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 <-- 1.734 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1m8pa3) 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 d1m8pa3 ATP sulfurylase C-​terminal 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 <-- 1.734 --> Hit
DALI alignment (Z-score: 5.5 Raw score:562.00) d1tf7a1 1 ehqAIAKmrtmiegfddishgglpIGRSTLVSGTSGTGKTLFSIQFLYNGIieFDEPgvf 60 :::: ::::::::::::::::::::::::::: :::: d1m8pa3 1 ---PRAT-----------------QGFTIFLTGYMNSGKDAIARALQVTLN--QQGG--- 35 d1tf7a1 61 vtfeetpqdiiknarsfgwdlaklvdegklfildaspdpegqevvggfdlsalierinya 120 d1m8pa3 36 ------------------------------------------------------------ 36 d1tf7a1 121 iqkyrARRVSIDS--VTSV-FQQYD----ASSVVRRELFRLVARLKQIGATTVMTTErie 173 :::::::: :::: ::::: :::::::::::::::::::::::::::: d1m8pa3 36 -----RSVSLLLGdtVRHElSSELGftreDRHTNIQRIAFVATELTRAGAAVIAAPI--- 87 d1tf7a1 174 eygpiARYG-VEEFVS--------DNVVILRNVLE------------------------- 199 :::: :::::: ::::::::::: d1m8pa3 88 -----APYEeSRKFARdavsqagsFFLVHVATPLEhceqsdkrgiyaaarrgeikgftgv 142 d1tf7a1 200 gerrrrtlEILKlrgtshmkgeyPFTItdhGINI--------fplgamrlt 242 :::: :::: :::: d1m8pa3 143 ddpyetpeKADL-------vvdfSKQS---VRSIvheiilvlesqgflerq 183 FAST alignment (Normalized score: 4.64 Raw score:977.20) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPI-----GRSTLVSGTSGTGKTLFSIQFLYNGIIEFD 55 :::::::::::::::::::::::::::::: d1m8pa3 1 -------------------------PRATQGFTIFLTGYMNSGKDAIARALQVTLNQQGG 35 d1tf7a1 56 EPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASP-------DPEGQEV---- 104 :::::::: :::: d1m8pa3 36 RSVSLLLG----------------------------------DTVRHELSSEL---GFTR 58 d1tf7a1 105 -VGGFDLSALIERINYAIQKYRA--RRVSIDSVTSVFQQYDASSV-----VRRELFRLVA 156 :::::::::::::::::: ::::: :::::::::: d1m8pa3 59 EDRHTNIQRIAFVATELTR----AGAAVIA---------------APIAPYEESRKFARD 99 d1tf7a1 157 RLKQIGATTVMTTERIEEYGPIARYGVE-------------------------------- 184 ::::: :::::::: d1m8pa3 100 AVSQA-GSFFLVHV--------------ATPLEHCEQSDKRGIYAAARRGEIKGFTGVDD 144 d1tf7a1 185 ----EFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMR 240 ::::::::: d1m8pa3 145 PYETPEKADLVVD----------------------------------------------- 157 d1tf7a1 241 LT-------------------------- 242 d1m8pa3 158 --FSKQSVRSIVHEIILVLESQGFLERQ 183 TMalign alignment (TM-score: 0.42 Raw score:102.04) d1tf7a1 1 EHQAIAKM--RTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPG 58 : : : ::::::::::: :::::::::::::::::::::: d1m8pa3 1 P----R-ATQ----------------GFTIFLTGYMN-SGKDAIARALQVTLNQQGGRSV 38 d1tf7a1 59 VFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDAS--PDPEGQE---VVGGFDLSAL 113 :::::: : ::: :: ::: :::::::::: d1m8pa3 39 SLLLGD-T---------------------------VRHELSS--ELGFTREDRHTNIQRI 68 d1tf7a1 114 IERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTT-ERI 172 :::::::::: :: :::::::: : ::::::::::::::::::::::: ::: d1m8pa3 69 AFVATELTRA-GA-AVIAAPIA--P--------YEESRKFARDAVSQAGSFFLVHVATPL 116 d1tf7a1 173 EEY--------------------GPIAR---YGVEEFVSDNVVILRNVLEGERRRRTLEI 209 ::: :: ::::::::::::::: :: d1m8pa3 117 EHCEQSDKRGIYAAARRGEIKGF---TGVDDPYETPEKADLVVDFS----------KQ-- 161 d1tf7a1 210 LKLRGTSHMKGEYPFTITDHGINI------------------FPLGAMRLT 242 : ::: d1m8pa3 162 --------------S------VRSIVHEIILVLESQGFLERQ--------- 183 HHsearch alignment (Probability: 0.97 E-value:0.00) d1tf7a1 24 PIGRSTLVSGTSGTGKTLFSIQFLYN 49 :::::::::::::::::::::::::: d1m8pa3 4 TQGFTIFLTGYMNSGKDAIARALQVT 29