| Motif (click icon to enlarge) | SCOPid | Range | SCOP Class | SCOP Fold | SCOP Superfamily | SCOP Family | Protein |
|---|---|---|---|---|---|---|---|
1l6r_Ah |
d1l6ra_ | A36-A82,A148-A164 | Alpha and beta proteins (a/b) | HAD-like | HAD-like | Predicted hydrolases Cof | Phosphoglycolate phosphatase, PGPase |
1ir6_Ac |
d1ir6a_ | A329-A402,A403-A433 | Alpha and beta proteins (a/b) | DHH phosphoesterases | DHH phosphoesterases | Exonuclease RecJ | Exonuclease RecJ |
Justification for analogy
The motif in 1l6r: two strands are insertions; hybrid motif in a Rossmann structure.
In 1ir6: comparing d1ir6a_ and d1k20a_ (same superfamily), domain 2 in these two homologs are not exactly the same. Anyway,
domain 2 does not have a Rossmann-like structure. So the motif in 1l6r and the motif in 1ir6 are analogs.
| Alignment-based scores | |||||
|---|---|---|---|---|---|
| Aligner | Aligned Length | Sequence Identity | RMSD | GDT-TS | COMPASS |
| manual | 52 | 0.15385 | 2.33533 | 65.86538 | -29.07214 |
| dali | 57 | 0.10526 | 2.44707 | 64.47368 | -25.68230 |
| tm | 61 | 0.13115 | 3.12977 | 55.32787 | -21.33369 |
| fast | 54 | 0.11111 | 2.36651 | 66.20370 | -26.57495 |
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 1l6r_Ah ltVSLLSGN-------VIPVVYALKIFLGinGPVFGEn--gGIMFDNd---------------------gSIKKFFs--geDKAFAVNKLKEMYSl------------ 1ir6_Ac -aKAIVLLDpeghpgvMGIVASRILEATL--RPVFLVaqgkGTVRSLapisavealrsaedlllrygghkEAAGFAmdealFPAFKARVEAYAARfpdpvrevalldl
DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1l6r_Ah -LTVSLLS-GNVIPVVYALKIFLG----iNGPVFGEngGIMFDN-------------------------DGSIKKFfsgeDKAFAVNKLKEMYSL---------------- 1ir6_Ac aKAIVLLDpEGHPGVMGIVASRILeatlrPVFLVAQ--GKGTVRslapisavealrsaedlllrygghkEAAGFAM----DEALFPAFKARVEAYaarfpdpvrevalldl
TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1l6r_Ah LTVSLLSG--N-V--IP-VVYALKIFLGINGPVFGEN-GGIMFDN-----------------------DGSIKKFFS-GEDKAFAVNKLKEMYSL------------- 1ir6_Ac AKAIVLLDPEGHPGVMGIVASRILE-ATLR-PVFLVAQGKGTVRSLAPISAVEALRSAEDLLLRYGGHKEAAGFAMDEALFPAFKARVEA-YAARFPDPVREVALLDL
FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1l6r_Ah L--TVSLLSG-NVIPVVYALKIFL--GIN--GPVFGENGGIMFDND---------------------------GSIKKFFSGEDKAFAVNKLKEMYSL----------------- 1ir6_Ac -AKAIVLLDPEGHPGVMGIVASRILEATLRPVFLVAQ--GKGTV--RSLAPISAVEALRSAEDLLLRYGGHKEAAGFAM----DEALFPAFKARVEA-YAARFPDPVREVALLDL