d1izna_d1gkza1

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1izn_Ai	d1izna_	A7-A42,B2-B33	Multi-domain proteins (alpha and beta)	Subunits of heterodimeric actin filament capping protein Capz	Subunits of heterodimeric actin filament capping protein Capz	Capz alpha-1 subunit	Capz alpha-1 subunit
1gkz_Ac	d1gkza1	A64-A104,A127-A174	All alpha proteins	Bromodomain-like	alpha-ketoacid dehydrogenase kinase, N-terminal domain	alpha-ketoacid dehydrogenase kinase, N-terminal domain	Branched-chain alpha-ketoacid dehydrogenase kinase (BCK)

Justification for analogy
In 1izn, the 4-helix bundle uses corresponding parts in the two chains. interface motif. Note that the two chains are not identical, but they are in the same superfamily in SCOP. In 1gkz, the 4-helix bundle is the core motif of that domain.

Alignment-based scores
Aligner	Aligned Length	Sequence Identity	RMSD	GDT-TS	COMPASS
manual	57	0.05263	3.07752	56.14035	-4.66805
dali	62	0.06452	3.02647	54.83871	-5.19767
tm	63	0.07937	3.03187	57.14286	-4.83633
fast	59	0.15254	4.25388	40.25424	-6.23377

Alignment-based scores

Aligner

manual

0.05263

3.07752

56.14035

-4.66805

dali

0.06452

3.02647

54.83871

-5.19767

0.07937

3.03187

57.14286

-4.83633

fast

0.15254

4.25388

40.25424

-6.23377

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 1izn_Ai -----rvSDEEKVRIAAKFithappgeFNEVFNDVRLLLNn-------SDQQLDCALDLMRRL-----PPQQIEKNLSDLIDLVP------ 1gkz_Ac lqqelpvRIAHRIKGFRSLpfii--gcNPTILHVHELYIRafqqllddHKDVVTLLAEGLRESrkhieDEKLVRYFLDKTLTSRLgirmla

DALI alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1izn_Ai --rvSDEEKVRIAAKFITHAPP-gEFNEVFNDVRLLLNN-------SDQQLDCALDLMR-----rlpPQQIEKNLSDLIDLVP------ 1gkz_Ac lqqeLPVRIAHRIKGFRSLPFIigCNPTILHVHELYIRAfqqllddHKDVVTLLAEGLResrkhiedEKLVRYFLDKTLTSRLgirmla

TM alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1izn_Ai R--VS-DEEKVRIAAKFITHAPPGEFNE-VFNDVRLLL-NN--------SDQQLDCALDLMR-R---LP-PQQ-IEKNLSDLI-DLVP------ 1gkz_Ac LQQ-ELPVRIAHRIKGFRSLPFIIGCNPTILHVHEL-YIRAFQQLLDDHK-DVVTLLAEGLRESRKHIEDEKLVR-YFLDKTLTS-RLGIRMLA

FAST alignment PDB format superposition aligned motifs in PyMol whole structures in PyMol 1izn_Ai RVSDEEKVRIAAKFITH---APPGE-----FNEVFNDVRLLLNN---SDQQLDCALDLMRRLPPQ------------QIEKNLSDLIDLVP------- 1gkz_Ac --LQQELPVRIAHRIKGFRSLPFIIGCNPTILHVHELYIRAF--QQLLDDHKDVVTLLAEG----LRESRKHIEDEKLVRYFLDKTLTSR-LGIRMLA