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 <-- 0.638 --> Intermediate <-- 1.430 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1f2t.1) 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 d1f2t.1 Rad50P-​loop containing nucleoside triphosphate hydrolasesP-​loop containing nucleoside triphosphate hydrolasesα/β

Supporting Alignments

Query <-- 0.638 --> Intermediate
DALI alignment (Z-score: 3.2 Raw score:303.50) 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---GATTVMTTE 170 query 92 drsesaqpkygqpagaprN-------aaavlhrgRVALTFAKHHLPNYgvfdefryfvpg 144 : :::::::::::::: d1tf7a1 171 ------------------RieeygpiarygveefVSDNVVILRNVLEG------------ 200 query 145 dtmpivrlhgvdialaicedlwqdggrvpaarsagaglllsvnaspyerdkddtrlelvr 204 d1tf7a1 201 ------------------------------------------------------------ 201 query 205 kraqeagcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcvvldldlpaaea 264 d1tf7a1 201 ------------------------------------------------------------ 201 query 265 epptgvvddglridrlviseeplpayeaelaggyadrldadeevysalvvglrayvakng 324 d1tf7a1 201 ------------------------------------------------------------ 201 query 325 frsvliglsggidsalvaaiacdalgaqnvygvsmpskyssdhskgdaaelarrtglnfr 384 d1tf7a1 201 ------------------------------------------------------------ 201 query 385 tvsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqeghivlapgnkselavgyst 444 d1tf7a1 201 ------------------------------------------------------------ 201 query 445 lygdsvgaygpikdvyktsifrlaewrnraaaergqtppipeasitkpdypvldailely 504 d1tf7a1 201 ------------------------------------------------------------ 201 query 505 vdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrw 564 d1tf7a1 201 ----------------------errrrtleilklrgtshmkgeypftitdhginifplga 238 query 565 regh 568 d1tf7a1 239 mrlt 242 FAST alignment (Normalized score: 1.90 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 LDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPS 361 d1tf7a1 198 ------------------------------------------------------------ 198 query 362 KYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAI 421 d1tf7a1 198 ------------------------------------------------------------ 198 query 422 SNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQT 481 d1tf7a1 198 ------------------------------------------------------------ 198 query 482 PPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQY 541 d1tf7a1 198 ------------------------------------------------------------ 198 query 542 PPGTKISAKGFGKDRRLPITNRWREGH--------------------------------- 568 d1tf7a1 198 ---------------------------LEGERRRRTLEILKLRGTSHMKGEYPFTITDHG 230 query 569 ------------ 569 d1tf7a1 231 INIFPLGAMRLT 242 TMalign alignment (TM-score: 0.21 Raw score:121.48) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 :: : : d1tf7a1 1 --------------EH--------------------------------Q-A--------- 4 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1tf7a1 5 ------------------------------------------------------------ 5 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1tf7a1 5 ------------------------------------------------------------ 5 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 ::::: d1tf7a1 5 ------------------------------------------IAKMR------------- 9 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 :: d1tf7a1 10 -------TM--------------------------------------------------- 11 query 301 RLDADEEVYSALVVGLRAYVAKN--------GFRSVLIGLSGG-IDSALVAAIACDALGA 351 :::::::::::: ::: : : :::::::::::::::: d1tf7a1 12 ----IEGFDDISHGGL-PIG--RSTLVSGTS-----------GTGKTLFSIQFLYNGIIE 53 query 352 -QNVYGVSMPSKYSSDHSKGDAAELAR--RTGL--NF-----RTVSIE-PMF--DAYMAS 398 ::::::::: : ::::::::::: :::: :: :::::: : d1tf7a1 54 FDEPGVFVTF---E--ETPQDIIKNARSFGWDLAKLVDEGKLFILDASP--DPE------ 100 query 399 LGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSE-L-----AV--GYSTL-YGDS 449 ::: ::::::::::::::::::::::::::::::::: : : ::::: ::: d1tf7a1 101 --GQE-VVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDA-SSVVRRELF-RLV 155 query 450 -VG----AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELY 504 :: :::::: :: ::: ::::: d1tf7a1 156 ARLKQIGATTVMT--TE--------------------------------RIE-EYGPI-- 178 query 505 VDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTK----------------IS 548 : : :: :: ::: : :::: :: d1tf7a1 179 A---------------------R--YG--VE-EFV-S-DNVVILRNVLEGERRRRTLEIL 210 query 549 AKGFGK----------------------------DRRLPITNRWREGH 568 : : :: d1tf7a1 211 K-L-RGTSHMKGEYPFTITDHGINIFPLGAMRLT-------------- 242 HHsearch alignment (Probability: 0.02 E-value:0.74) query 324 GFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTG--L 381 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: : d1tf7a1 26 GRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLV 85 query 382 NFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTT 417 :::::::::::::::::::::::::::::::::::: d1tf7a1 86 DEGKLFILDASPDPEGQEVVGGFDLSALIERINYAI 121
Intermediate <-- 1.430 --> Hit
DALI alignment (Z-score: 7.1 Raw score:807.80) d1tf7a1 1 ehqaiakMRTMI--------EGFDdishgGLPIgRSTLVSGTSGTGKTLFSIQFLYNGII 52 ::::: :::: :::: :::::::::::::::::::::::::: d1f2t.1 1 -----mkLERVTvknfrshsDTVV-----EFKE-GINLIIGQNGSGKSSLLDAILVGLYW 49 d1tf7a1 53 efdepgvfvtfeetpqdiikNARSFG---------------------------------- 78 :::::: d1f2t.1 50 ------------------plRIKDIKkdeftkvgardtyidlifekdgtkyritrrflkg 91 d1tf7a1 79 --------------------------wdlAKLVdEGKLFI------lDASP--------- 97 :::: :::::: :::: d1f2t.1 92 eihamkrlvgnewkhvtepsskaisafmeKLIP-YNIFLNaiyirqgQIDAilesareaa 150 d1tf7a1 98 -----------------------------------------dpegQEVVGGFDLSALIER 116 ::::::::::::::: d1f2t.1 151 lskigelaseifaeftegkysevvvraeenkvrlfvvwegkerplTFLSGGERIALGLAF 210 d1tf7a1 117 INYAIQKY--RARRVSIDSVtSVFQqydasSVVRRELFRLVA-RLKQiGATTVMTTErie 173 :::::::: :::::::::: :::: :::::::::::: :::: ::::::::: d1f2t.1 211 RLAMSLYLagEISLLILDEP-TPYL----dEERRRKLITIMErYLKK-IPQVILVSH--- 261 d1tf7a1 174 eygpiaryGVEEFVSDNVVILRNVLegerRRRTLEILKlrgtshmkgeypftitdhgini 233 ::::::::::::::::: ::::::::: d1f2t.1 262 -------dEELKDAADHVIRISLEN----GSSKVEVVS---------------------- 288 d1tf7a1 234 fplgamrlt 242 d1f2t.1 289 --------- 289 FAST alignment (Normalized score: 4.74 Raw score:1250.00) d1tf7a1 1 EHQAIAK---MRTMIEGFDDISHG------------GLPIGRSTLVSGTSGTGKTLFSIQ 45 :::: :::: ::::::::::::::::::: d1f2t.1 1 -------MKLERVT----------VKNFRSHSDTVVEFKE-GINLIIGQNGSGKSSLLDA 42 d1tf7a1 46 FLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEV- 104 ::::: d1f2t.1 43 ILVGL------------------------------------------------------Y 48 d1tf7a1 105 ------------------------------------------------------------ 105 d1f2t.1 49 WPLRIKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLKGEIHAMKRLVGNEWKHVT 108 d1tf7a1 105 ------------------------------------------------------------ 105 d1f2t.1 109 EPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESAREAALSKIGELASEIFAEFTEG 168 d1tf7a1 105 ------------------------------VGGFDLSALIERINYAIQK--YRARRVSID 132 ::::::::::::::::::: ::::::::: d1f2t.1 169 KYSEVVVRAEENKVRLFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILD 228 d1tf7a1 133 SVTSVFQQYDASSV----VRRELFRLVA----RLKQIGATTVMTTERIEEYGPIARYGVE 184 :: :::::::::: ::::: :::::: :::::: d1f2t.1 229 EP------------TPYLDEERRRKLITIMERYLKKI-PQVILV----------SHDEEL 265 d1tf7a1 185 EFVSDNVVILRNVLEGER--RRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT 242 :::::::::::: ::::::: d1f2t.1 266 KDAADHVIRISL------ENGSSKVEV--------------------------------- 286 d1tf7a1 243 -- 243 d1f2t.1 287 VS 288 TMalign alignment (TM-score: 0.43 Raw score:104.70) d1tf7a1 1 EHQAIAKMRTMI---------EGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGI 51 ::::::: :::: ::: :::::::::::::::::::::: : d1f2t.1 1 -----MKLERVTVKNFRSHSDTVVE-----FKE--GINLIIGQNGSGKSSLLDAILV--G 46 d1tf7a1 52 IEFDEPGVFVTFEETPQDIIKNARS---------FGW-----------------D--LAK 83 :::: :: :::::: ::: : :: d1f2t.1 47 -----LYWP------LR--IKDIKKDEFTKVGARDTYIDLIFEKDGTKYRITRRFLK-GE 92 d1tf7a1 84 -L----------------VDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRA 126 : :::::: ::::::: d1f2t.1 93 IHAMKRLVGNEWKHVTEPSSKAIS-----------------------------AFMEKLI 123 d1tf7a1 127 RR--V----SIDS-VTSVFQQY-------------------------------------- 141 :: : :::: :::::::: d1f2t.1 124 PYNIFLNAIYIRQGQIDAILESAREAALSKIGELASEIFAEFTEGKYSEVVVRAEENKVR 183 d1tf7a1 142 -----------D--A----S-SVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGV 183 : : : ::::::::::::::::::::::::::::::::::: ::: d1f2t.1 184 LFVVWEGKERPLTFLSGGERIALGLAFRLAMSLYLAGEISLLILDEPTPYLDEERR-RKL 242 d1tf7a1 184 EEF---VS--D--NVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPL 236 ::: :: : :::::::: ::::::: :: ::::::::: ::::: d1f2t.1 243 ITIMERYLKKIPQVILVSHDE--------ELKDAAD----HV--IRISLENGS-SKVEV- 286 d1tf7a1 237 GAMRLT 242 :: d1f2t.1 287 VS---- 288 HHsearch alignment (Probability: 0.98 E-value:0.00) d1tf7a1 121 IQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIAR 180 :::::::::::::::::: ::: ::::::::::::::::::::::::::: d1f2t.1 217 YLAGEISLLILDEPTPYL----DEE-RRRKLITIMERYLKKIPQVILVSHDEE------- 264 d1tf7a1 181 YGVEEFVSDNVVILRNVLEGERR 203 :::::::::::::::::::: d1f2t.1 265 ---LKDAADHVIRISLENGSSKV 284