d1hbnb2d1aisb2

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1hbn_Bh	d1hbnb2	B49-B60,B73-B100,B117-B163	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	Methyl-coenzyme M reductase alpha and beta chain N-terminal domain	Beta chain
1ais_Bc	d1aisb2	B1200-B1220,B1221-B1242,B1243-B1300	All alpha proteins	Cyclin-like	Cyclin-like	Transcription factor IIB (TFIIB), core domain	Transcription factor IIB (TFIIB), core domain

Justification for analogy
In 1hbn_B, the 4-helix bundle uses two helices from the ferredoxin core and two inserted helices. This is a hybrid 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

1hbn_Bh   -----------NLEGIENALKtaeldlDIVGNAESIAAAAKEMIQVtedddpsarfdvaaeysaaplVTATAFVQAIINEFDvs--myDANMVKAAVLgr----------------------
1ais_Bc   tpkklfvkptdYVNKFADELG------LSEKVRRRAIEILDEAYKRglt---------------sgkSPAGLVAAALYIASLlegekrTQREVAEVARvtevtvrnrykelveklkikvpia

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

1hbn_Bh   ---------------NLEGIEnalktaeldldivgnAESIAAAAKEMIQVteddDPSARFdvaaeYSAAPLVTATAFVQAIINEFdvsmydanmVKAAVLG--------------------------r
1ais_Bc   tpkklfvkptdyvnkFADELG--------------lSEKVRRRAIEILDE--ayKRGLTS-----GKSPAGLVAAALYIASLLEG------ekrTQREVAEvarvtevtvrnrykelveklkikvpia

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

1hbn_Bh   ----------N-LEGIENALKTAELDLDIVGN-AESIAAAAKEMI-QVTEDDDPSARFDVAAEYSAAPLVTATAFVQAIINEF-----DVSMYDANMVKAA-----------------------VLGR
1ais_Bc   TPKKLFVKPTDYVNKFAD-E----LGLS--EKVRRRAIEILDEAYKRGL----T--S--------GK-S-PAGLVAAALYIASLLEGEKRTQREVAEVARVTEVTVRNRYKELVEKLKIKVPIA----

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

1hbn_Bh   ---------------NLEGIENALKTAELDLDIVGNA---ESIAAAAKEMIQVTEDDDPSARFDVA--------AEYSAAPLVTATAFVQAIINEFDVSMYD-----ANMVKAAVLGR-------------------------
1ais_Bc   TPKKLFVKPTDYVNKFADEL-----------------GLSEKVRRRAIEILD--------------EAYKRGLTSGKS-PAGLVAAALYIASLLE-------GEKRTQREVAEVA---RVTEVTVRNRYKELVEKLKIKVPIA