d1g99a1d1gqyb3

Motif (click icon to enlarge)	SCOPid	Range	SCOP Class	SCOP Fold	SCOP Superfamily	SCOP Family	Protein
1g99_Ah	d1g99a1	A11-A80	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Actin-like ATPase domain	Acetate kinase	Acetate kinase
1gqy_Bc	d1gqyb3	B244-B321	Alpha and beta proteins (a/b)	Ribokinase-like	MurD-like peptide ligases, catalytic domain	MurCDEF	UDP-N-acetylmuramate-alanine ligase MurC

Justification for analogy
The motif in 1g99: compared to d1ig8a1 (same superfamily), two strands are insertion to the RNaseH core. hybrid motif. The motif in 1gqy: although it looks like a dsRBD, the helix belongs to the Rossmann core because without it, half of the Rossmann sheet is not covered. So this motif cannot be dsRBD and thus has nothing to do with RNaseH domains (RNaseH is thought to originated from dsRBD).

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

1g99_Ah   sslkyqlidmtneSALAVGL-CErIGIDNSIITQKKFDGKKLEKLTDLPTHKDALEEVVKALTDdefgvik-----------
1gqy_Bc   ---rqvitygfseQADYRIEdYE-QTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAkeegianeailealadfq

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

1g99_Ah   ---sslkYQLIdmtnesALAVG-LCERigIDNSIITQKKFDGKKLEKLTDLPTHKDALEEVVKALTDdefGVIK--------------
1gqy_Bc   rqvitygFSEQ------ADYRIeDYEQ-tGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVA---KEEGianeailealadfq

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

1g99_Ah   ------SSLKY-QLIDMTNESALAVGLCERIGID-NSIITQKKFDGKKLEKLTDLPTHKDALEEVVKALTDD--EF-------------GVIK
1gqy_Bc   RQVITY--GFSEQA--------DYRIEDYEQ-TGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIANEAILEALADFQ----

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

1g99_Ah   SSLKYQLIDMTNES-----------ALAVGLCERIGI------DNSIITQKKFDGKKLEKLTDLP--THKDALEEVVKALTDDEFGVIK-------------------
1gqy_Bc   --------------RQVITYGFSEQADYRIE------DYEQTGFQGHYTVICPNNERINVLLN--VPGKHNALNATAALAV--------AKEEGIANEAILEALADFQ