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 | d1rq8a_ | Hypothetical protein SAV1595 | YhbY-like | IF3-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 <-- 1.022 --> HitDALI alignment (Z-score: 2.6 Raw score:211.00) d2dnja_ 1 -------------lkiAAFNIrtFGETKMSnATLASYIVRIVRRYDIVLIQeVRDSH--- 44 ::::: ::::::: :::::::::::::::::::: ::::: d1rq8a_ 1 mltgkqkrylrslahnIDPIF-qIGKGGIN-ENMIKQIDDTLENRELIKVH-VLQNNfdd 57 d2dnja_ 45 -LVAVGKLLDYLnqddpnTYHY-VVSEplgrnsykeRYLFLFRPN----kVSVLdtyqyd 98 ::::::::::: :::: :::: ::::::::: :::: d1rq8a_ 58 kKELAETLSEAT------RSELvQVIG---------SMIVIYRESkenkeIELP------ 96 d2dnja_ 99 ddsfsrepavvkfsshstkvkefaivalhsapsdavaeinslydvyldvqqkwhlndvml 158 d1rq8a_ 97 ------------------------------------------------------------ 97 d2dnja_ 159 mgdfnadcsyvtssqwssirlrtsstfqwlipdsadttatstncaydrivvagsllqssv 218 d1rq8a_ 97 ------------------------------------------------------------ 97 d2dnja_ 219 vpgsaapfdfqaayglsnemalaisdhypvevtlt 253 d1rq8a_ 97 ----------------------------------- 97 FAST alignment (Normalized score: 2.50 Raw score:388.90) d2dnja_ 1 LKIA-------------------AFNIRTFGETKM----SNATLASYIVRIVRRYDIVLI 37 :::: ::::::::::::::::::::: d1rq8a_ 1 ----MLTGKQKRYLRSLAHNIDPIFQI--------GKGGINENMIKQIDDTLENRELIKV 48 d2dnja_ 38 QEVRDSH-----LVAVGKLLDYLNQDDPNTYH-----YVVSEPLGRNSYKE-RYLFLFRP 86 ::::: :::::::::: :::: ::::::: d1rq8a_ 49 -HVLQN-NFDDKKELAETLSEA----------TRSELVQVI----------GSMIVIYR- 85 d2dnja_ 87 NKVSVLDTYQYDDDSFSREPAVVKFSSHSTKVKEFAIVALHSAPSDAVAEINSLYDVYLD 146 d1rq8a_ 86 ------------------------------------------------------------ 86 d2dnja_ 147 VQQKWHLNDVMLMGDFNADCSYVTSSQWSSIRLRTSSTFQWLIPDSADTTATSTNCAYDR 206 d1rq8a_ 86 ------------------------------------------------------------ 86 d2dnja_ 207 IVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT----------- 253 d1rq8a_ 86 -----------------------------------------------ESKENKEIELP 96 TMalign alignment (TM-score: 0.23 Raw score:59.21) d2dnja_ 1 -------------LKI--AAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEV-RDS- 43 : :::::: :::::: ::::::::::::::::::::::: ::: d1rq8a_ 1 MLTGKQKRYLRSL--AHNIDPIFQ-IGKGGI-NENMIKQIDDTLENRELIKVHVLQNNFD 56 d2dnja_ 44 H-LVAVGKLLDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPN-----KVSVLDTYQY 97 : :::::::::::: ::::::: :::::::::: ::: d1rq8a_ 57 DKKELAETLSEATR------SELVQVI--------GSMIVIYRESKENKEIEL------- 95 d2dnja_ 98 DDDSFSREPAVVKFSSHSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVM 157 : d1rq8a_ 96 --------------P--------------------------------------------- 96 d2dnja_ 158 LMGDFNADCSYVTSSQWSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSS 217 d1rq8a_ 97 ------------------------------------------------------------ 97 d2dnja_ 218 VVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT 253 d1rq8a_ 97 ------------------------------------ 97 HHsearch alignment (Probability: 0.02 E-value:0.29) d2dnja_ 12 GETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDPNTYHYVVSEPL 71 ::::::: ::::::::::::::::::::: ::::::::::::::::::::::::: : d1rq8a_ 24 GKGGINE-NMIKQIDDTLENRELIKVHVL-QNNFDDKKELAETLSEATRSELVQV----I 77 d2dnja_ 72 GRNSYKERYLFLFRPNKV 89 : ::::::::::: d1rq8a_ 78 G------SMIVIYRESKE 89