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: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.427 --> Intermediate <-- 1.891 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1sr4b_) 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 d1sr4b_ Cytolethal distending toxin subunit BDNase I-​likeDNase I-​likeα+β

Supporting Alignments

Query <-- 1.427 --> Intermediate
DALI 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 <-- 1.891 --> Hit
DALI 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