d1m9na2d1j27a_

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1m9n_Ai	d1m9na2	A235-A278,A412-A439,A440-A450	Alpha and beta proteins (a/b)	Cytidine deaminase-like	Cytidine deaminase-like	AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC	AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC
1j27_Ac	d1j27a_	A16-A62,A63-A98,A1-A15	Alpha and beta proteins (a+b)	Ferredoxin-like	Hypothetical protein TT1725	Hypothetical protein TT1725	Hypothetical protein TT1725

Justification for analogy
The motif in 1m9n: occurs in the interface of the two duplicates.

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

1m9n_Ai   --spGFINLCDALNAWQLVKELkqalgiPAAASFkh------vspAGAAVGI---PESAVRDLIVASIAVKYTQSns-VCYAKD----------GQViGIGAGqq
1j27_Ac   arslKEKRALIKPALERLKARF------PVSAARlygldawgyevVGFTLLGndpAWVEETMRAAARFLAEAGGFqvaLEEFRLeafelmkaylGLY-TARLEtp

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

1m9n_Ai   --SPGFINLCDALNAWQLVKELKqalgipAAASFK------hvspAGAAVGIPESAVRDLIVASIAVKYT----qSNSVCYAKD----------GQVIgIGAGqq
1j27_Ac   arSLKEKRALIKPALERLKARFP------VSAARLygldawgyevVGFTLLGNDPAWVEETMRAAARFLAeaggfQVALEEFRLeafelmkaylGLYT-ARLEtp

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

1m9n_Ai   ---SPGFINLCDALNAWQLVKELKQALGIPAAASF--K-----HVSPAGAAVGIPESAVRDLIVASIAVKYT-----QSNSVCYAK---------DGQVIGIGAG--QQ
1j27_Ac   ARS-LKEKRALIKPALERLKARFP------VSAARLYGLDAWGYE-VVGFTLLGNDPAWVEETMRAAARFLAEAGGFQVALEEFRLEAFELMKAYLGLY-TARLETP--

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

1m9n_Ai   SP----GFINLCDALNAWQLVKELKQALGIP-AAASFKHVSPA-----------GAAVGI----PESAVRDLIVASIAVKYTQSNS-----VCYAKDGQVI--------------GIGAGQQ---
1j27_Ac   --ARSLKEKRALIKPALERLKARF-------PVSAARL-----YGLDAWGYEVVGFTLL-GNDPAWVEETMRAAARFLAEAG----GFQVALEEFR-----LEAFELMKAYLGLYTARL---ETP