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 <-- 0.816 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1o14a_) 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 d1o14a_ Putative sugar kinase TM0828Ribokinase-​likeRibokinase-​likeα/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 <-- 0.816 --> Hit
DALI alignment (Z-score: 3.8 Raw score:582.90) d1tf7a1 1 ehqaiakmrtmiegfddishgglpigrstlvsgtsgtgktlfsiqflyngiiefdePGVF 60 :::: d1o14a_ 1 --------------------------------------------------------MVLT 4 d1tf7a1 61 VTFEET------------------------pqdiiknarsfgwDLAKLvdEGKLFILdAS 96 :::::: ::::: ::::::: :: d1o14a_ 5 VTLNPAldreifiedfqvnrlyrindlsktqmspggkginvsiALSKL--GVPSVAT-GF 61 d1tf7a1 97 PDPEG----------------------------------------------qeVVGGFDL 110 ::::: ::::::: d1o14a_ 62 VGGYMgkilveelrkisklittnfvyvegetrenieiideknktitainfpgpDVTDMDV 121 d1tf7a1 111 SALIERINYAIQkyRARRVSIDSvtSVFQQydassvVRRELFRLVARLKQIGATTVMTTE 170 :::::::::::: ::::::::: ::::: :::::::::::::::::::::::: d1o14a_ 122 NHFLRRYKMTLS--KVDCVVISG--SIPPG-----vNEGICNELVRLARERGVFVFVEQT 172 d1tf7a1 171 RieeygpiaRYGVEEFV--------------------------------------sDNVV 192 : :::::::: :::: d1o14a_ 173 P-------rLLERIYEGpefpnvvkpdlrgnhasflgvdlktfddyvklaeklaekSQVS 225 d1tf7a1 193 ILRNVlegerRRRTLEILklrgtsHMKGEYPFT--------------------------- 225 ::::: :::::::: ::::::::: d1o14a_ 226 VVSYE-----VKNDIVAT------REGVWLIRSkeeidtshllgagdayvagmvyyfikh 274 d1tf7a1 226 --------------ITDHG------------------inIFPLgamrlt 242 ::::: :::: d1o14a_ 275 ganflemakfgfasALAATrrkekympdleaikkeydhfTVER----vk 319 FAST alignment (Normalized score: 3.76 Raw score:1046.00) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKT-------------------- 40 d1o14a_ 1 ----------------------------------------MVLTVTLNPALDREIFIEDF 20 d1tf7a1 41 -------------------LFSIQFLYNGIIEFDEPGVFVTFEE-----TPQDIIKNARS 76 :::::::::::: ::::::::: ::::::::::: d1o14a_ 21 QVNRLYRINDLSKTQMSPGGKGINVSIALSK-LGVPSVATG---FVGGYMGKILVEELRK 76 d1tf7a1 77 FGWDLAKLVDE--GKLFILDASPDPEGQEVV----------------------------G 106 :::::::::: : d1o14a_ 77 -----------ISKLITTNFVYV--------EGETRENIEIIDEKNKTITAINFPGPDVT 117 d1tf7a1 107 GFDLSALIERINYAIQKYRARRVSIDSVTSVFQ-----QYDASSVVRRELFRLVARLKQI 161 :::::::::::::::: ::::::: :::: :::::::::::::: d1o14a_ 118 DMDVNHFLRRYKMTLS--KVDCVVI--------SGSIPPGVN----EGICNELVRLARER 163 d1tf7a1 162 GATTVMTTERIEEYGPIAR----YGVEEF----VSDNVVILRNVLEGERRR--------- 204 :::::::: ::::: ::::::::: d1o14a_ 164 GVFVFVEQ-----------TPRLLERIY-EGPEFPNVVKPDL---------RGNHASFLG 202 d1tf7a1 205 -----------------------------RTLEILKLRGTSHMKGEYPFTITDHGINIFP 235 ::::: :::::::: d1o14a_ 203 VDLKTFDDYVKLAEKLAEKSQVSVVSYEVKNDIV--ATREGVWL---------------- 244 d1tf7a1 236 LGAMRLT----------------------------------------------------- 242 d1o14a_ 245 -------IRSKEEIDTSHLLGAGDAYVAGMVYYFIKHGANFLEMAKFGFASALAATRRKE 297 d1tf7a1 243 ---------------------- 243 d1o14a_ 298 KYMPDLEAIKKEYDHFTVERVK 319 TMalign alignment (TM-score: 0.46 Raw score:112.45) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLV----SGTSG-------------------- 36 : ::::::: : d1o14a_ 1 -------M----------------VLTVTLNPALD----REIFIEDFQVNRLYRINDLSK 33 d1tf7a1 37 -----TGKTLFSIQFLYNGIIEFDEPGVFVTFEE-TPQDIIKNARSFGWDLAKLVDEGKL 90 :::::::::::::::::::::::::: ::::::: :::::: :::: d1o14a_ 34 TQMSP---GGKGINVSIALSKLGVPSVATGFVGGYMGKILVE-------ELRKIS-KLIT 82 d1tf7a1 91 FILDASPDP----------------------EGQEVVGGFDLSALIERINYAIQKYRARR 128 ::::::::: ::::: :::::::::::::::: :::: d1o14a_ 83 TNFVYVEGETRENIEIIDEKNKTITAINFPG-PDVTD--MDVNHFLRRYKMTLSK-VDCV 138 d1tf7a1 129 VSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFV- 187 ::::::::::: :: ::::::::::::::::::::: ::: :::::: d1o14a_ 139 VISGSIPPGVN-------EG-ICNELVRLARERGVFVFVEQT-------PRL-LERIYEG 182 d1tf7a1 188 --SD--NVVILRNV--------------LEGERRRRTLE--IL--KL--RGTSHMKGEYP 223 :: :::::::: : :: :: ::::::::::: d1o14a_ 183 PEFPNVVKPDLRGNHASFLGVDLKTFDD----------YVKLAEKLAEKSQVSVVSYEVK 232 d1tf7a1 224 ------------------F----TI----------------------------------- 226 : :: d1o14a_ 233 NDIVATREGVWLIRSKEEIDTSHLLGAGDAYVAGMVYYFIKHGANFLEMAKFGFASALAA 292 d1tf7a1 227 ---TDHGIN-------IFP-LGAMRL---T 242 :::::: :: ::::: d1o14a_ 293 TRRKEKYMPDLEAIKK-EYD-HFTVERVK- 319 HHsearch alignment (Probability: 0.01 E-value:0.76) d1tf7a1 51 IIEFDEPGVFVTFE--ETPQDIIKNARSFGWDLA 82 :::::::::::::: :::::::::::::::::: d1o14a_ 49 LSKLGVPSVATGFVGGYMGKILVEELRKISKLIT 82