d1fy2a_d1qmha1

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1fy2_Ah	d1fy2a_	A1-A31,A114-A120,A192-A209	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Aspartyl dipeptidase PepE	Aspartyl dipeptidase PepE
1qmh_Ac	d1qmha1	A185-A218,A219-A231,A232-A279	Alpha and beta proteins (a/b)	Thioredoxin fold	RNA 3'-terminal phosphate cyclase, RPTC, insert domain	RNA 3'-terminal phosphate cyclase, RPTC, insert domain	RNA 3'-terminal phosphate cyclase, RPTC, insert domain

Justification for analogy
The motif in 1fy2: part of the motif comes from the permuted flavodoxin core, part comes from C-terminal insertion. The insertion looks different in different family, e.g. d1gpma2. So this is a hybrid motif and is analog to the thioredoxin 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

1fy2_Ah   ------MELLLLSNstlpgkawLEHALPLIANQLngraLYIGWS--------EGNWIQVSN----GQAVLGGPn------------------------
1qmh_Ac   ergnivQMRGEVLLagvprhvaEREIATLAGSFS---lHEQNIHnlprdqgpGNTVSLEVEseniTERFFVVGekrvsaevvaaqlvkevkrylasta

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

1fy2_Ah   ------MELLLLSNstlPGKAW-LEHALPLIANQLngraLYIGWS--------EGNWIQVSN----GQAVLGGPN------------------------
1qmh_Ac   ergnivQMRGEVLL-agVPRHVaEREIATLAGSFS---lHEQNIHnlprdqgpGNTVSLEVEseniTERFFVVGEkrvsaevvaaqlvkevkrylasta

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

1fy2_Ah   ------MELLLLSN--STLPGKAW--LEHALPLIANQLNGRALYIGWS--------EGNWIQVSNG----QAVLGGPN------------------------
1qmh_Ac   ERGNIVQMRGEVLLAG--VP--RHVAEREIATLAGSFS---LHEQNIHNLPRDQGPGNTVSLEVESENITERFFVVGEKRVSAEVVAAQLVKEVKRYLASTA

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

1fy2_Ah   --------MELLLLSNSTLPGKAW--LEHALPLIANQLN--GRA-LYIGWS-----EGNWIQVSNG----------QAVLGGPN------------------------
1qmh_Ac   ERGNIVQMRGEVLLAG--------VPRHVAEREIATLAGSFSLHEQNIHN-LPRDQGPGNTVSL--EVESENITERFFVVGE--KRVSAEVVAAQLVKEVKRYLASTA