HorA Server Transitive Detail

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


Query <-- 1.411 --> Intermediate <-- 1.780 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1i9za_) through the intermediate protein (d2dnja_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d2dnja_ Deoxyribonuclease IDNase I-​likeDNase I-​likeα+β
Hit d1i9za_ Synaptojanin,​ IPP5C domainDNase I-​likeDNase I-​likeα+β

Supporting Alignments

Query <-- 1.411 --> Intermediate
DALI 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 <-- 1.780 --> Hit
DALI alignment (Z-score: 14.0 Raw score:1443.70) d2dnja_ 1 --------------------------LKIAAFNIRTFGetkmsnatlASYIvRIVRR--- 31 :::::::::::: :::: ::::: d1i9za_ 1 ydpiheyvnhelrkrenefsehknvkIFVASYNLNGCS--------aTTKL-ENWLFpen 51 d2dnja_ 32 -----yDIVLIQEVR---dSHLVAVGKLLDYLNQ--------ddPNTYHYVVSEPlgrns 75 ::::::::: ::::::::::::::: ::::::::::: d1i9za_ 52 tpladiYVVGFQEIVqltsADPAKRREWESCVKRllngkctsgpGYVQLRSGQLV----- 106 d2dnja_ 76 ykeRYLFLFRPN-----kVSVLDTYQYDDDSFSREPAVVKFSSHstkvKEFAIVALHSAP 130 ::::::::: :::::::::::::::::::::::::: :::::::::::: d1i9za_ 107 ---GTALMIFCKesclpsIKNVEGTVKKTGLGNKGAVAIRFDYE---dTGLCFITSHLAA 160 d2dnja_ 131 S--DAVAEINSLYDVYLDVQ--qKWHLN---DVMLMGDFNADCS---------------- 167 : ::::::::::::::::: ::::: ::::::::::::: d1i9za_ 161 GytNYDERDHDYRTIASGLRfrrGRSIFnhdYVVWFGDFNYRISltyeevvpciaqgkls 220 d2dnja_ 168 ------YVTSsQWSS-IRLRtssTFQWLiPDSADTTAT-------------STNCAYDRI 207 :::: :::: :::: ::::: ::::::::: ::::::::: d1i9za_ 221 ylfeydQLNK-QMLTgKVFP---FFSELpITFPPTYKFdigtdiydtsdkhRVPAWTDRI 276 d2dnja_ 208 VVAGSllqSSVVpgSAAPFDFQaayglsnemalaISDHYPVEVTLT-------------- 253 ::::: :::: :::::::: :::::::::::: d1i9za_ 277 LYRGE---LVPH--SYQSVPLY------------YSDHRPIYATYEanivkvdrekkkil 319 d2dnja_ 254 ----------------- 254 d1i9za_ 320 feelynqrkqevrdasq 336 FAST alignment (Normalized score: 7.27 Raw score:2120.00) d2dnja_ 1 --------------------------LKIAAFNIRTFGETKMSNAT--LASYIVRIVRRY 32 :::::::::: ::::::::: d1i9za_ 1 YDPIHEYVNHELRKRENEFSEHKNVKIFVASYNLNG----------CSATTKLENWL--- 47 d2dnja_ 33 ----------DIVLIQEVRDSH------------LVAVGKLLDYLNQ--DDPNTYHYVVS 68 ::::::: ::::::::::::: :::::::: d1i9za_ 48 FPENTPLADIYVVGFQE-----IVQLTSADPAKRREWESCVKRLLNGKCTSGPGYVQ--- 99 d2dnja_ 69 EPLGRNSY-------KERYLFLFRPNKVSV-------LDTYQYDDDSF-----SREPAVV 109 ::::::::::: :::::: ::::::: d1i9za_ 100 --------LRSGQLVGTALMIFCKES----CLPSIKNVEGTVK-----KTGLGNKGAVAI 142 d2dnja_ 110 KFSSHSTKV--KEFAIVALHSA--PSDAVAEIN-SLYDVYLDVQQK---------WHLND 155 :::: ::::::::::: ::: ::::: :::::::: ::::: d1i9za_ 143 RFDY-----EDTGLCFITSHLAAGYTN-YDERDHDYRTIASG----LRFRRGRSIFNHDY 192 d2dnja_ 156 VMLMGDFNADCSYV----------------TSSQWSSI--RLRTS--------STFQWLI 189 :::::::::: :::::: :::: ::::: : d1i9za_ 193 VVWFGDFNYR----ISLTYEEVVPCIAQGKLSYLFE--YDQLNK-QMLTGKVFPFFSE-L 244 d2dnja_ 190 PDSADTTAT-------------------STNCAYDRIVVAGSLLQSSVV---PGSAAPFD 227 :::: ::::::::::::: :::::::: d1i9za_ 245 PITF-----PPTYKFDIGTDIYDTSDKHRVPAWTDRILYRG--------ELVPHSYQSVP 291 d2dnja_ 228 FQAAYGLSNEMALA--ISDHYPVEVTLT-------------------------------- 253 ::::::::::: d1i9za_ 292 --------------LYYSDHRPIYATY-EANIVKVDREKKKILFEELYNQRKQEVRDASQ 336 TMalign alignment (TM-score: 0.67 Raw score:168.42) d2dnja_ 1 -------------------------LKIAAFNIRTFGETKMSNATLASYIVRIV--RRY- 32 :::::::::::: ::: : ::::::::: ::: d1i9za_ 1 YDPIHEYVNHELRKRENEFSEHKNVKIFVASYNLNGC-SAT--T-KLENWLFPENTPLAD 56 d2dnja_ 33 DIVLIQE-VR-----DSH--LVAVGKLLDYLNQ-D--DPNTYHYVVSEPLGRNSYKERYL 81 ::::::: :: ::: ::::::::::::: : ::::::::::::: :::: d1i9za_ 57 IYVVGFQEIVQLTSADPAKRREWESCVKRLLNGKCTSGPGYVQLRSGQLV------GTAL 110 d2dnja_ 82 FLFRP-NKV--S-VLDTYQYDDDSFSREPAVVKFSSHSTKVKEFAIVALHSAPS--DAVA 135 ::::: ::: : :::::::::::::::::::::::: :::::::::::::: :::: d1i9za_ 111 MIFCKESCLPSIKNVEGTVKKTGLGNKGAVAIRFDYE---DTGLCFITSHLAAGYTNYDE 167 d2dnja_ 136 EINSLYDVYLDVQ--QKWH--LND-VMLMGDFNADCSY-----------------VTSSQ 173 ::::::::::::: :::: ::: ::::::::::::: ::::: d1i9za_ 168 RDHDYRTIASGLRFRRGRSIFNHDYVVWFGDFNYRISLTYEEVVPCIAQGKLSYLFEYDQ 227 d2dnja_ 174 WSSIRLRTS--STFQWLIPDSADTT--A----TST--------NCAYDRIVVAGSLLQSS 217 :::: :::: :::::::::::::: : ::: :::::::::: : :: d1i9za_ 228 LNKQ-MLTGKVFPFFSELPITFPPTYKFDIGTDIYDTSDKHRVPAWTDRILYR---G-EL 282 d2dnja_ 218 VVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT------------------------ 253 :: :::: ::: ::::::::::::::: d1i9za_ 283 VP--HSYQ-SVP---------LYYSDHRPIYATYEANIVKVDREKKKILFEELYNQRKQE 330 d2dnja_ 254 ------ 254 d1i9za_ 331 VRDASQ 336 HHsearch alignment (Probability: 1.00 E-value:0.00) d2dnja_ 1 LKIAAFNIRTFGETKMSNATLASYIVRI-VRRYDI--VLIQEVRDSHLVAV-------GK 50 :::::::::::: :::::::::::: :::::: :::::::::::::: :: d1i9za_ 27 IFVASYNLNGCS----ATTKLENWLFPENTPLADIYVVGFQEIVQLTSADPAKRREWESC 82 d2dnja_ 51 LLDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQY---DDDSFSREPA 107 :::::::::::::::::::::: ::::::::::::::::::::::: :::::::::: d1i9za_ 83 VKRLLNGKCTSGPGYVQLRSGQ--LVGTALMIFCKESCLPSIKNVEGTVKKTGLGNKGAV 140 d2dnja_ 108 VVKFSSHSTKVKEFAIVALHSAPSDA--VAEINSLYDVYLDVQQ-----KWHLNDVMLMG 160 :::::: ::::::::::::::::: :::::::::::::::: ::::::::::: d1i9za_ 141 AIRFDY---EDTGLCFITSHLAAGYTNYDERDHDYRTIASGLRFRRGRSIFNHDYVVWFG 197 d2dnja_ 161 DFNADCSYVTSSQWSSI-----------------RL--RTSSTFQ----WLIP-----DS 192 ::::::::::::::::: :: ::::::: :::: :: d1i9za_ 198 DFNYRISLTYEEVVPCIAQGKLSYLFEYDQLNKQMLTGKVFPFFSELPITFPPTYKFDIG 257 d2dnja_ 193 ADTTATSTNCAY----DRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPV 248 :::::::::::: :::::::::::::::: ::::::::::: d1i9za_ 258 TDIYDTSDKHRVPAWTDRILYRGELVPHSYQS-----------------VPLYYSDHRPI 300 d2dnja_ 249 EVTLT 253 ::::: d1i9za_ 301 YATYE 305