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 <-- 1.086 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1m7ga_) 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 d1m7ga_ Adenosine-​5'​phosphosulfate kinase (APS kinase)P-​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 <-- 1.086 --> Hit
DALI alignment (Z-score: 5.0 Raw score:567.60) d1tf7a1 1 ---------------EHQAIAkmrtmiegfddishgglpiGRSTLVSGTSGTGKTLFSIQ 45 :::::: :::::::::::::::::::: d1m7ga_ 1 stnitfhasaltrseRTELRN-----------------qrGLTIWLTGLSASGKSTLAVE 43 d1tf7a1 46 FLYNGIIEFDEpgvfvtfeetpqdiiknarsfgwdlaklvdegklfildaspdpegqevv 105 ::::::::::: d1m7ga_ 44 LEHQLVRDRRV------------------------------------------------- 54 d1tf7a1 106 ggfdlsalierinyaiqkyraRRVSIDS-VTSV--FQQYD----ASSVVRRELFRLVARL 158 ::::::: :::: ::::: :::::::::::::::: d1m7ga_ 55 ---------------------HAYRLDGdNIRFglNKDLGfseaDRNENIRRIAEVAKLF 93 d1tf7a1 159 KQIGATTVMTTErieeygpiARYG-VEEFVS---------------DNVVILRNVLE--- 199 :::::::::::: :::: :::::: ::::::::::: d1m7ga_ 94 ADSNSIAITSFI--------SPYRkDRDTARqlhevatpgeetglpFVEVYVDVPVEvae 145 d1tf7a1 200 ---------------------gerrrrtlEILKlrgtshmkgeyPFTItdhGINI----- 233 :::: :::: :::: d1m7ga_ 146 qrdpkglykkaregvikeftgisapyeapANPE------vhvknYELP---VQDAvkqii 196 d1tf7a1 234 ---fplgamrlt 242 d1m7ga_ 197 dyldtkgylpak 208 FAST alignment (Normalized score: 4.33 Raw score:970.90) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPI-----------------------GRSTLVSGTSGT 37 :::::::::::: d1m7ga_ 1 -------------------------STNITFHASALTRSERTELRNQRGLTIWLTGLSAS 35 d1tf7a1 38 GKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASP 97 ::::::::::::::::::::::::: d1m7ga_ 36 GKSTLAVELEHQLVRDRRVHAYRLD----------------------------------- 60 d1tf7a1 98 DPEGQE----------------VVGGFDLSALIERINYAIQKYRA--RRVSIDSVTSVFQ 139 ::::::::::::::::::: ::::: d1m7ga_ 61 ------GDNIRFGLNKDLGFSEADRNENIRRIAEVAKLFAD----SNSIAIT-------- 102 d1tf7a1 140 QYDASSV-----VRRELFRLVARLKQI---------GATTVMTTERIEEYGPIARYGVE- 184 :::::::::::: :::::::::: d1m7ga_ 103 -------SFISPYRKDRDTARQLH---EVATPGEETGLPFVEVYVD-------------V 139 d1tf7a1 185 ----------------------------------EFVSDNVVILRNVLEGERRRRTLEIL 210 :::::::::: d1m7ga_ 140 PVEVAEQRDPKGLYKKAREGVIKEFTGISAPYEAPANPEVHVKN---------------- 183 d1tf7a1 211 KLRGTSHMKGEYPFTITDHGINIFPLGAMRLT------------------------- 242 d1m7ga_ 184 --------------------------------YELPVQDAVKQIIDYLDTKGYLPAK 208 TMalign alignment (TM-score: 0.43 Raw score:104.01) d1tf7a1 1 ----------EHQ--AIAK------MRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLF 42 ::: :: ::::::::::: :::::: d1m7ga_ 1 STNITFHASALTRSE--RTELRNQR-----------------GLTIWLTGLSA-SGKSTL 40 d1tf7a1 43 SIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPD-PEG 101 ::::::::::::::::::::: : ::::: ::: d1m7ga_ 41 AVELEHQLVRDRRVHAYRLDG--D---------------------------NIRFGLNKD 71 d1tf7a1 102 QE---VVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARL 158 :: :::::::::::::::::::: :: :::::::: : :::::::::::: d1m7ga_ 72 LGFSEADRNENIRRIAEVAKLFADS-NS-IAITSFIS--P--------YRKDRDTARQLH 119 d1tf7a1 159 K--------QIGATTVMTTERIEEY--------------------GPIAR---YGVEEFV 187 : :::::::::::::::: :: ::::::: d1m7ga_ 120 EVATPGEETGLPFVEVYVDVPVEVAEQRDPKGLYKKAREGVIKEF---TGISAPYEAPAN 176 d1tf7a1 188 SDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIF-P----------- 235 :::::::: :: : :::: : d1m7ga_ 177 PEVHVKNY---------EL-----------------P------VQDAVKQIIDYLDTKGY 204 d1tf7a1 236 ----LGAMRLT 242 d1m7ga_ 205 LPAK------- 208 HHsearch alignment (Probability: 0.97 E-value:0.00) d1tf7a1 24 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFE 64 ::::::::::::::::::::::::::::::::::::::::: d1m7ga_ 22 QRGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGD 62