d3pmga1d1e8ca1

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
3pmg_Ah	d3pmga1	A54-A89,A167-A190	Alpha and beta proteins (a/b)	Phosphoglucomutase, first 3 domains	Phosphoglucomutase, first 3 domains	Phosphoglucomutase, first 3 domains	Phosphoglucomutase
1e8c_Ac	d1e8ca1	A3-A67,A68-A103	Alpha and beta proteins (a/b)	MurF and HprK N-domain-like	MurE/MurF N-terminal domain	MurE/MurF N-terminal domain	UDP-N-acetylmuramyl tripeptide synthetase MurE

Justification for analogy
The motif in 3pmg: comparing the three duplicates, the C-terminal beta hairpin in the first duplicate is an addition. Hybrid motif. These three duplicates apparently have a mini-Rossmann core. The motif in 1e8c: compare 1e8c_A with d1gg4a3 (same family), it appears that the antiparallel strand in 1e8c_A is originally a helix or loop connecting the two parallel strands. Anyway, this can be regarded as a core motif.

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

3pmg_Ah   --------------------------------ATLVVGGdgrfymkeAIQLIVRIAAANGIGRLVIGQ----gvlGKQQFDlenkfkPFTVEIVDS---------------
1e8c_Ac   rnlrdllapwvpdapsralremtldsrvaaagDLFVAVVgh----qaDGRRYIPQAIAQGVAAIIAEAkdeatdgEIREMH------GVPVIYLSQlnerlsalagrfyhe

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

3pmg_Ah   --------------------------------ATLVVGGDgrFYMKeaIQLIVRIAAANGIGRLVIGQ----GVLGKQQFDlenkfkPFTVEIVDS---------------
1e8c_Ac   rnlrdllapwvpdapsralremtldsrvaaagDLFVAVVG--HQAD--GRRYIPQAIAQGVAAIIAEAkdeaTDGEIREMH------GVPVIYLSQlnerlsalagrfyhe

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

3pmg_Ah   --------------------------------ATLVVGGDGRFYMKEAIQLIVRIAAANGIGRLVIGQ--GVL--GKQQFDLENKFKPFTVEIVDS---------------
1e8c_Ac   RNLRDLLAPWVPDAPSRALREMTLDSRVAAAGDLFVAVVG-HQ-AD-GRR-YIPQAIAQGVAAIIAEAKDEATDGEIREMH------GVPVIYLSQLNERLSALAGRFYHE

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

3pmg_Ah   --------------------------------ATLVVGGDG-RFYMKEAIQLIVRIAAANGIGRLVIGQGV-------LGKQQFDLENKFKP-FTVEIVDS----------------
1e8c_Ac   RNLRDLLAPWVPDAPSRALREMTLDSRVAAAGDLFVAVV--GHQAD---GRRYIPQAIAQGVAAIIAE---AKDEATDGEIREMH-------GVPVIYLS-QLNERLSALAGRFYHE