d1gx3a_d1epaa_

Motif
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SCOPidRangeSCOP ClassSCOP FoldSCOP SuperfamilySCOP FamilyProtein
1gx3_Ah
d1gx3a_A85-A185Alpha and beta proteins (a+b)Cysteine proteinasesCysteine proteinasesArylamine N-acetyltransferaseArylamine N-acetyltransferase
1epa_Ac
d1epaa_A3-A162All beta proteinsLipocalinsLipocalinsRetinol binding protein-likeRetinoic acid-binding protein

Justification for analogy
The motif in 1gx3: compare d1gx3a_ with classic cysteine proteinase papain d1ppn__ (same superfamily), half of the barrel in 1gx3 is absent in 1ppn. So this is a hybrid motif and is analog to true barrels in all-beta class. Note that the cysteine proteinase superfamily is very diverged in structures.


Alignment-based scores
AlignerAligned LengthSequence IdentityRMSDGDT-TSCOMPASS
manual770.051954.4227546.10390-18.48876
dali790.050633.3573454.74684-18.29170
tm870.080463.5060552.58621-19.27938
fast700.042863.1930756.78571-16.24640

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

1gx3_Ah   --------gfEVERL-SGRVVwmraddaplpaQTHNVLSVAVPGa--dGRYLVDVgfggqtltSPIRLEA-------GPVQQTRHEPYRLTRHG------DDHTLAAQVRGEWQPlYTFTTEPRP-----------------------------------------
1epa_Ac   vkdfdiskflGFWYEiAFASKmgtp--glahkEEKMGAMVVELKenllALTTTYYse---dhcVLEKVTAtegdgpaKFQVTRLSGKKEVVVEAtdyltyAIIDITSLVAGAVHR-TMKLYSRSLddngealynfrkitsdhgfsetdlyilkhdltcvkvlqsaa

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

1gx3_Ah   ------gfeVERLSG-RVVWMraddaplpaq--THNVLSVAVpgADGRYLVDvGFGG--qtltSPIR-----leAGPVQQTRHEPYRLTRHG------DDHTLAAQVRGEWQPLYTFTTEPRP----------------------------------------
1epa_Ac   vkdfdiskfLGFWYEiAFASKmgtpglahkeekMGAMVVELK--ENLLALTT-TYYSedhcvlEKVTategdgpAKFQVTRLSGKKEVVVEAtdyltyAIIDITSLVAGAVHRTMKLYSRSLDdngealynfrkitsdhgfsetdlyilkhdltcvkvlqsaa

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

1gx3_Ah   ---------GFEVERLSGRVVWMR----------ADDAPLPAQTHNVLSVAVPGADGRYLVDVGFGG---QTLTSPIRLE----AGPVQQTRHEPYRLTRHGD------DHTLAAQVRGEWQPLYTFTTEPRP-----------------------------------------
1epa_Ac   VKDFDISKF--LGFWYEIAFASKMGTPGLAHKEE---------KMGAMVVEL-KENLLALTTTYYSEDHC-VLEKVTATEGDGPAKFQVTRLSGKKEVVVEATDYLTYAIIDITSLVAGAVHRTMKLY-SRSLDDNGEALYNFRKITSDHGFSETDLYILKHDLTCVKVLQSAA

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

1gx3_Ah   GFEV----------ERLSG-RVVWMRADDAPLPAQT--------------HNVLSVAVPGADGRYLVDVGFGGQTLT---------SPIRLEA-----GPVQQTRHEPYRLTRHGD-------DHTLAAQVRGEWQPL-YTFTTEPRP-------------------------------------------
1epa_Ac   ----VKDFDISKFLGFWYEIAFAS------------KMGTPGLAHKEEKMGAMVVELKE--NLLALTTT--------YYSEDHCVLEKVTATEGDGPAKFQVTRLSGKKEVVVEA-TDYLTYAIIDITSLVAGAVHRTMKLYSR----SLDDNGEALYNFRKITSDHGFSETDLYILKHDLTCVKVLQSAA