d1qd1b1d1itwa_

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1qd1_Bh	d1qd1b1	B2083-B2180	Alpha and beta proteins (a+b)	Ferredoxin-like	Formiminotransferase domain of formiminotransferase-cyclodeaminase.	Formiminotransferase domain of formiminotransferase-cyclodeaminase.	Formiminotransferase domain of formiminotransferase-cyclodeaminase.
1itw_Ac	d1itwa_	A166-A379	Alpha and beta proteins (a/b)	Isocitrate/Isopropylmalate dehydrogenase-like	Isocitrate/Isopropylmalate dehydrogenase-like	Monomeric isocitrate dehydrogenase	Monomeric isocitrate dehydrogenase

Justification for analogy
The motif in 1qd1: uses the last strand in ferredoxin and the C-terminal extensions, hybrid. Compare the two duplicates. The motif in 1itw: Each duplicate in Isocitrate dehydrogenase has five strands, 1~5. The rudimant ICDH fold, or the large insertion as described in SCOP, uses strands 5, 1, 3. So this is a core motif. Note that the dimerization strands are after strand 5 in both the complete and the rudiment ICDH subunits.

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

1qd1_Bh   prmgalDVCPFipvr--------------------------------------------gvtMDECVRCAQAFGQRLAEELGVPVYLYGeaar----------------------------------------------------------------------------------------tagrqSLPALRAgeyealpeklkqaewapdfgpsafvpswGATVAGARk
1itw_Ac   sadsksHVAHMdngdfygsekaaligapgsvkieliakdgsstvlkaktsvqageiidssvmSKNALRNFIAAEIEDAKKQGVLLSVHLkatmmkvsdpimfgqivsefykdaltkhaevlkqigfdvnngigdlyariktlpeakqkeieadiqavyaqrpqlamvnsdkgitnlhvpsdvivdaSMPAMIRdsgk---------------mwgpdgklhDTKAVIPD-

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

1qd1_Bh   prmgALDVCPF---IPVRG-----------------------------------------vTMDECVRCAQAFGQRLAEELGVPVYL-------------------------------------------------------------------------------------ygeaarTAGRqSLPALRAGEYEAL--pekLKQAewapdfgpsafvpsWGATVAGArk
1itw_Ac   sadsKSHVAHMdngDFYGSekaaligapgsvkieliakdgsstvlkaktsvqageiidssvMSKNALRNFIAAEIEDAKKQGVLLSVhlkatmmkvsdpimfgqivsefykdaltkhaevlkqigfdvnngigdlyariktlpeakqkeieadiqavyaqrpqlamvnsdkgitnlhvPSDV-IVDASMPAMIRDSgkmwgPDGK-------------lHDTKAVIP-d

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

1qd1_Bh   ------------------------------------------------------------------------------------------P------R--MG--AL----------------------D-VC--PF-I-PVRGVT-MDEC-VRCAQAFGQRLAEELGVPVYLY-GEAARTAGR---QSL-PALRAGE-YEALPEK---LKQAEWAPDF--GPS-AFVPSW-GATVAGARK
1itw_Ac   SADSKSHVAHMDNGDFYGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIEDAKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYARIKTLPEAK--QKE-IE-ADI-QAVYAQRPQLAMVNS---DKG--ITNL-HVPS-DVIVDA-SMPAMIRDSGKM---WGPDGK-LHDTKAVIPD---------

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

1qd1_Bh   PRMGAL------DVCPFIPVRGVTM---------------------------------------------------DECVRCAQAFGQRLAEELGVPVYLYGEAARTAGRQ----------------------------------------------------------------------------------------------SLPALRAGEYEALPEKL-------KQAEWAPDFGPSAFVPSWG--ATVAGARK
1itw_Ac   ------SADSKSHVAHMD-------NGDFYGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIEDAKKQGVLLSVH----------LKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRD-----SGKMWGPDGKL---------------HDTKAVIPD-