d1rwha2d1n67a2

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1rwh_Ai	d1rwha2	A462-A526,A642-A709	All beta proteins	Hyaluronate lyase-like, C-terminal domain	Hyaluronate lyase-like, C-terminal domain	Hyaluronate lyase-like, C-terminal domain	Chondroitinase AC
1n67_Ah	d1n67a2	A370-A499,A500-A560	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	Bacterial adhesins	Fibrinogen-binding domain	Clumping 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.

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