Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets.
J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu
Query: T0542_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d2dnja_ | Deoxyribonuclease I | DNase I-like | DNase I-like | α+β |
| Hit | d1wdua_ | Endonuclease domain of TRAS1 retrotransposon (ORF2) | DNase I-like | DNase I-like | α+β |
Query <-- 1.411 --> IntermediateDALI alignment (Z-score: 4.0 Raw score:601.80) query 1 slqLRLALNQIDS-tvGDIAG--NAEAILRWTRHsaeqgAHLVAFPEMaltgypvedlal 57 :::::::::: ::::: ::::::::::: ::::::::: d2dnja_ 1 ---LKIAAFNIRTfgeTKMSNatLASYIVRIVRR-----YDIVLIQEV------------ 40 query 58 rssfveaSRTALRELAARLAEEGFGELPvlvgyldrsesaqpkygqpagaprnaaavlhr 117 ::::::::::::::::::::: d2dnja_ 41 ----rdsHLVAVGKLLDYLNQDDPNTYH-------------------------------- 64 query 118 grvALTFAKHhlpnygVFDEfryfvpgdtmpivrLHGVDialaiceDLWQD--------g 169 ::::::: :::: ::::: ::::: d2dnja_ 65 ---YVVSEPL-----gRNSY--kerylflfrpnkVSVLD-----tyQYDDDsfsrepavv 109 query 170 grvpaarsagAGLLLSVNaSPYErdkdDTRLELVRKRAQEAG------CTTAYLA--mig 221 :::::::: :::: ::::::::::::::: ::::::: d2dnja_ 110 kfsshstkvkEFAIVALH-SAPS--daVAEINSLYDVYLDVQqkwhlnDVMLMGDfnadc 166 query 222 gqdelvfdgdsivvdrdgEVVAR---aPQFS----------------------------- 249 ::::: :::: d2dnja_ 167 syvtssqwssirlrtsstFQWLIpdsaDTTAtstncaydrivvagsllqssvvpgsaapf 226 query 250 ------------------EGCVVLDLDlpaaeaepptgvvddglridrlviseeplpaye 291 ::::::::: d2dnja_ 227 dfqaayglsnemalaisdHYPVEVTLT--------------------------------- 253 query 292 aelaggyadrl 302 d2dnja_ 254 ----------- 254 FAST alignment (Normalized score: 3.85 Raw score:1064.00) query 1 SLQLRLALNQIDSTVGD---------IAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYP 51 :::::::: ::::::::::::: :::::::: d2dnja_ 1 ---LKIAAFNI------RTFGETKMSNATLASYIVRIVR-----RYDIVLIQ-------- 38 query 52 VEDLALRSSFVEAS------RTALRELAARLAEEGFG-ELPVLVGYLDRSESAQPKYGQP 104 :::::::::::: :::: :::::: d2dnja_ 39 --------------EVRDSHLVAVGKLLDYLN-QDDPNTYHYVV---------------- 67 query 105 AG-------APRNAAAVLHRGRVALTFAK------------HHLPNYGVFDEFRYFVPGD 145 ::::::::: ::::::: d2dnja_ 68 --SEPLGRNSYKERYLFL-----------FRPNKVSVLDTYQYDDDSF------------ 102 query 146 T-----MPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA-------GLLLSVNASPYER 193 ::::: :::::::::: d2dnja_ 103 -SREPAVVKFS-----------------------------SHSTKVKEFAIVALHSA--- 129 query 194 DKD--------DTRLELVRKRAQEAG-CTTAYLAMIGGQDELVF---------------- 228 ::::::::::::::: :::::: d2dnja_ 130 ---PSDAVAEINSLYDVYLDVQQKWHLNDVMLM-----------GDFNADCSYVTSSQWS 175 query 229 ----------------------------DGDSIVVDRDGEVVARAPQFS----------- 249 ::::::: d2dnja_ 176 SIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVA--------------GSLLQSSVVPG 221 query 250 -----------------------EGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEP 286 :::::::: d2dnja_ 222 SAAPFDFQAAYGLSNEMALAISDHYPVEVTL----------------------------- 252 query 287 LPAYEAELAGGYADRL- 302 d2dnja_ 253 ----------------T 253 TMalign alignment (TM-score: 0.46 Raw score:140.16) query 1 SLQLRLALNQIDSTVG-DIA-G--NAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLA 56 :::::::::::: ::: : :::::::::: :: ::::: :: :: d2dnja_ 1 ----LKIAAFNIRTFGETKMSNATLASYIVRIVR-RY----DIVLI-QE-VR-------- 41 query 57 LRSSFVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLH 116 ::: ::::::::::::::::::::::: ::::: :: :::::::::: d2dnja_ 42 ----DSH--LVAVGKLLDYLNQDDPNTYHYVV-SEPLG--------RN--SYKERYLFLF 84 query 117 RG----RVA-LTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLH----GVDIALAICE---- 163 :: : :::::::::: : : :: :::::::: :::::::::: d2dnja_ 85 RPNKVS--VLDTYQYDDDSF-----S---R-EP-AVVKFSSHSTKVKEFAIVALHSAPSD 132 query 164 ---DLWQDGGRVPAARS-A-GAGLLLSVNASPYER--DKDDTR-LELVRKRAQEAGCTTA 215 :::::::::::::: : ::::::::::::::: :::::: ::::::::: ::: d2dnja_ 133 AVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQWSS-IRLRTSSTF---QWL 188 query 216 YL---AMIGGQDELVFDGDSIVVDRD--GE-V-VA-RAP-Q----------------FSE 250 :: :::::: ::::::::::::: :: : :: ::: : ::: d2dnja_ 189 IPDSADTTATS--TNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHY 246 query 251 GCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRL 302 :::::: : d2dnja_ 247 PVEVTL-----------------------------------T---------- 253 HHsearch alignment (Probability: 0.07 E-value:0.01) query 4 LRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPE 44 ::::::::::: :::::::::::::::::::: :::::::: d2dnja_ 1 LKIAAFNIRTF-GETKMSNATLASYIVRIVRR-YDIVLIQE 39
Intermediate <-- 2.043 --> HitDALI alignment (Z-score: 18.0 Raw score:1653.80) d2dnja_ 1 --LKIAAFNIRTFGetkmsnatlaSYIVRIVR--RYDIVLIQEVRDshlvavgKLLDyln 56 :::::::::::: :::::::: :::::::::::: :::: d1wdua_ 1 ppYRVLQANLQRKK-------latAELAIEAAtrKAAIALIQEPYV-------KGFR--- 43 d2dnja_ 57 qddpnTYHYVVSEPlgRNSYKERYLFLFRPNKVSVlDTYQYdddsfsREPAVVKFSSHSt 116 ::::::::: ::::::::::::::::::: ::::: :::::::::::: d1wdua_ 44 -----GVRVFQSTA--QGDGTVKAAIAVFDHDLDV-IQYPQ---lttNNIVVVGIRTRA- 91 d2dnja_ 117 kvKEFAIVALHSAP-SDAVAEINSLYDVYLDVQqkwhLNDVMLMGDFNAD---csyvTSS 172 :::::::::::: :::::::::::::::::: ::::::::::::: ::: d1wdua_ 92 --WEITLVSYYFEPdKPIESYLEQIKRVERKMG----PKRLIFGGDANAKstwwgskEDD 145 d2dnja_ 173 Q-WSSI-RLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSlLQSSVVpgSAAPFDFqa 230 : :::: ::::::::::::::::::::::::::::::::::: :::::: ::::::: d1wdua_ 146 ArGDQLmGTLGELGLHILNEGDVPTFDTRYQSRVDVTFCTED-MLDLID--GWRVDED-- 200 d2dnja_ 231 ayglsnemalaISDHYPVEVTLT--- 253 :::::::::::: d1wdua_ 201 ---------lvSSDHNGMVFNIRlqk 217 FAST alignment (Normalized score: 10.87 Raw score:2547.00) d2dnja_ 1 --LKIAAFNIRTFGETKMS-NATLASYIVRIVR--RYDIVLIQEVRDSHLVAVGKLLDYL 55 ::::::::: ::::::::::::: :::::::::: d1wdua_ 1 PPYRVLQANLQ--------RKKLATAELAIEAATRKAAIALIQEP--------------- 37 d2dnja_ 56 NQDDPN------TYHYVVSEPLGRN--SYKE-RYLFLFRPNKVSV-----LDTYQYDDDS 101 :::::::: :::: ::::::: :::: d1wdua_ 38 ------YVKGFRGVRVFQST-----AQGDGTVKAAIAVF------DHDLDVIQY------ 74 d2dnja_ 102 FSR------EPAVVKFSSHSTKV-KEFAIVALHSAPSDAVA--EINSLYDVYLDVQQKWH 152 :::::::::: :::::::::::: :::::::::::::::: d1wdua_ 75 ---PQLTTNNIVVVGIRTR----AWEITLVSYYFEP-----DKPIESYLEQIKRVERKM- 121 d2dnja_ 153 -LNDVMLMGDFNADCSYVT-----------SSQWSSIRLRTSS-----TFQWLIPDSADT 195 ::::::::::: ::::: :::: :::::::::::: d1wdua_ 122 GPKRLIFGGDAN-------AKSTWWGSKEDDARGD--QLMG--TLGELGLHILNEGDVPT 170 d2dnja_ 196 TATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALA----ISDHYPVEVT 251 ::::::::::::: :::::::::: ::::: :::::::::: d1wdua_ 171 FDTRYQSRVDVTF-CTEDMLDLID--GWRVD---------------EDLVSSDHNGMVFN 212 d2dnja_ 252 LT---- 253 : d1wdua_ 213 I-RLQK 217 TMalign alignment (TM-score: 0.67 Raw score:169.98) d2dnja_ 1 --LKIAAFNIRTFGETKMSNATLASYIVRIVR-R-YDIVLIQEVRDSHLVAVGKLLDYLN 56 ::::::::::: :: :::::::::: : ::::::::::: :::: d1wdua_ 1 PPYRVLQANLQRK---KL----ATAELAIEAATRKAAIALIQEPYV-------KGFR--- 43 d2dnja_ 57 QDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDDSFSREPAVVKFSSHST 116 : ::::::::: ::::::::::::::::::::::::: : ::::::::::: d1wdua_ 44 ----G-VRVFQSTAQ--GDGTVKAAIAVFDHDLDVIQYPQLT---T-NNIVVVGIRTR-- 90 d2dnja_ 117 KVKEFAIVALHSAPSDAVAEINS-LYDVYLDVQQKWHLNDVMLMGDFNADC----SYVTS 171 : ::::::::::::::::::::: ::::::::: :::::::::::::: :::: d1wdua_ 91 A-WEITLVSYYFEPDKPIESYLEQIKRVERKMG----PKRLIFGGDANAKSTWWG-SKED 144 d2dnja_ 172 SQ-WSSI-RLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQ 229 :: :::: ::::::::::::::::::::::::::::::::::: :::::: :::::::: d1wdua_ 145 DARGDQLMGTLGELGLHILNEGDVPTFDTRYQSRVDVTFCTED-MLDLID--GWRVDEDL 201 d2dnja_ 230 AAYGLSNEMALAISDHYPVEVTLT--- 253 : :::::::::::: d1wdua_ 202 ---------V--SSDHNGMVFNIRLQK 217 HHsearch alignment (Probability: 1.00 E-value:0.00) d2dnja_ 1 LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDP 60 ::::::::::: ::::::::::::: ::::::::::::::::: d1wdua_ 3 YRVLQANLQRK---KLATAELAIEAAT--RKAAIALIQEPYVKGFR-------------- 43 d2dnja_ 61 NTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDDSFSREPAVVKFSSHSTKVKE 120 ::::::::: ::::::::::::::::::::::::::: :::::::::: :::: d1wdua_ 44 GVRVFQSTA---QGDGTVKAAIAVFDHDLDVIQYPQLTT----NNIVVVGIRT---RAWE 93 d2dnja_ 121 FAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQ--W--S- 175 :::::::::::::::::: :::::::::::::::::::::::::::::::: : : d1wdua_ 94 ITLVSYYFEPDKPIESYL---EQIKRVERKMGPKRLIFGGDANAKSTWWGSKEDDARGDQ 150 d2dnja_ 176 SIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLS 235 :::::::::::::::::::::::::::::::::::::::::: :::::: d1wdua_ 151 LMGTLGELGLHILNEGDVPTFDTRYQSRVDVTFCTEDMLDLI---DGWRVD--------- 198 d2dnja_ 236 NEMALAISDHYPVEVTLT 253 :::::::::::::::: d1wdua_ 199 --EDLVSSDHNGMVFNIR 214