d1jdbc2d1r9ca_

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1jdb_Ch	d1jdbc2	C262-C280,C322-C356	Alpha and beta proteins (a/b)	Flavodoxin-like	Class I glutamine amidotransferase-like	Class I glutamine amidotransferases (GAT)	Carbamoyl phosphate synthetase, small subunit C-terminal domain
1r9c_Ac	d1r9ca_	A1-A27,A28-A65	Alpha and beta proteins (a+b)	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Antibiotic resistance proteins	Fosfomycin resistance protein FosX

Justification for analogy
Comparing d1jdbc2 with d1gg9a1 and d1g2ia_, they are homologs (same SCOP superfamily but different family). Note the angle of the helix after strand 4. The motif in 1jdb is a hybrid because two strands in it do not belong to the flavodoxin core.

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

1jdb_Ch   ----diPVFGIC----LGHQLLALASGpaNL-RVThkslfdGTLqGIHRT--DKPAFSFQGHPea--
1r9c_Ac   mieglsHMTFIVrdleRMTRILEGVFD-aREvYASdteqfsLSR-EKFFLigDIWVAIMQGEKlaer

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

1jdb_Ch   ----DIPVFGICLGHQLLALASG---paNLRVTHKsLFDGTLQGIHRTD--KPAFSFQGHPEA--
1r9c_Ac   miegLSHMTFIVRDLERMTRILEgvfdaREVYASDtEQFSLSREKFFLIgdIWVAIMQGEKLAer

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

1jdb_Ch   ----D-IPVF-G--ICLGHQLLALASGPANLRVTH-KS--------LFDGTLQGIHR-TDKPAFSFQGHPE------A
1r9c_Ac   MIEGLSHMTFIVRDLERMTRILEGVFD--AREVYASDTEQFSLSRE-------KFFLIGDIWVAIM---QGEKLAER-

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

1jdb_Ch   ----DIPVFGI----CLGHQLLALASGPAN-LRVTHKSLFDGTLQ------------GIHRTDKPAFSFQGHPEA------
1r9c_Ac   MIEGLSHMTFIVRDLERMTRILEGVF----DAREVYA--------SDTEQFSLSREKFFLIGDIWVAIMQG----EKLAER