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 <-- 1.007 --> Intermediate <-- 0.924 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1n25a_) through the intermediate protein (d1tf7a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1tf7a1 Circadian clock protein KaiCP-​loop containing nucleoside triphosphate hydrolasesP-​loop containing nucleoside triphosphate hydrolasesα/β
Hit d1n25a_ Papillomavirus large T antigen helicase domainP-​loop containing nucleoside triphosphate hydrolasesP-​loop containing nucleoside triphosphate hydrolasesα/β

Supporting Alignments

Query <-- 1.007 --> Intermediate
DALI alignment (Z-score: 2.3 Raw score:411.50) query 1 ----------------------------------------------------sLQLRLAL 8 ::::::: d1tf7a1 1 ehqaiakmrtmiegfddishgglpigrstlvsgtsgtgktlfsiqflyngiieFDEPGVF 60 query 9 NQID------------------------------------stvgDIAGNAEAILRWTRHS 32 :::: :::::::::::::::: d1tf7a1 61 VTFEetpqdiiknarsfgwdlaklvdegklfildaspdpegqevVGGFDLSALIERINYA 120 query 33 A-EQGAHLVAFPemALTGypvedlalrssFVEASRTALRELAARLAEEgfgELPVLVGYl 91 : :::::::::: :::: ::::::::::::::::::: :::::::: d1tf7a1 121 IqKYRARRVSID--SVTS-----vfqqydASSVVRRELFRLVARLKQI---GATTVMTT- 169 query 92 drsesaqpkygqpagAPRNaaavlhrgrVALTFAKHHLPNygvfdefryfvpgdtmpivr 151 :::: :::::::::::: d1tf7a1 170 ---------erieeyGPIA-rygveefvSDNVVILRNVLE---------------gerrr 204 query 152 lhgvdialaicedlwqdgGRVPaarsagaglllsvnaspyerdkddtrlelvrkRAQEAg 211 :::: ::::: d1tf7a1 205 rtleilklrgtshmkgeyPFTI--------------------------------TDHGI- 231 query 212 cttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcvvldldlpaaeaePPTGvv 271 :::: d1tf7a1 232 ---------------------------------------------------nifPLGA-- 238 query 272 ddglridrlviseeplpayeaelaggyadrl 302 d1tf7a1 239 ---------------------------mrlt 242 FAST alignment (Normalized score: 2.60 Raw score:703.80) query 1 ----------------------------------------------------SLQLRLAL 8 :::::::: d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVF 60 query 9 NQIDST-----------------------------------------VGDIAGNAEAILR 27 : ::::::::::::: d1tf7a1 61 V-----TFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIE 115 query 28 WTRHSA-EQGAHLVAFPEMALTGYPVEDLALRSS----------FVEASRTALRELAARL 76 :::::: :::::::::: :::::::::::::::: d1tf7a1 116 RINYAIQKYRARRVSID-----------------SVTSVFQQYDASSVVRRELFRLVARL 158 query 77 AEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRG---------------RVA 121 ::: :::::::::: ::: d1tf7a1 159 KQI---GATTVMTTER--------------------------IEEYGPIARYGVEEFVSD 189 query 122 LTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAG 181 :::::::: d1tf7a1 190 NVVILRNV---------------------------------------------------- 197 query 182 LLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEV 241 d1tf7a1 198 ------------------------------------------------------------ 198 query 242 VARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADR 301 d1tf7a1 198 ------------------------------------------------------------ 198 query 302 L--------------------------------------------- 302 d1tf7a1 198 -LEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT 242 TMalign alignment (TM-score: 0.33 Raw score:100.58) query 1 -----SLQL------------RL-----ALNQIDSTVGDIAGNAEAILRWTRHSAEQGAH 38 :::: :: ::::::: : :: :: d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTS-------G--TG--KT--------- 40 query 39 LVAF--------PEMALTGYPVEDLALRSSFVEASRTALRELAARLAEEGFGE------L 84 :::: : d1tf7a1 41 LFSIQFLYNGII----------------------------------------EFDEPGV- 59 query 85 PVL-VG-YLDRSESAQPKYGQPAGAPRNAAA-VLHRGRVALT--------FAKHHLPNYG 133 : : ::: ::::: :::::::::: :::::: d1tf7a1 60 --FV-TFEET----------------PQDIIKNARSFGWDLAKLVDEGKLFILDAS---- 96 query 134 VFDEFRYF-------VPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGAGLLLSV 186 ::::: :::::::::::::::::::::::: d1tf7a1 97 ---PDPEGQEVVGGF---------------------DLSALIERINYAIQKYRARRVSID 132 query 187 N-AS--P-YERDKD-DT-RLELVRKRAQEAGCTTAYLAMIGG-----QDELVFDGDSIVV 235 : :: : :::::: :: :::::::::: ::::::::::::: ::::::::: d1tf7a1 133 SVTSVFQQYDASSVVRRELFRLVARLKQ-IGATTVMTTERIEEYGPI----ARYGVEEFV 187 query 236 DRDGEVVARAP--QFSE--------GCVV-LDLDLPAAEAEPPTGVVDDGLRIDRLVISE 284 :::::: :: :::: :::: d1tf7a1 188 -----SDNVVILR--NVLEGERRRRTLEILKLRG-------------------------- 214 query 285 EPLPAYEAELAGG----------------------YADRL 302 :::::: d1tf7a1 215 -------TSHMKGEYPFTITDHGINIFPLGAMRLT----- 242 HHsearch alignment (Probability: 0.01 E-value:0.33) query 203 VRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQFSEGC 252 :::::::::::::::::::::::::::::::::::::::::::::::::: d1tf7a1 154 LVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERR 203
Intermediate <-- 0.924 --> Hit
DALI alignment (Z-score: 5.7 Raw score:669.50) d1tf7a1 1 ------------------------------------------------------------ 1 d1n25a_ 1 kqvswklvteyametkcddvllllgmylefqysfemclkcikkeqpshykyhekhyanaa 60 d1tf7a1 1 ------------------------------------------------------------ 1 d1n25a_ 61 ifadsknqkticqqavdtvlakkrvdslqltreqmltnrfndlldrmdimfgstgsadie 120 d1tf7a1 1 -ehqaiakmrtmieGFDDISHG-GLPI------gRSTLVSGTSGTGKTLFSIQFLYNGIi 52 :::::::: :::: ::::::::::::::::::::::::: d1n25a_ 121 ewmagvawlhcllpKMDSVVYDfLKCMvynipkkRYWLFKGPIDSGKTTLAAALLELCG- 179 d1tf7a1 53 efdepGVFVTfeetpqdiiknarsfgwdlaklvdegklfildaspdpegqevvGGFDlsa 112 ::::: :::: d1n25a_ 180 -----GKALN----------------------------------------vnlPLDR--- 191 d1tf7a1 113 LIERInYAIQkyRARRVSIDSVTS------vfQQYDassvvrRELFRLVARLKQ------ 160 ::::: :::: :::::::::::: :::: :::::::::::: d1n25a_ 192 LNFEL-GVAI--DQFLVVFEDVKGtggesrdlPSGQ----giNNLDNLRDYLDGsvkvnl 244 d1tf7a1 161 ----------IGATTVMTTERieeygpiaRYGV--EEFVSDNVVILRNVLEgerrrrtle 208 ::::::::::: :::: :::::::::::::::: d1n25a_ 245 ekkhlnkrtqIFPPGIVTMNE--------YSVPktLQARFVKQIDFRPKDY--------- 287 d1tf7a1 209 ilklrgtshmkgeypftiTDHGI------nifpLGAMRL--------------------- 241 ::::: :::::: d1n25a_ 288 -----lkhclerseflleKRIIQsgialllmliWYRPVAefaqsiqsrivewkerldkef 342 d1tf7a1 242 -------------------t 242 d1n25a_ 343 slsvyqkmkfnvamgigvld 362 FAST alignment (Normalized score: 3.41 Raw score:1008.00) d1tf7a1 1 EHQAIAKMRTM------------------------------------------------- 11 d1n25a_ 1 -----------KQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHY 49 d1tf7a1 12 ------------------------------------------------------------ 12 d1n25a_ 50 KYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDI 109 d1tf7a1 12 --------------------------IEGFDDISHGGLPIG------------RSTLVSG 33 ::::::: ::::::: d1n25a_ 110 MFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYD--------FLKCMVYNIPKKRYWLFKG 161 d1tf7a1 34 TSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFIL 93 :::::::::::::::: ::::::: d1n25a_ 162 PIDSGKTTLAAALLEL------CGGKALN------------------------------- 184 d1tf7a1 94 DASPDPEGQEVV---GGFDLSALIERINYAIQK--YRARRVSIDSVTSVFQQYDAS---- 144 :::::::::: :::::::::: d1n25a_ 185 ------------VNLPLDRLNFELG--------VAIDQFLVVFED-----------VKGT 213 d1tf7a1 145 ---------SVVRRELFRLVARLKQI-------------------GATTVMTTERIEEYG 176 :::::::::::::: :::::::: d1n25a_ 214 GGESRDLPSGQGINNLDNLRDYL---DGSVKVNLEKKHLNKRTQIFPPGIVTM------- 263 d1tf7a1 177 PIA----RYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGIN 232 :::::::::::::::::: d1n25a_ 264 ---NEYSVPKTLQARFVKQIDFRPK----------------------------------- 285 d1tf7a1 233 IFPLGAMRLT-------------------------------------------------- 242 d1n25a_ 286 ----------DYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWK 335 d1tf7a1 243 --------------------------- 243 d1n25a_ 336 ERLDKEFSLSVYQKMKFNVAMGIGVLD 362 TMalign alignment (TM-score: 0.36 Raw score:88.28) d1tf7a1 1 ------------------------------------------------------------ 1 d1n25a_ 1 KQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAA 60 d1tf7a1 1 -----------------------------------EHQAIAKM---RTM----------- 11 : : d1n25a_ 61 IFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQM-------LTNR--FNDLLDRMDIMF 111 d1tf7a1 12 -------------IE--GF--DDISHGGL-P---I-------GRSTLVSGTSGTGKTLFS 43 :: :: :::::::: : : :::::::::::::::::: d1n25a_ 112 GSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLA 171 d1tf7a1 44 IQFLYNGIIEFDEPGVFVTFEE----------TPQDIIKNARSFGWDLAKLVDEGKLFIL 93 :::::::: :::::::: :::::::::: d1n25a_ 172 AALLELCG------GKALNVNLPLDRLNFELG------------------VAIDQFLVVF 207 d1tf7a1 94 DASP----------DPEGQEVVGGFDLSALIERI-N---Y-A--------IQKYRARRVS 130 :::: ::::::::::::::: : : : ::::: ::: d1n25a_ 208 EDVKGTGGESRDLP-----SGQGINNLDNLRDYLDGSVKVNLEKKHLNKR-TQIFP-PGI 260 d1tf7a1 131 IDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDN 190 ::::: : :: : :::::::: :: d1n25a_ 261 VTMNE--Y--------SV-P-KTLQARFV-----------------------------KQ 279 d1tf7a1 191 VVILRNVLEGERRRRT----LEILKLRGTSHMKGEYPFTI-TDHGI---N---I------ 233 :::::::: ::::: ::: ::::: : : d1n25a_ 280 IDFRPKDY---LKHCLERSE-----------------FLLEKRIIQSGIALLLMLIWYRP 319 d1tf7a1 234 ---------------------------FP--LG----------AMRLT 242 :: :: d1n25a_ 320 VAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD----- 362 HHsearch alignment (Probability: 0.98 E-value:0.00) d1tf7a1 14 GFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEE 65 ::::::: ::::::::::::::::::::::::::: :: ::::::::::: d1n25a_ 143 FLKCMVY-NIPKKRYWLFKGPIDSGKTTLAAALLE--LC--GGKALNVNLPL 189