d1b65a_

DomainSCOPidRangeSCOP ClassSCOP FoldSCOP SuperfamilySCOP familyProtein
1b65_A1d1b65a_A9-A193Alpha and beta proteins (a+b)DmpA/ArgJ-likeDmpA/ArgJ-likeDmpA-likeL-aminopeptidase D-Ala-esterase/amidase DmpA
1b65_A2d1b65a_A194-A375Alpha and beta proteins (a+b)DmpA/ArgJ-likeDmpA/ArgJ-likeDmpA-likeL-aminopeptidase D-Ala-esterase/amidase DmpA

Alignment-based scores

AlignerAligned LengthSequence IdentityRMSDGDT-TSCOMPASS
manual710.084512.7872362.67606-5.80923
dali900.066673.7644758.33333-7.03223
tm970.072163.5185155.67010-5.95331
fast710.084513.1198457.74648-6.17646

In the alignments below, two upper-case letters are aligned, and two lower-case letters are NOT aligned. The superposition files 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. The coordinates of the first domain are transformed, while the coordinates of the second domain are the same as in the original PDB file.


MANUAL alignment      superposition in PDB format     colored superposition in PyMol

1b65_A1   kprardlglpftgvtgpynaitdvdGVGVGFQTIIENeprpgrkrPARSGVTAILPHmqsetpvpvyagvhrfngngemtgthwiedggyflGPVVITN----thgIGMAHHATVRWMVDRYastyqtddFLWIMPVVAETYdga-------------lndingfpvTEADVRKALDNVasgpvqegncgggtgmitygfkg-----------------
1b65_A2   -------------------------GTGTASRVVEFG--------GRSFTIGALVQAnhgqrdwltiagvp-vgqhmrdgtpqsql----siIVVLATDlplmphqLKRLARRASIGIGRNGtpg---gnNSGDIFIAFSTAnqrpmqhrsapfldvemvndepldtVYLAAVDSVEEAvvnamiaaedmggtpfdrllvqaidherlravlrqygrla

DALI alignment      superposition in PDB format     colored superposition in PyMol

1b65_A1   kprardlglpftgvtgpynaitdvdGVGVGFQTIIENeprpgrkrPARSGVTAILPhMQSETpvpvyagvhrfngngemtgthwiedggyflGPVVITNTH----gIGMAHHATVRWMVDRYAsTYQTddFLWIMPVVAETY----------dgalndINGF---pvTEADVRKALDNV--ASGP---------------vqegncgggtgmitygfkg
1b65_A2   -------------------------GTGTASRVVEFG--------GRSFTIGALVQ-ANHGQ----rdwltiagvpvgqhmrdgtpqsqlsiIVVLATDLPlmphqLKRLARRASIGIGRNGT-PGGN--NSGDIFIAFSTAnqrpmqhrsapfldveMVNDepldtVYLAAVDSVEEAvvNAMIaaedmggtpfdrllvqaidherlravlrqygrla

TM alignment      superposition in PDB format     colored superposition in PyMol

1b65_A1   KPRARDLGLPFTGVTGPYNAITDVDGVGVGFQTIIENEPRPGRKRPARSGVTAILPHMQSETP------------------------VPVYAGVHRFNGNGEMTGTHWIEDGGYFLGPVVIT-NTH---GIGMAHHATVRWMVDRYASTYQTDDFLWIMPVVAETYDG-------------ALNDINGF-PVT--EADVRKALDNV--AS--G---------------------------------PVQEGNCGGGTGMITYGFKG
1b65_A2   -------------------------GTGTASRVVEF--G------GRSFTIGALVQA--NHGQRDWLTIAGVPVGQHMRDGTPQSQL---------------------------SIIVVLATDLPLMPHQLKRLARRASIGIGRNGTPGG---NNSGDIFIAFSTANQRPMQHRSAPFLDV---EMVNDEPLDTVYLAAVDSVEEAVVNAMIAAEDMGGTPFDRLLVQAIDHERLRAVLRQYGRLA--------------------

FAST alignment      superposition in PDB format     colored superposition in PyMol

1b65_A1   KPRARDLGLPFTGVTGPYNAITDVDG-VGVGFQTIIENEPRPGRKRP--ARSGVTAILPHMQSETPVPVYAGVHRFNGNGEMTGTHWIEDGGYFL-------------------------------GPVVITN-----THGIGMAHHATVRWMVDRYASTYQTDD------FLWIMPVVAETYDGAL------------------NDINGFPVT---EADVRKALDNVASGPVQEGNCGGGTGMITYGFKG-----------------------------------------
1b65_A2   --------------------------GTGTASRVVEF----------GGRSFTIGALVQ------------------------------------ANHGQRDWLTIAGVPVGQHMRDGTPQSQLSIIVVLAT-DLPLMPHQLKRLARRASIGIGRN---------GTPGGNNSGDIFIAFST-----ANQRPMQHRSAPFLDVEMVNDEPL---DTVYLAAVDSVEE------------------------AVVNAMIAAEDMGGTPFDRLLVQAIDHERLRAVLRQYGRLA