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: T542_A.pdb A
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 | d1vyba_ | Endonuclease domain of LINE-1 reverse transcriptase homolog | DNase I-like | DNase I-like | α+β |
Query <-- 1.427 --> IntermediateDALI alignment (Z-score: 4.0 Raw score:586.90) 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 aelaggyadrldadeevysalvvglrayvakngfrsvliglsggidsalvaaiacdalga 351 d2dnja_ 254 ------------------------------------------------------------ 254 query 352 qnvygvsmpskyssdhskgdaaelarrtglnfrtvsiepmfdaymaslgltglaeenlqs 411 d2dnja_ 254 ------------------------------------------------------------ 254 query 412 rlrgttlmaisnqeghivlapgnkselavgystlygdsvgaygpikdvyktsifrlaewr 471 d2dnja_ 254 ------------------------------------------------------------ 254 query 472 nraaaergqtppipeasitkpdypvldailelyvdrdtgadaivaagydrelvvktlrmv 531 d2dnja_ 254 ------------------------------------------------------------ 254 query 532 dtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d2dnja_ 254 ------------------------------------- 254 FAST alignment (Normalized score: 2.81 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 ---PSDAVAEINSLYDVYLDVQQKWHLNDVMLMG----------DFNADCSYVTSSQWSS 176 query 229 ---------------------------DGDSIVVDRDGEVVARAPQFS------------ 249 ::::::: d2dnja_ 177 IRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVA--------------GSLLQSSVVPGS 222 query 250 ----------------------EGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPL 287 :::::::: d2dnja_ 223 AAPFDFQAAYGLSNEMALAISDHYPVEVTL------------------------------ 252 query 288 PAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACD 347 d2dnja_ 253 ------------------------------------------------------------ 253 query 348 ALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEE 407 d2dnja_ 253 ------------------------------------------------------------ 253 query 408 NLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRL 467 d2dnja_ 253 ------------------------------------------------------------ 253 query 468 AEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKT 527 d2dnja_ 253 ------------------------------------------------------------ 253 query 528 LRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH- 568 d2dnja_ 253 -----------------------------------------T 253 TMalign alignment (TM-score: 0.28 Raw score:157.74) query 1 SLQLRLALNQIDSTVGDIAGNAE--AILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALR 58 :::::::: ::: ::::::: ::::::::::: :::::: :: :: d2dnja_ 1 ---LKIAAFNI-RTF-GETKMSNATLASYIVRIVRR--YDIVLI-QE-VR---------- 41 query 59 SSFVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRG 118 ::: ::::::::::::::::::::::: ::::: : ::::::::::::: d2dnja_ 42 --DSH--LVAVGKLLDYLNQDDPNTYHYVV-SEPLG--------R--NSYKERYLFLFRP 86 query 119 ----RVA-LTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLH----GVDIALAICE------ 163 : :::::::::: : : :: :::::::: :::::::::: d2dnja_ 87 NKVS--VLDTYQYDDDSF-----S---R-EP-AVVKFSSHSTKVKEFAIVALHSAPSDAV 134 query 164 -DLWQDGGRVPAARS-A-GAGLLLSVNASP-YERDKDDTRLEL-VRKRAQEAGCTTAY-- 216 :::::::::::::: : :::::::::::: :::::::::::: ::::::: ::::: d2dnja_ 135 AEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQWSSIRLRTSSTF--QWLIPDS 192 query 217 -LAMIGG-QDELVFDGDSIVVDRD---G--E-VV-ARAPQ------------F---SEGC 252 ::::: :::::::::::: : : :: ::::: : :::: d2dnja_ 193 A-DTTATS----TNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYP 247 query 253 VVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSAL 312 :::::: d2dnja_ 248 VEVTLT------------------------------------------------------ 253 query 313 VVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDA 372 d2dnja_ 254 ------------------------------------------------------------ 254 query 373 AELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAP 432 d2dnja_ 254 ------------------------------------------------------------ 254 query 433 GNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKP 492 d2dnja_ 254 ------------------------------------------------------------ 254 query 493 DYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGF 552 d2dnja_ 254 ------------------------------------------------------------ 254 query 553 GKDRRLPITNRWREGH 568 d2dnja_ 254 ---------------- 254 HHsearch alignment (Probability: 0.05 E-value:0.03) query 4 LRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPE 44 ::::::::::: :::::::::::::::::::: :::::::: d2dnja_ 1 LKIAAFNIRTF-GETKMSNATLASYIVRIVRR-YDIVLIQE 39
Intermediate <-- 2.033 --> HitDALI alignment (Z-score: 20.2 Raw score:1880.90) d2dnja_ 1 -----LKIAAFNIRTFGETKMsnatlASYIVRIVR--RYDIVLIQEVRDS--HLVAVgkl 51 :::::::::::::::: ::::::::: ::::::::::::: ::::: d1vyba_ 1 gsnshITILTLNINGLNSAIK-----RHRLASWIKsqDPSVCCIQETHLTcrDTHRL--- 52 d2dnja_ 52 LDYLnqddpnTYHYVVSEPlgrnSYKERYLFLFRPNK-VSVLDTYQYDddsfSREPAVVK 110 :::: ::::::::: :::::::::::::: :::::::::: :::::::: d1vyba_ 53 KIKG------WRKIYQANG---kQKKAGVAILVSDKTdFKPTKIKRDK----EGHYIMVK 99 d2dnja_ 111 FSSHstkvKEFAIVALHSAPSDAVAEINSLYDVYLDVQqkwhLNDVMLMGDFNAD----- 165 :::: :::::::::::::::::::::::::::::: ::::::::::::: d1vyba_ 100 GSIQ---qEELTILNIYAPNTGAPRFIKQVLSDLQRDL----DSHTLIMGDFNTPlstld 152 d2dnja_ 166 --csyvTSSQWSSI-RLRTSSTFQWLIP-----dSADTTATS---TNCAYDRIVVAGSlL 214 :::::::: ::::::::::::: :::::::: ::::::::::::: : d1vyba_ 153 rstrqkVNKDTQELnSALHQADLIDIYRtlhpksTEYTFFSAphhTYSKIDHIVGSKA-L 211 d2dnja_ 215 QSSVVpgSAAPFDFqaayglsnemalAISDHYPVEVTLT 253 ::::: ::::::: ::::::::::::: d1vyba_ 212 LSKCK--RTEIITN------------YLSDHSAIKLELR 236 FAST alignment (Normalized score: 12.88 Raw score:3148.00) d2dnja_ 1 -----LKIAAFNIRTFGETKMSNATLASYIVRIVR--RYDIVLIQEVRDSH-LVAVGKLL 52 ::::::::::: :::::::::::::: :::::::::::: :::::: d1vyba_ 1 GSNSHITILTLNINGL-----NSAIKRHRLASWIKSQDPSVCCIQETHL--TCRDTHR-- 51 d2dnja_ 53 DYLNQDDPNT------YHYVVSEPLGRNSYKERYLFLFRPN-KVSVLDTYQYDDDSFSR- 104 :::::: ::::: ::::::::::: :::::::::: d1vyba_ 52 ----------LKIKGWRKIYQA--NGKQK-KAGVAILVSDKTDFKPTKIKRD-------K 91 d2dnja_ 105 --EPAVVKFSSHSTKV---KEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWH--LNDVM 157 :::::::: :::::::::::::::::::: :::::::: ::::: d1vyba_ 92 EGHYIMVKGS------IQQEELTILNIYAPNTGAPRFIK---QVLSDLQR---DLDSHTL 139 d2dnja_ 158 LMGDFNADCSYV-------------TSSQWSS--IRLRTSSTFQWLIP-------DSADT 195 :::::: ::::::: :::::: ::::: ::::: d1vyba_ 140 IMGDFN------TPLSTLDRSTRQKVNKDTQELNSALHQA-DLIDI--YRTLHPKSTEYT 190 d2dnja_ 196 TAT----STNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVT 251 :: :::::::::: :::::::::: :::::: :::::::::::: d1vyba_ 191 FF-SAPHHTYSKIDHIV-GSKALLSKCK--RTEIIT------------NYLSDHSAIKLE 234 d2dnja_ 252 LT-- 253 d1vyba_ 235 --LR 236 TMalign alignment (TM-score: 0.71 Raw score:180.58) d2dnja_ 1 -----LKIAAFNIRTFGETKMSNATLASYIVRIVR-R-YDIVLIQEVRDS--HLVAVGKL 51 :::::::::::: : ::: ::: :::::: : :::::::::::: :::::: d1vyba_ 1 GSNSHITILTLNINGLN-S-AIK--RHR-LASWIKSQDPSVCCIQETHLTCRDTHRLK-- 53 d2dnja_ 52 LDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDDSFSREPAVVKF 111 : : ::::::::::: ::::::::::::::::::::::::: ::::::::: d1vyba_ 54 I--K------GWRKIYQANGK--QKKAGVAILVSDKTDFKPTKIKRDK---EGHYIMVKG 100 d2dnja_ 112 SSHSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNAD-----C 166 ::: ::::::::::::::::::::::::::::::: ::::::::::::: : d1vyba_ 101 SIQ---QEELTILNIYAPNTGAPRFIKQVLSDLQRDL----DSHTLIMGDFNTPLSTLDR 153 d2dnja_ 167 -S-YVTSSQ-WSSI-RLRTSSTFQWLIP-----DSADTTATS---TNCAYDRIVVAGSLL 214 : ::::: :::: ::::::::::::: ::::::::: ::::::::::::: : d1vyba_ 154 STR-QKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTFFSAPHHTYSKIDHIVGSKA-L 211 d2dnja_ 215 QSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT 253 ::::: ::::::: : :::::::::::: d1vyba_ 212 LSKCK--RTEIITN----------Y--LSDHSAIKLELR 236 HHsearch alignment (Probability: 1.00 E-value:0.00) d2dnja_ 1 LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDP 60 :::::::::::::: :::::::::::: ::::::::::::::::::: :: :::: d1vyba_ 6 ITILTLNINGLNSA-IKRHRLASWIKS--QDPSVCCIQETHLTCRDTH-----RL-KIKG 56 d2dnja_ 61 NTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDDSFSREPAVVKFSSHSTKVKE 120 ::::::::::: ::::::::::::::::::::::: ::::::::: ::::::: d1vyba_ 57 WRKIYQANGKQ----KKAGVAILVSDKTDFKPTKIKRD-----KEGHYIMVK-GSIQQEE 106 d2dnja_ 121 FAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTS--------- 171 ::::::::::::::::::::::::: : ::::::::::::::::::::: d1vyba_ 107 LTILNIYAPNTGAPRFIKQVLSDLQ---R-DLDSHTLIMGDFNTPLSTLDRSTRQKVNKD 162 d2dnja_ 172 -SQWSSIRLRTSST--FQWLIPDSADTTA----TSTNCAYDRIVVAGSLLQSSVVPGSAA 224 ::::::::::::: ::::::::::::: ::::::::::::::::::::: ::: d1vyba_ 163 TQELNSALHQADLIDIYRTLHPKSTEYTFFSAPHHTYSKIDHIVGSKALLSKCK---RTE 219 d2dnja_ 225 PFDFQAAYGLSNEMALAISDHYPVEVTL 252 : ::::::::::::::: d1vyba_ 220 I------------ITNYLSDHSAIKLEL 235