d1b05a_d1nkia_

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1b05_Ah	d1b05a_	A9-A24,A31-A46,A188-A207,A217-A227	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	Oligo-peptide binding protein (OPPA)
1nki_Ac	d1nkia_	A1-A13,A14-A25,A26-A43,A44-A57	Alpha and beta proteins (a+b)	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Antibiotic resistance proteins	Fosfomycin resistance protein A (FosA)

Justification for analogy
The babbb motif in 1b05: a hybrid motif, because a beta-hairpin is absent in the majority of homologs in this superfamily and therefore is an insertion. Other parts of the motif come from the core of this superfamily. The babbb motif in 1nki: a core motif. Thus, these two motifs are analogs.

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

1b05_Ah   -ladkqTLVRNNGsevqiegVPESNVSRDLFEgnGAYKLKNWVVnERIVLERnVInQVTYLPIS----
1nki_Ac   mltglnHLTLAVA-------DLPASIAFYRDL--LGFRLEARWD-QGAYLELgSL-WLCLSREPqygg

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

1b05_Ah   -LADKQTLVRNNGSevqiegvPESNVSRDLFEgnGAYKLKNWVVnERIVLERnVINQVTYLPIS----
1nki_Ac   mLTGLNHLTLAVAD-------LPASIAFYRDL--LGFRLEARWD-QGAYLEL-GSLWLCLSREPqygg

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

1b05_Ah   --LADKQTLVRNNGSEVQIEGVPESNVSRDLFEGNGAYKLKNWVVNERIVLERNVINQVTYLPIS----
1nki_Ac   ML-TGLNHLTLAVADLP------A-SIAFYRDL-LG-FRLEARWD-QGAYLELG-SLWLCLSREPQYGG

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

1b05_Ah   LAD----KQTLVRNNGSEVQIEGVPESNVSRDLFEGN-GAYKLKNWVVNERIVLERNVIN----QVTYLPIS----
1nki_Ac   ---MLTGLNHLTLAVAD-------LPASIAFYRD---LLGFRLEARWD-QGAYLE-----LGSLWLCLSREPQYGG