d1j22a_d1m2aa_

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1j22_Ah	d1j22a_	A5-A50,A116-A135	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Restriction endonuclease-like	XPF/Rad1/Mus81 nuclease	Putative ATP-dependent RNA helicase Hef, nuclease domain
1m2a_Ac	d1m2aa_	A1-A77,A78-A103	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Thioredoxin-like 2Fe-2S ferredoxin	Thioredoxin-like 2Fe-2S ferredoxin

Justification for analogy
The motif in 1j22: From the paper for 1j22, in Fig. 2, d1j22a_ have similar catalytic residues as Hjc (d1gefa_). Thus, d1j22a_ IS an endonuclease superfamily member. Therefore, one strand and one helix in the motif are insertion. In other families, the insertion adopts different conformations, e.g. d1ckqa_. So this hybrid motif is analogous to thioredoxin.

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

1j22_Ah   ---VKVVVDSR-------------elrSEVVKRLKLLG---------VKLEVKT-LDV----gDYIISE-DVAIERkstPEETAQYIFL-IAKREqee-------
1m2a_Ac   aefKHVFVCVQdrppghpqgscaqrgsREVFQAFMEKIqtdpqlfmtTVITPTGcMNAcmmgpVVVVYPdGVWYGQv--KPEDVDEIVEkHLKGGepverlvisk

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

1j22_Ah   ---VKVVVDSR-------------elrSEVVKRLKLLG---------vKLEVK-TLDV----gDYIIS-EDVAIERkstPEETAQYIFL-IAKREQ-------ee
1m2a_Ac   aefKHVFVCVQdrppghpqgscaqrgsREVFQAFMEKIqtdpqlfmttVITPTgCMNAcmmgpVVVVYpDGVWYGQ--vKPEDVDEIVEkHLKGGEpverlvisk

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

1j22_Ah   ---VKVVVDSR----------EL---RSEVVKRLKLLG---------VKLEVKT-LDV---G-DYIIS-EDVAIERKSTPEETAQYIFL-IAK-RE---------QEE
1m2a_Ac   AEFKHVFVCVQDRPPGHPQGSCAQRGSREVFQAFMEKIQTDPQLFMTTVITPTGCMNACMMGPVVVVYPDGVWYGQV-KP-EDVDEIVEKHLKGGEPVERLVISK---

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

1j22_Ah   ---VKVVVD------------------SRELRSEVVKRLKLLG-----VKLEVKTLDVGD----------YIISE-DVAIERKST------PEETAQYIFLIAKREQEE-----------
1m2a_Ac   AEFKHVFVCVQDRPPGHPQGSCAQRGSREVFQ-AFMEKIQTDPQLFMTTVITPTG-----CMNACMMGPVVVVYPDGVWYG----QVKPEDVDEIVEK---HLKG----GEPVERLVISK