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 <-- 2.017 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1akoa_) 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 d1akoa_ DNA-​repair enzyme exonuclease IIIDNase 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 <-- 2.017 --> Hit
DALI alignment (Z-score: 19.6 Raw score:1911.60) d2dnja_ 1 LKIAAFNIRTFGetkmsnatLASYIVRIVR--RYDIVLIQEVRDSHLVAVGKLLDYLnqd 58 :::::::::::: :::::::::: ::::::::::::::::::::::::: d1akoa_ 1 MKFVSFNINGLR-------aRPHQLEAIVEkhQPDVIGLQETKVHDDMFPLEEVAKL--- 50 d2dnja_ 59 dpnTYHYVVSEPlgrnsYKERYLFLFRPnkvSVLDTYQ-YDDDsFSRE--PAVVKFSSHS 115 ::::::::: ::::::::::: ::::::: :::: :::: :::::::::: d1akoa_ 51 ---GYNVFYHGQ----kGHYGVALLTKE---TPIAVRRgFPGDdEEAQrrIIMAEIPSLL 100 d2dnja_ 116 tkvKEFAIVALHSAPS----------DAVAEINSLYDVYLDVQQkwhlNDVMLMGDFNAD 165 ::::::::::::: :::::::::::::::::: :::::::::::: d1akoa_ 101 ---GNVTVINGYFPQGesrdhpikfpAKAQFYQNLQNYLETELK--rdNPVLIMGDMNIS 155 d2dnja_ 166 --------------------cSYVTSSQWSS-IRLRtSSTFQWLIP------dSADTTAT 198 :::::::::: :::: ::::::::: ::::::: d1akoa_ 156 ptdldigigeenrkrwlrtgkCSFLPEEREWmDRLM-SWGLVDTFRhanpqtaDRFSWFD 214 d2dnja_ 199 --------STNCAYDRIVVAgSLLQSSVVpgSAAPFD-FQAAYglsnemalAISDHYPVE 249 :::::::::::: :::::::: :::::: ::::: ::::::::: d1akoa_ 215 yrskgfddNRGLRIDLLLAS-QPLAECCV--ETGIDYeIRSME--------KPSDHAPVW 263 d2dnja_ 250 VTLT- 253 :::: d1akoa_ 264 ATFRr 268 FAST alignment (Normalized score: 11.87 Raw score:3091.00) d2dnja_ 1 LKIAAFNIRTFGETKMSNAT---LASYIVRIVR--RYDIVLIQEVRDSHLVAVGK-LLDY 54 :::::::::: :::::::::: :::::::::::: :::: :::: d1akoa_ 1 MKFVSFNING----------LRARPHQLEAIVEKHQPDVIGLQETKV-HDDM---FPLEE 46 d2dnja_ 55 LNQDDPN---TYHYVVSEPLGR-NSYKERYLFLFRPNKVSVLDTYQYDDDSFSR------ 104 : ::::::: ::::::::::: :::::::: d1akoa_ 47 V------AKLGYNVFYH-----GQKGHYGVALLT---KETPIAVR---------RGFPGD 83 d2dnja_ 105 ------EPAVVKFSSHSTKV--KEFAIVALHSAPS------------DAVAEINSLYDVY 144 ::::::::: ::::::::::: ::::::::::::: d1akoa_ 84 DEEAQRRIIMAEIPS-----LLGNVTVINGYFP--QGESRDHPIKFPAKAQFYQNLQNYL 136 d2dnja_ 145 LDVQQKWHL------NDVMLMGDFNADC-----------------------SYVTSSQWS 175 : :::::::::: ::::::::: d1akoa_ 137 E--------TELKRDNPVLIMGDMN---ISPTDLDIGIGEENRKRWLRTGKCSFLPEERE 185 d2dnja_ 176 S-IRLRTSSTFQWLI-------PDSADTTATS-----------TNCAYDRIVVAGSLLQS 216 : ::::: :::::: ::::::: :::::::::: :::::: d1akoa_ 186 WMDRLMS-WGLVDT-FRHANPQTADRFSW---FDYRSKGFDDNRGLRIDLLLA-SQPLAE 239 d2dnja_ 217 SVVPGSAAPF-DFQAAYGLSNEMA-LAISDHYPVEVTLT-- 253 :: :::::: :::: ::::::::::::: d1akoa_ 240 CC--VETGIDYEIRS---------MEKPSDHAPVWATF-RR 268 TMalign alignment (TM-score: 0.73 Raw score:184.13) d2dnja_ 1 LKIAAFNIRTFGETKMSNATLASYIVRIVR-R-YDIVLIQEVRDSHLVAVGKLLDYLNQD 58 :::::::::::: : :::::::::: : :::::::::::::::::::::::: d1akoa_ 1 MKFVSFNINGLR--A-----RPHQLEAIVEKHQPDVIGLQETKVHDDMFPLEEVAKL--- 50 d2dnja_ 59 DPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQ-YDDDSFSRE--PAVVKFSSHS 115 :::::: ::: :::::::::::: ::::::: ::::::::: ::::::::: d1akoa_ 51 ---GYNVFY-HGQ---KGHYGVALLTKE---TPIAVRRGFPGDDEEAQRRIIMAEIPSL- 99 d2dnja_ 116 TKVKEFAIVALHSAPS--------D--AVAEINSLYDVYLDVQQKWHLNDVMLMGDFNAD 165 :::::::::::::: : ::::::::::::::::: :::::::::::::: d1akoa_ 100 --LGNVTVINGYFPQGESRDHPIKFPAKAQFYQNLQNYLETELK--RDNPVLIMGDMNIS 155 d2dnja_ 166 -----C--------------SYVTSSQ-WSSI-RLRTSSTFQWLIP-----DS-ADTTAT 198 : ::::::: :::: ::: ::::::::: :: :::::: d1akoa_ 156 PTDLDIGIGEENRKRWLRTGKCSFLPEEREWMDRLM-SWGLVDTFRHANPQTADRFSWFD 214 d2dnja_ 199 ----S----TNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEV 250 : ::::::::::: :::::::: ::::::::: :: : :::::::::: d1akoa_ 215 YRSKGFDDNRGLRIDLLLAS-QPLAECCV--ETGIDYEIR--SM---E--KPSDHAPVWA 264 d2dnja_ 251 TLT- 253 ::: d1akoa_ 265 TFRR 268 HHsearch alignment (Probability: 1.00 E-value:0.00) d2dnja_ 1 LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDP 60 ::::::::::: ::::::::::::: :::::::::::::::::::::::: : d1akoa_ 1 MKFVSFNINGL---RARPHQLEAIVEK--HQPDVIGLQETKVHDDMFPLEEVA------K 49 d2dnja_ 61 NTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDDSFSREPAVVKFSSHSTKVKE 120 :::::::::::: :::::::::::::::::::::::::::: ::::::: :::::: d1akoa_ 50 LGYNVFYHGQKG----HYGVALLTKETPIAVRRGFPGDDEEAQR--RIIMAEI-PSLLGN 102 d2dnja_ 121 FAIVALHSAPSDAV-------AEINSLYDVYLDVQQK-WHLNDVMLMGDFNADCSYVTSS 172 :::::::::::::: :::::::::::::::: :::::::::::::::::::::: d1akoa_ 103 VTVINGYFPQGESRDHPIKFPAKAQFYQNLQNYLETELKRDNPVLIMGDMNISPTDLDIG 162 d2dnja_ 173 QWS--------------------------SIRLRTSSTFQWLIPDS--ADTT-------- 196 ::: ::::: :::::::::: :::: d1akoa_ 163 IGEENRKRWLRTGKCSFLPEEREWMDRLMSWGLV--DTFRHANPQTADRFSWFDYRSKGF 220 d2dnja_ 197 ATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT 253 :::::::::::::::::::::: :::::: ::::::::::::::::::: d1akoa_ 221 DDNRGLRIDLLLASQPLAECCV---ETGIDY-------EIRSMEKPSDHAPVWATFR 267