d1qysa_d1i7b.1

Motif
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SCOPidRangeSCOP ClassSCOP FoldSCOP SuperfamilySCOP FamilyProtein
1qys_Aa
d1qysa_A3-A13,A14-A94Designed proteinsNew fold designsNew fold designsalpha+beta foldsTop7
1i7b_Ac
d1i7b.1B4-B23,A74-A166Alpha and beta proteins (a+b)S-adenosylmethionine decarboxylaseS-adenosylmethionine decarboxylaseS-adenosylmethionine decarboxylaseS-adenosylmethionine decarboxylase

Justification for analogy
Top7 is a de novo designed protein, and thus is analog to the natural protein 1i7b. Top7 paper mentioned that there is no significant BLAST hit when Top7 sequence is used as query to search nr database.


Alignment-based scores
AlignerAligned LengthSequence IdentityRMSDGDT-TSCOMPASS
manual760.092112.3682670.06579-0.26971
dali800.100002.4780265.00000-0.27048
tm790.101273.0581562.65823-0.11867
fast720.097222.9675762.84722-0.27435

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

1qys_Aa   -----DIQVQVNIDDN----GKNFDYTYTVtteselqKVLNELMDYIKKQG-------AKRVRISITArtkke----aekFAAILIKVFAELgYNDINVTFDG-----DTVTVEGQL--
1i7b_Ac   ahffeGTEKLLEVWFSrqqpKRRFILKTCG-----ttLLLKALVPLLKLARdysgfdsIQSFFYSRKNfmkpshqgyphrNFQEEIEFLNAI-FPNGAGYCMGrmnsdCWYLYTLDFpe

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

1qys_Aa   -----DIQVQVNIDDN----GKNFDYTYtVTTEselqKVLNELMDYIKKQ-------GAKRVRISITART----kkeaeKFAAILIKVFAELgYNDINVTFDG-----DTVTVEGQ--l
1i7b_Ac   ahffeGTEKLLEVWFSrqqpKRRFILKT-CGTT----LLLKALVPLLKLArdysgfdSIQSFFYSRKNFMkpshqgyphRNFQEEIEFLNAI-FPNGAGYCMGrmnsdCWYLYTLDfpe

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

1qys_Aa   -------DIQVQVNIDDN--GKNFDYTYTVT--TESELQKVLNELMD-YIK--KQGAKRVRISITART-----------KKEAEKFAAILIKVFAELGYNDINVTFDG--------DTVTVEGQ-L
1i7b_Ac   AHFFEGTEKLLEVWFSRQQP--KRRFILKTCGTTL-LLK-ALVPLLKLARDYSGFDS-IQSFFYSRKNFMKPSHQGYPH-RNFQEEIEFLNAIF-----P-NGAGYCMGRMNSDCWYLYTLDFPE-

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

1qys_Aa   D------IQVQVNIDDN-----GKNFDYTYTVTTESELQK----VLNELMDYIKKQG--------AKRVRISIT-ARTKKE--------AEKFAAILIKVFAELGYNDINVTFDGD-------TVTVEGQL--
1i7b_Ac   -AHFFEGTEKLLEVWF-SRQQPKRRFILKTC---------GTTLLLKALVPLLKLA-RDYSGFDSIQSFFYSRKNFMKPS-HQGYPHRNFQEEIEFLNAIF-----PNGAGYCM--GRMNSDCWYLYTLDFPE