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 | d1sr4b_ | Cytolethal distending toxin subunit B | 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 <-- 1.891 --> HitDALI alignment (Z-score: 18.0 Raw score:1744.00) d2dnja_ 1 ----LKIAAFNIRTfGETKMsnaTLASYI-VRIVR---RYDIVLIQEVRDshlvAVGKL- 51 :::::::::: ::::: :::::: ::::: :::::::::::: ::::: d1sr4b_ 1 nlsdFKVATWNLQG-SSAVN--eSKWNINvRQLLSgeqGADILMVQEAGS----LPSSAv 53 d2dnja_ 52 ----------------LDYLNQD-DPNTYHYVVSEPLgrNSYK-ERYLFLFRpnkVSVLD 93 ::::::: ::::::::::::: :::: :::::::: ::::: d1sr4b_ 54 rtsrviqhggtpieeyTWNLGTRsRPNMVYIYYSRLD--VGANrVNLAIVSR---RQADE 108 d2dnja_ 94 TYQYDDDS---fSREPAVVKFSshstkvkEFAIVALHSAPSDAVaEINS-LYDVYLDVQQ 149 :::::::: :::::::::: ::::::::::::::: :::: :::::::::: d1sr4b_ 109 AFIVHSDSsvlqSRPAVGIRIG-------TDVFFTVHALATGGS-DAVSlIRNIFTTFNS 160 d2dnja_ 150 K--WHLNDVMLMGDFNADcsyvtssqWSSIR--lrtSSTFQWLIPdSADTTAtsTNCAYD 205 : ::::::::::::::: ::::: ::::::::: :::::: :::::: d1sr4b_ 161 PpeRRVYSWMVVGDFNRA----panlEVALRqepavSENTIIIAP-TEPTHR--SGNILD 213 d2dnja_ 206 RIVVAGSL------lQSSVvpgSAAPFDFqaAYGLsnemalAISDHYPVEVTLT- 253 :::::::: :::: ::::::: :::: ::::::::::::: d1sr4b_ 214 YAILHDAHlprreqaRERI---GASLMLN-qLRSQ------ITSDHFPVSFVRDr 258 FAST alignment (Normalized score: 9.88 Raw score:2525.00) d2dnja_ 1 L-----KIAAFNIRTFGETKMS-NATLA-SYIVRIVR----RYDIVLIQEVRDSHLVAVG 49 ::::::: ::::: ::::: ::::::: :::::::::: d1sr4b_ 1 -NLSDFKVATWNL-QGSSA---VNESKWNINVRQLL-SGEQGADILMVQEA--------- 45 d2dnja_ 50 KLLDYL-----------------------------NQDDPN--TYHYVVSEPLGRNSYK- 77 :::: :::::: ::::: d1sr4b_ 46 ------GSLPSSAVRTSRVIQHGGTPIEEYTWNLGTRSR--PNMVYIYY-SRLDV----G 92 d2dnja_ 78 ---ERYLFLFRPNKVSVLDTYQYDDDSF--------SREPAVVKFSSHSTKVKEFAIVAL 126 ::::::: :::::::::: ::::::::: :::::::: d1sr4b_ 93 ANRVNLAIVS---RRQADEAFIV-----HSDSSVLQSRPAVGIRI-------GTDVFFTV 137 d2dnja_ 127 HSAPSDAVAEINSLYDVYLDVQQKWHL---------NDVMLMGDFNADCSYVTSS-QWSS 176 :::::: :::::::::::::: :::::::::: :::: d1sr4b_ 138 HALATG----GSDAVSLIRNIFTT---FNSPPERRVYSWMVVGDFN---------RAPAN 181 d2dnja_ 177 IRLRT-----------SSTFQWLIPDSADTTATSTNCAYDRIVVAG------SLLQSSVV 219 ::::::::: ::::: :::::::::::: ::::: d1sr4b_ 182 -----LEVALRQEPAVSENTIIIAP-TEPTH--RSGNILDYAILH-DAHLPRREQAR--- 229 d2dnja_ 220 PG---SAAPFDFQAAYGLSNEMALA--ISDHYPVEVTLT--- 253 ::::: :::::: :::::::::: d1sr4b_ 230 --ERIGASLM--LNQLRS-------QITSDHFPVSFV--RDR 258 TMalign alignment (TM-score: 0.71 Raw score:180.19) d2dnja_ 1 ----LKIAAFNIRTFGETKMSNATLASYIVRIVR---RYDIVLIQEVRDSHLVAVGK--- 50 :::::::::::::::: : ::::::::::: :::::::::::: :::::: d1sr4b_ 1 NLSDFKVATWNLQGSSAVNE-S-KWNINVRQLLSGEQGADILMVQEAGS--LPSSAVRTS 56 d2dnja_ 51 ------------LLDYLNQ-DDPNTYHYVVSEPLGRNSYK-ERYLFLFRPNKVSVLDTYQ 96 ::::::: ::::::::::: ::: :::: ::::::::: ::::::: d1sr4b_ 57 RVIQHGGTPIEEYTWNLGTRSRPNMVYIYYS-RLD-VGANRVNLAIVSRR---QADEAFI 111 d2dnja_ 97 YDD-DS--FSREPAVVKFSSHSTKVKEFAIVALHSAPSDAVAEINS-LYDVYLDVQQK-- 150 ::: :: ::::::::::: :::::::::::::: ::::: ::::::::::: d1sr4b_ 112 VHSDSSVLQSRPAVGIRIG-------TDVFFTVHALATGG-SDAVSLIRNIFTTFNSPPE 163 d2dnja_ 151 WHLNDVMLMGDFNADCSYVTSSQWSSIRLRT--SSTFQWLIPDSADTTATSTNCAYDRIV 208 ::::::::::::::: ::: ::::::::: ::::::::: ::::: : ::::::::: d1sr4b_ 164 RRVYSWMVVGDFNRA---PAN-LEVALRQEPAVSENTIIIAP-TEPTH-R-SGNILDYAI 216 d2dnja_ 209 VAGSLL----QSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT- 253 :::::: :::::: :::::::: :: : :: :::::::::::: d1sr4b_ 217 LHDAHLPRREQARERI-GASLMLNQ-LR-S---QI--TSDHFPVSFVRDR 258 HHsearch alignment (Probability: 1.00 E-value:0.00) d2dnja_ 1 LKIAAFNIRTFGETKMSNAT-LASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDD 59 :::::::::::::::::::: :::::::::::::::::::::::::::::: :::::::: d1sr4b_ 5 FKVATWNLQGSSAVNESKWNINVRQLLSGEQGADILMVQEAGSLPSSAVRT-SRVIQHGG 63 d2dnja_ 60 PNTYHYV--------------VSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDDSFSRE 105 ::::::: ::::::::::::::::::::::::::::::::::::::: d1sr4b_ 64 TPIEEYTWNLGTRSRPNMVYIYYSRLDVGANRVNLAIVSRRQADEAFIVHSDSSVLQSRP 123 d2dnja_ 106 PAVVKFSSHSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHL---NDVMLMGDF 162 :::::: :::::::::::::::: :::::::::::::::::: ::::::::: d1sr4b_ 124 AVGIRI-------GTDVFFTVHALATGGS-DAVSLIRNIFTTFNSPPERRVYSWMVVGDF 175 d2dnja_ 163 NADCSYVTSSQWSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVV--P 220 :::::::::::::::: ::::::::::::: ::::::::::::::::::::::: : d1sr4b_ 176 NRAPANLEVALRQEPA--VSENTIIIAPTEP---THRSGNILDYAILHDAHLPRREQARE 230 d2dnja_ 221 GSAAPFDFQAAYGLSNEMALAISDHYPVEV 250 :::: :::::::::::::::::::: d1sr4b_ 231 RIGA------SLMLNQLRSQITSDHFPVSF 254