d1rwha2d1n67a2

Motif
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SCOPidRangeSCOP ClassSCOP FoldSCOP SuperfamilySCOP FamilyProtein
1rwh_Ai
d1rwha2A462-A526,A642-A709All beta proteinsHyaluronate lyase-like, C-terminal domainHyaluronate lyase-like, C-terminal domainHyaluronate lyase-like, C-terminal domainChondroitinase AC
1n67_Ah
d1n67a2A370-A499,A500-A560All beta proteinsCommon fold of diphtheria toxin/transcription factors/cytochrome fBacterial adhesinsFibrinogen-binding domainClumping factor A

Justification for analogy
The motif in 1rwh: This protein has two all-beta domains: Hyaluronate lyase-like (H) and Supersandwich (S). All proteins containing H have S, but not vice versa. Since H and S are two separate domains, this motif is an interface motif, using some strands in H and some in S. The motif in 1n67: uses immunoglobulin core elements as well as a C-terminal extension, hybrid.


Alignment-based scores
AlignerAligned LengthSequence IdentityRMSDGDT-TSCOMPASS
manual710.042254.7005947.53521-7.25096
dali670.029854.3840055.97015-8.81353
tm710.084514.8491841.54930-5.72837
fast670.044784.9063444.40299-6.96899

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

1rwh_Ai   egqwgaavpadewSGATALGEVAAVGQH-LVGPgRTGLTARKSWFVsg--------------------------------------------------------------------------------DVTVCLGAdISTASgakvegnkysvirndaTAQSVEFK---TAKTTAATFWKpgmag--dlgasGPACVVFSrhgnelslavseptqkaag
1n67_Ah   -------------EKYGKFYNLSIKGTIdQIDK-TNNTYRQTIYVNpsgdnviapvltgnlkpntdsnalidqqntsikvykvdnaadlsesyfvnpenfedvtnsvnitfpnpnqykvefntpddqiTTPYIVVV-NGHIDpns--------kgdlaLRSTLYGYnsnIIWRSMSWDNEvafnngsgsgdgIDKPVVPEqpdepgeiepipek-----

DALI alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1rwh_Ai   egqwgaavpadewsgaTALG----EVAAVG-QHLVGpgrtgLTARKSWFVSGDvtvclgadistasgakveGNKYSVIR-----------------------------------------------------------------------------------ndATAQSVEFKT-------aKTTAATFWKpgmagdlgaSGPACVVFS-RHGNelslavseptqkaag
1n67_Ah   ---------------eKYGKfynlSIKGTIdQIDKT-----NNTYRQTIYVNP------------sgdnviAPVLTGNLkpntdsnalidqqntsikvykvdnaadlsesyfvnpenfedvtnsvnitfpnpnqykvefntpddqittpyivvvnghidpnskgDLALRSTLYGynsniiwrSMSWDNEVA--fnngsgsGDGIDKPVVpEQPD----epgeiepipek

TM alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1rwh_Ai   ---EGQWGAAVPADEWSGATALGEVAAVGQHLVGPGRTGLTARKSWFV-SGD--------------------------VTVCLGADISTASGAKVEGNKYSVIRNDATAQSVEFKTA----------------KTTAATFWKPGMAGDLGASG-----PACVVFSRHGNELSL-------------------------AV---------S---------------------------------EPTQK--AAG
1n67_Ah   EKY---------------GKFYNLSIKGTIDQID--KTNNTYRQTIYVNPSGDNVIAPVLTGNLKPNTDSNALIDQQN----------------------------TSIKVYKVDNAADLSESYFVNPENFED-----------VTNSVNITFPNPNQYKVEFNTP---DDQITTPYIVVVNGHIDPNSKGDLALRSTLYGYNSNIIWRSMSWDNEVAFNNGSGSGDGIDKPVVPEQPDEPGEIEPIPEK---

FAST alignment     PDB format superposition    aligned motifs in PyMol   whole structures in PyMol

1rwh_Ai   EGQWGAAVPADEWSGATALGEVAAVGQHL-VGPGRTGLTARKSWFVSG-----------------------------------------------------------------------------------DVTVCLGADISTASGAKVEGNKYSVIRNDAT-------AQSVEFKT----AKTTAATFWKPGMAGDLGASG--------------PACVVFSRHGNELSLAVSEPTQKAAG---------------
1n67_Ah   -------------EKYGKFYNLSIKGTIDQIDKT-NNTYRQTIYV---NPSGDNVIAPVLTGNLKPNTDSNALIDQQNTSIKVYKVDNAADLSESYFVNPENFEDVTNSVNITFPNPNQYKVEFNTPDDQITTPYIVVVNGHIDPN----------------SKGDLALRSTLYGY-NSNIIWRSMSWDN------------EVAFNNGSGSGDGIDKPVVP--------------------EQPDEPGEIEPIPEK