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 <-- 1.860 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1knqa_) 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 d1knqa_ Gluconate kinaseP-​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 <-- 1.860 --> Hit
DALI alignment (Z-score: 4.8 Raw score:497.80) d1tf7a1 1 ehqaiakmrtmiegfddishgglpIGRSTLVSGTSGTGKTLFSIQFLYNGiiefdepgvf 60 :::::::::::::::::::::::::: d1knqa_ 1 --------------------ttnhDHHIYVLMGVSGSGKSAVASEVAHQL---------- 30 d1tf7a1 61 vtfeetpqdiiknarsfgwdlaklvdegklfildaspdpegqevvggfdlsalierinya 120 d1knqa_ 31 ------------------------------------------------------------ 31 d1tf7a1 121 iqkyraRRVSIDsVTSVFQQYD-------------ASSVVRRELFRLVARLKQIGATTVM 167 :::::: ::::::::: ::::::::::::::::::::::::: d1knqa_ 31 ------HAAFLD-GDFLHPRRNiekmasgeplnddDRKPWLQALNDAAFAMQRTNKVSLI 83 d1tf7a1 168 TTErieeygpiARYG-VEEFVS-----DNVVILRNVLE---------------------- 199 ::: :::: :::::: ::::::::::: d1knqa_ 84 VCS--------ALKKhYRDLLRegnpnLSFIYLKGDFDviesrlkarkghffktqmlvtq 135 d1tf7a1 200 -gerrrrtleILKLrgtshmkgeyPFTItdHGINifplgamrlt 242 :::: :::: :::: d1knqa_ 136 fetlqepgadETDV-----lvvdiDQPL--EGVV-astievikk 171 FAST alignment (Normalized score: 3.78 Raw score:769.40) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPI-----GRSTLVSGTSGTGKTLFSIQFLYNGIIEFD 55 :::::::::::::::::::::::: d1knqa_ 1 -------------------------TTNHDHHIYVLMGVSGSGKSAVASEVAHQ------ 29 d1tf7a1 56 EPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIE 115 d1knqa_ 30 ------------------------------------------------------------ 30 d1tf7a1 116 RINYAIQKYRA-RRVSIDSV-TSVFQQYD------------------ASSVVRRELFRLV 155 ::::: :::: ::::::::::::: d1knqa_ 30 -----------LHAAFL---DGDFL----HPRRNIEKMASGEPLNDDDRKPWLQALNDAA 71 d1tf7a1 156 ARLKQIG--ATTVMTTERIEEYGPI-ARYGVEEFVS-------DNVVILRNVLEGERRRR 205 ::::: ::::::: ::::::::: ::::::::: d1knqa_ 72 FAMQR--TNKVSLIVC---------SALKKHYRDL-LREGNPNLSFIYLKGD-------- 111 d1tf7a1 206 TLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT----------------------- 242 d1knqa_ 112 -------------------------------------FDVIESRLKARKGHFFKTQMLVT 134 d1tf7a1 243 ------------------------------------- 243 d1knqa_ 135 QFETLQEPGADETDVLVVDIDQPLEGVVASTIEVIKK 171 TMalign alignment (TM-score: 0.38 Raw score:93.12) d1tf7a1 1 ----EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDE 56 : ::::::::::: ::::::::::::::: d1knqa_ 1 TTNH-------D----------------HHIYVLMGVSG-SGKSAVASEVAHQLH----- 31 d1tf7a1 57 PGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPD--PEGQ-----E--VVGG 107 ::::::: ::::: :::: : :::: d1knqa_ 32 AAFLDGD------------------------------FLHPRRNIEKMASGEPLNDDDRK 61 d1tf7a1 108 FDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATTVM 167 ::::::::::::::: ::::::::::: : ::::::::::::: :: ::: d1knqa_ 62 PWLQALNDAAFAMQR--TNKVSLIVCSA--L--------KKHYRDLLREGNP--NL-SFI 106 d1tf7a1 168 TTERIEEY--------------------GPIAR--YGVEEF-VSDNVVILRNVLEGERRR 204 :::::::: :: :::::: :::::::::: d1knqa_ 107 YLKGDFDVIESRLKARKGHFFKTQMLVT---QFETLQEPGADETDVLVVDID-------- 155 d1tf7a1 205 RTLEILKLRGTSHMKGEYPFTITDHGINI-------FPLGAMRLT 242 : ::: ::::: d1knqa_ 156 Q-------------------PLE-GVVASTIEVIKK--------- 171 HHsearch alignment (Probability: 0.97 E-value:0.00) d1tf7a1 24 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKN 73 ::::::::::::::::::::::::::: ::::::::::::::::: d1knqa_ 4 HDHHIYVLMGVSGSGKSAVASEVAHQL------HAAFLDGDFLHPRRNIE 47