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: T542_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.638 --> Intermediate <-- 1.803 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1oywa2) 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 d1oywa2 RecQ helicase domainP-​loop containing nucleoside triphosphate hydrolasesP-​loop containing nucleoside triphosphate hydrolasesα/β

Supporting Alignments

Query <-- 0.638 --> Intermediate
DALI alignment (Z-score: 3.2 Raw score:303.50) 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---GATTVMTTE 170 query 92 drsesaqpkygqpagaprN-------aaavlhrgRVALTFAKHHLPNYgvfdefryfvpg 144 : :::::::::::::: d1tf7a1 171 ------------------RieeygpiarygveefVSDNVVILRNVLEG------------ 200 query 145 dtmpivrlhgvdialaicedlwqdggrvpaarsagaglllsvnaspyerdkddtrlelvr 204 d1tf7a1 201 ------------------------------------------------------------ 201 query 205 kraqeagcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcvvldldlpaaea 264 d1tf7a1 201 ------------------------------------------------------------ 201 query 265 epptgvvddglridrlviseeplpayeaelaggyadrldadeevysalvvglrayvakng 324 d1tf7a1 201 ------------------------------------------------------------ 201 query 325 frsvliglsggidsalvaaiacdalgaqnvygvsmpskyssdhskgdaaelarrtglnfr 384 d1tf7a1 201 ------------------------------------------------------------ 201 query 385 tvsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqeghivlapgnkselavgyst 444 d1tf7a1 201 ------------------------------------------------------------ 201 query 445 lygdsvgaygpikdvyktsifrlaewrnraaaergqtppipeasitkpdypvldailely 504 d1tf7a1 201 ------------------------------------------------------------ 201 query 505 vdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrw 564 d1tf7a1 201 ----------------------errrrtleilklrgtshmkgeypftitdhginifplga 238 query 565 regh 568 d1tf7a1 239 mrlt 242 FAST alignment (Normalized score: 1.90 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 LDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPS 361 d1tf7a1 198 ------------------------------------------------------------ 198 query 362 KYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAI 421 d1tf7a1 198 ------------------------------------------------------------ 198 query 422 SNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQT 481 d1tf7a1 198 ------------------------------------------------------------ 198 query 482 PPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQY 541 d1tf7a1 198 ------------------------------------------------------------ 198 query 542 PPGTKISAKGFGKDRRLPITNRWREGH--------------------------------- 568 d1tf7a1 198 ---------------------------LEGERRRRTLEILKLRGTSHMKGEYPFTITDHG 230 query 569 ------------ 569 d1tf7a1 231 INIFPLGAMRLT 242 TMalign alignment (TM-score: 0.21 Raw score:121.48) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 :: : : d1tf7a1 1 --------------EH--------------------------------Q-A--------- 4 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1tf7a1 5 ------------------------------------------------------------ 5 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1tf7a1 5 ------------------------------------------------------------ 5 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 ::::: d1tf7a1 5 ------------------------------------------IAKMR------------- 9 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 :: d1tf7a1 10 -------TM--------------------------------------------------- 11 query 301 RLDADEEVYSALVVGLRAYVAKN--------GFRSVLIGLSGG-IDSALVAAIACDALGA 351 :::::::::::: ::: : : :::::::::::::::: d1tf7a1 12 ----IEGFDDISHGGL-PIG--RSTLVSGTS-----------GTGKTLFSIQFLYNGIIE 53 query 352 -QNVYGVSMPSKYSSDHSKGDAAELAR--RTGL--NF-----RTVSIE-PMF--DAYMAS 398 ::::::::: : ::::::::::: :::: :: :::::: : d1tf7a1 54 FDEPGVFVTF---E--ETPQDIIKNARSFGWDLAKLVDEGKLFILDASP--DPE------ 100 query 399 LGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSE-L-----AV--GYSTL-YGDS 449 ::: ::::::::::::::::::::::::::::::::: : : ::::: ::: d1tf7a1 101 --GQE-VVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDA-SSVVRRELF-RLV 155 query 450 -VG----AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELY 504 :: :::::: :: ::: ::::: d1tf7a1 156 ARLKQIGATTVMT--TE--------------------------------RIE-EYGPI-- 178 query 505 VDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTK----------------IS 548 : : :: :: ::: : :::: :: d1tf7a1 179 A---------------------R--YG--VE-EFV-S-DNVVILRNVLEGERRRRTLEIL 210 query 549 AKGFGK----------------------------DRRLPITNRWREGH 568 : : :: d1tf7a1 211 K-L-RGTSHMKGEYPFTITDHGINIFPLGAMRLT-------------- 242 HHsearch alignment (Probability: 0.02 E-value:0.74) query 324 GFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTG--L 381 ::::::::::::::::::::::::::::::::::::::::::::::::::::::::: : d1tf7a1 26 GRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKLV 85 query 382 NFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTT 417 :::::::::::::::::::::::::::::::::::: d1tf7a1 86 DEGKLFILDASPDPEGQEVVGGFDLSALIERINYAI 121
Intermediate <-- 1.803 --> Hit
DALI alignment (Z-score: 6.8 Raw score:690.60) d1tf7a1 1 -ehqaiakmrtMIEG----------------fddishGGLPigrSTLVSGTSGTGKTLFS 43 :::: :::: :::::::::::::::: d1oywa2 1 maqaevlnlesGAKQvlqetfgyqqfrpgqeeiidtvLSGR---DCLVVMPTGGGKSLCY 57 d1tf7a1 44 IQFLYNGiiefDEPGVFVTFEE-TPQDIIKNARSFGWDLA-----------------klv 85 ::::::: ::::::::::: ::::::::::::::::: d1oywa2 58 QIPALLL----NGLTVVVSPLIsLMKDQVDQLQANGVAAAclnstqtreqqlevmtgcrt 113 d1tf7a1 86 DEGKLFILDAspdpegqevvggfdlsALIE--RINYAiQKYRARRVSIDSVTSV-----F 138 :::::::::: :::: ::::: :::::::::::::::: : d1oywa2 114 GQIRLLYIAP---------------eRLMLdnFLEHL-AHWNPVLLAVDEAHCIsqwghD 157 d1tf7a1 139 QQYdassvvrrelFRLVaRLKQIG--ATTVMTTERieeygpiaRYGV-EEFVS------- 188 ::: :::: :::::: ::::::::: :::: ::::: d1oywa2 158 FRP--------eyAALG-QLRQRFptLPFMALTAT--------ADDTtRQDIVrllglnd 200 d1tf7a1 189 DNVVILrnvlegerrrrtleilklrgtshmkgeypftitdhginifplgamrlt 242 :::::: d1oywa2 201 PLIQIS------------------------------------------------ 206 FAST alignment (Normalized score: 5.26 Raw score:1175.00) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLP------------------------------------ 24 d1oywa2 1 ------------------------MAQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDT 36 d1tf7a1 25 --IGRSTLVSGTSGT---GKTLFSIQFLYNGIIEFDEPGVFVTFEE---TPQDIIKNARS 76 :::::::::: :::::::::::: :::::::::: ::::::::::: d1oywa2 37 VLSGRDCLVVMP---TGGGKSLCYQIPALL----LNGLTVVVSP--LISLMKDQVDQLQA 87 d1tf7a1 77 FGWDLAKLVD-----------------------EGKLFILDASPDPEGQEVVGGFDLS-- 111 :::: ::::::: d1oywa2 88 NGVA------AACLNSTQTREQQLEVMTGCRTGQIRLLYI------------------AP 123 d1tf7a1 112 ------ALIERINYAIQKYRARRVSIDSVTSVFQQYDA--------SSVVRRELFRLVAR 157 ::::::: :::::::::::::: ::::: :::::::: d1oywa2 124 ERLMLDNFLEHLA----HWNPVLLAVDEAHC-------ISQWGHDFRPEYA-ALGQLRQR 171 d1tf7a1 158 LKQ-IGATTVMTTERIEEYGPIAR-------YGVEEFVS--DNVVILRNVLEGERRRRTL 207 ::::::::: :::::::: ::::::: d1oywa2 172 ---FPTLPFMALT-----------ATADDTTRQDIVRLLGLNDPLIQI------------ 205 d1tf7a1 208 EILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT- 242 d1oywa2 206 -----------------------------------S 206 TMalign alignment (TM-score: 0.47 Raw score:113.99) d1tf7a1 1 --------EHQAIAKMRT-MIE-----------G--FDDISHGGL-PIGRSTLVSGTSGT 37 :: ::: : ::::::::: :: ::::::::::: d1oywa2 1 MAQAEVLN--------LESGAKQVLQETFGYQQFRPGQEEIIDTVLSG-RDCLVVMPTGG 51 d1tf7a1 38 GKTLFSIQFLYNGIIEFDEPGVFVTFEE-TPQDIIKNARSFGWDLAK------------- 83 ::::::::::::: ::::::::::: ::::::::::: :::::: d1oywa2 52 GKSLCYQIPALLL----NGLTVVVSPLISLMKDQVDQLQA-NGVAAACLNSTQTREQQLE 106 d1tf7a1 84 LV--D---EGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVF 138 : : :::::::::: :::::::: ::::::::::::::::::::: d1oywa2 107 -VMTGCRTGQIRLLYIAP------------ERLMLDNF-LEHLAHWNPVLLAVDEAHCIS 152 d1tf7a1 139 QQYDAS--SVV--RRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFV---S-DN 190 ::: :: :::::::::::: ::::::::::: :: :::::::: : :: d1oywa2 153 ---QWGHD-FRPE-YAALGQLRQRFP-TLPFMALTATA----DD-TTRQDIVRLLGLNDP 201 d1tf7a1 191 VVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT 242 ::::: d1oywa2 202 LIQIS----------------------------------------------- 206 HHsearch alignment (Probability: 0.96 E-value:0.00) d1tf7a1 24 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQ-DIIKNARSFGWDLA 82 :::::::::::::::::::::::::: ::::::::::::::: :::::::::::::: d1oywa2 38 LSGRDCLVVMPTGGGKSLCYQIPALL----LNGLTVVVSPLISLMKDQVDQLQANGVAAA 93 d1tf7a1 83 KLVDEGKLFILDASPDP----EGQEVVGGFDLSALIER-INYAIQKYRARRVSIDSVTSV 137 ::::::::::::::: ::::::::::::::::: ::::::::::::::::::::: d1oywa2 94 --CLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFLEHLAHWNPVLLAVDEAHCI 151 d1tf7a1 138 FQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEE 174 :::::::::::::::::::: ::::::::::::::: d1oywa2 152 SQWGHDFRPEYAALGQLRQR--FPTLPFMALTATADD 186