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 <-- 0.607 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1q0ua_) 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 d1q0ua_ Probable DEAD box RNA helicase YqfRP-​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 <-- 0.607 --> Hit
DALI alignment (Z-score: 5.0 Raw score:566.40) d1tf7a1 1 ehqaiakmrtmiEGFDD----------------------ishgGLPIGRSTLVSGTSGTG 38 ::::: ::::::::::::::::: d1q0ua_ 1 ----------tqFTRFPfqpfiieaiktlrfykpteiqeriipGALRGESMVGQSQTGTG 50 d1tf7a1 39 KTLFSIQFLYNGIIEFD--ePGVFVTFE-ETPQDIIKNARSFGW-----dlAKLV----- 85 ::::::::::::::::: :::::::: ::::::::::::::: :::: d1q0ua_ 51 KTHAYLLPIMEKIKPERaevQAVITAPTrELATQIYHETLKITKfcpkdrmIVARcligg 110 d1tf7a1 86 -----------dEGKLFILDAspdpegqevvggfdlsaLIER--inYAIQkyRARRVSID 132 ::::::::: :::: :::: :::::::: d1q0ua_ 111 tdkqkaleklnvQPHIVIGTP--------------griNDFIreqaLDVH--TAHILVVD 154 d1tf7a1 133 SVTS-VFQQydassvvrrelfrlvarlkqIGATTVMTTErieeygpiARYGVEEFVS--- 188 :::: :::: :::::::::: :::::::::: d1q0ua_ 155 EADLmLDMG-------fitdvdqiaarmpKDLQMLVFSA--------TIPEKLKPFLkky 199 d1tf7a1 189 ---DNVVILRnvlegerrrrtleilklrgtshmkgeypftitdhginifplgamrlt 242 ::::::: d1q0ua_ 200 menPTFVHVL----------------------------------------------- 209 FAST alignment (Normalized score: 4.49 Raw score:1009.00) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLP------------------------------------ 24 d1q0ua_ 1 ------------------------TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGAL 36 d1tf7a1 25 IGRSTLVSGTSGT---GKTLFSIQFLYNG-IIEFDE--PGVFVTFEE---TPQDIIKNAR 75 :::::::::: ::::::::::::: ::::: ::::::: :::::::::: d1q0ua_ 37 RGESMVGQSQ---TGTGKTHAYLLPIMEKIKPERA-EVQAVITAP--TRELATQIYHETL 90 d1tf7a1 76 SFGWDLAKLVDE--------------------------------GKLFILDASPDPEGQE 103 : :::::: d1q0ua_ 91 K-----------ITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIG---------- 129 d1tf7a1 104 VVGGFDLSALIERINYAIQKY-----------------RARRVSIDSVTSVFQQYDASSV 146 ::::::::::::::: d1q0ua_ 130 ---------------------TPGRINDFIREQALDVHTAHILVVDEADLMLD------- 161 d1tf7a1 147 VRRE------LFRLVARLKQ--IGATTVMTTERIEEYGPIA--RYGVEEFVS-------D 189 ::::::: ::::::::: :::::::: : d1q0ua_ 162 ----MGFITDVDQIAAR---MPKDLQMLVFS----------ATIPEKLKPF-LKKYMENP 203 d1tf7a1 190 NVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT-- 242 :::: d1q0ua_ 204 TFVH-------------------------------------------------VL 209 TMalign alignment (TM-score: 0.44 Raw score:106.88) d1tf7a1 1 -----EHQAIAKMRTMI--------------------EGFDDISHGGLPIGRSTLVSGTS 35 ::: ::::::: :::: ::::::: d1q0ua_ 1 TQFTR---------FPFQPFIIEAIKTLRFYKPTEIQERIIPGA-LRGE----SMVGQSQ 46 d1tf7a1 36 GT-GKTLFSIQFLYNGIIEFDEP---GVFVTF----EET--PQDIIKNARSFGWDLAKLV 85 :: :::::::::::::: :::: :::::: ::: :::::: :::::: d1q0ua_ 47 TGTGKTHAYLLPIMEKI--KPERAEVQAVITAPTRELATQIYHETLK-------ITKFCP 97 d1tf7a1 86 DEGKLFILDASPDPE-GQ--------------EVVGGFDLSALI-ERINYAIQKYRARRV 129 ::::::::::::::: :: :::::::::: ::::: :: ::: d1q0ua_ 98 KDRMIVARCLIGGTDKQKALEKLNVQPHIVIG--TPGRINDFIREQALDV-HT----AHI 150 d1tf7a1 130 SIDSVT-SVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVS 188 :::::: ::::: : :: :::::::::::: : ::::::::: :::::::::::: d1q0ua_ 151 LVVDEADLMLDM-G---FI-TDVDQIAARMPK-D-LQMLVFSAT----IPEKLKPFLKKY 199 d1tf7a1 189 DN-VVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT 242 :: ::::::: d1q0ua_ 200 MENPTFVHVL--------------------------------------------- 209 HHsearch alignment (Probability: 0.97 E-value:0.00) d1tf7a1 23 LPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEF--DEPGVFVTFEE-TPQDIIKNARSFGW 79 :::::::::::::::::::::::::::::::: ::::::::::: :::::::::::::: d1q0ua_ 35 ALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITK 94 d1tf7a1 80 DLAKLVDEGKLF------ILDASPDPEGQEVVGGFDLSALIERINYA-IQKYRARRVSID 132 :::::::::::: ::::::::::::::::::::::::::::: :::::::::::: d1q0ua_ 95 FCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVD 154 d1tf7a1 133 SVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTER 171 ::::::::: :::::::::::::::::: :::::: d1q0ua_ 155 EADLMLDMG-----FITDVDQIAARMPKDLQM-LVFSAT 187