLTFVSVYN-------------------------------------------------------------------------------------------------------------------a 1vk0_Ah sasfdgpkfkmtdgsYVQTKTIDVGSS-TDISPYLSLIREDsiLNGN-----RAVIFDVYWDVGFtKTSGWSLSSVKLSTRNLCLFLRLPkpfhdnlkdlyrffaskfvtfvgvqieedldllrenhglvirnainvgklaaeargtlvleflgtrelahrvlwsdlgqldsieakwekagpeeqleaaaiegwlivnvwdqlsde
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1ac5__h ---------------IEIVLFNGDK-DLICNNKGVLDTIDNLKWGGIKGFSDDAVSFDWIHKSKSTDDS-------EEFSGYVKYDRNLTFVSVYNA------------------------------------------------------------------------------------------------------------------- 1vk0_Ah SASFDGPKFKMTDGSYVQTKTIDVGSST--DISPYLSLIREDS---ILNGNRAVIFDVYWD-------VGFTKTSGWSLSSVKLSTRNLCLFLRLPKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1ac5__h ---------------IEIVLFNGDKD-LICNNKGVLDTIDNL---KWGGIKGFSD-DAVSFDWIHKSKSTD---DSEEFSGYVKYDRNLTFVSVYNA--------------------------------------------------------------------------------------------------------------------- 1vk0_Ah SASFDGPKFKMTDGSYVQTKTIDV--GSSTDISPYLSLIRE-DSILNGN------RAVIFDVYWDVGF---TKTSGWSLSSVKLSTRNLCLFLRL--PKPFHDNLKDLYRFFASKFVTFVGVQIEEDLDLLRENHGLVIRNAINVGKLAAEARGTLVLEFLGTRELAHRVLWSDLGQLDSIEAKWEKAGPEEQLEAAAIEGWLIVNVWDQLSDE