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 <-- 2.499 --> Hit

SVM
score
SVM
score

The query (T542_A.pdb A) is transitively linked to the hit (d1g6ha_) 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 d1g6ha_ MJ1267P-​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 <-- 2.499 --> Hit
DALI alignment (Z-score: 8.5 Raw score:892.40) d1tf7a1 1 ehqaIAKMRTmIEGF---------ddishgGLPIGRSTLVSGTSGTGKTLFSIQFLY--- 48 :::::: :::: ::::::::::::::::::::::::::: d1g6ha_ 1 ----TMEILR-TENIvkyfgefkaldgvsiSVNKGDVTLIIGPNGSGKSTLINVITGflk 55 d1tf7a1 49 ------NGIIEFD----------EPGVFVTFeetpqdiiknarsfgwdlaklvdegklFI 92 ::::::: :::::::: :: d1g6ha_ 56 adegrvYFENKDItnkepaelyhYGIVRTFQ------tpqplkemtvlenlligeicpGE 109 d1tf7a1 93 LD-------------------------------aspdpeGQEVVGGFDLsALIERINYAI 121 :: :::::::::: :::::::::: d1g6ha_ 110 SPlnslfykkwipkeeemvekafkileflklshlydrkaGELSGGQMKL-VEIGRALMTN 168 d1tf7a1 122 qkyrARRVSIDSVTSVFqqydASSVVRRELFRlVARLKQIGATTVMTTErieeygpIARY 181 ::::::::::::: ::::::::::: :::::::::::::::: :::: d1g6ha_ 169 ----PKMIVMDEPIAGV----APGLAHDIFNH-VLELKAKGITFLIIEH-------RLDI 212 d1tf7a1 182 gvEEFVSDNVVILRNvlegerrrRTLEILKLRGtshmkgeypftitdhginifplgamrl 241 ::::::::::::: :::::::::: d1g6ha_ 213 --VLNYIDHLYVMFN--------GQIIAEGRGE---------eeiknvlsdpkvveiyig 253 d1tf7a1 242 t 242 d1g6ha_ 254 e 254 FAST alignment (Normalized score: 5.47 Raw score:1357.00) d1tf7a1 1 EHQAIAKM---RTMIEGFDDISHG-----------------GLPIGRSTLVSGTSGTGKT 40 ::::: ::::::::::::::::::: d1g6ha_ 1 --------TMEILRTE--------NIVKYFGEFKALDGVSISVNKGDVTLIIGPNGSGKS 44 d1tf7a1 41 LFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARS------------------FGWDLA 82 :::::: :::::: d1g6ha_ 45 TLINVI------------------------------TGFLKADEGRVYFENKDITNKEPA 74 d1tf7a1 83 KLVDEGKLFILDASPDPEGQ---------------------------------------- 102 ::::: ::::: :::::: d1g6ha_ 75 ELYHY-GIVRT-FQTPQP--LKEMTVLENLLIGEICPGESPLNSLFYKKWIPKEEEMVEK 130 d1tf7a1 103 --------------------EVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQ-QY 141 ::::: :::::::::: :::::::::::: :: d1g6ha_ 131 AFKILEFLKLSHLYDRKAGELSGGQ-MKLVEIGRAL----MTNPKMIVMDEP-----IAG 180 d1tf7a1 142 DASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIAR--YGVEEFVSDNVVILRNVLE 199 :::::::::::: ::::::::::::::: :::::::::::::: d1g6ha_ 181 VAPGLAHDIFNH-VLELKAKGITFLIIE-----------HRLDIVLNYIDHLYVM----- 223 d1tf7a1 200 GERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT----------------- 242 d1g6ha_ 224 -------------------------------------------FNGQIIAEGRGEEEIKN 240 d1tf7a1 243 -------------- 243 d1g6ha_ 241 VLSDPKVVEIYIGE 254 TMalign alignment (TM-score: 0.52 Raw score:124.76) d1tf7a1 1 EHQAIAKMRTMIE------------GFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLY 48 ::::::::: ::: : ::::::::::::::::::::::::::: d1g6ha_ 1 ----TMEILRTENIVKYFGEFKALDGVS--I--SVNKGDVTLIIGPNGSGKSTLINVITG 52 d1tf7a1 49 --------NGI--IEF-------D--EPGVFVTFEET-------------PQDIIKNARS 76 ::: ::: : ::::::::::: d1g6ha_ 53 FLKADEGRVYFENKDITNKEPAELYHYGIVRTFQTPQPLKEMTVLENLLI---------- 102 d1tf7a1 77 FGWDLAKLV--DEGKLFILDA-----------------------------------SPDP 99 : : :::::: d1g6ha_ 103 --------GEI--C-PGESPLNSLFYKKWIPKEEEMVEKAFKILEFLKLSHLYDRK---- 147 d1tf7a1 100 EGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLK 159 ::::::::::: ::::::::: : ::::::::::: :: : : :::::::::::::: d1g6ha_ 148 AGELSGGQMKL-VEIGRALMT-N---PKMIVMDEPIA--GV-A-P-GLAHDIFNHVLELK 197 d1tf7a1 160 QIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRG-TS-- 216 ::::::::::: :: ::::::::::::::: :::::::::: : d1g6ha_ 198 AKGITFLIIEH-------RL--DIVLNYIDHLYVMFN--------GQIIAEGRGEE-EIK 239 d1tf7a1 217 -HMK--G-E--------YPFTITDHGINIFPLGAMRLT 242 : : : d1g6ha_ 240 N--VLSDPKVVEIYIGE--------------------- 254 HHsearch alignment (Probability: 0.98 E-value:0.00) d1tf7a1 22 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEE----TPQDIIKNARSF 77 :::::::::::::::::::::::: :: :::::::::::::::: :::::::: :: d1g6ha_ 26 SVNKGDVTLIIGPNGSGKSTLINV-IT-GFLKADEGRVYFENKDITNKEPAELYHY--GI 81 d1tf7a1 78 GWDLAKLVDEGKLFILDA--------------------------------------SP-D 98 :::::::::::::::::: :: : d1g6ha_ 82 VRTFQTPQPLKEMTVLENLLIGEICPGESPLNSLFYKKWIPKEEEMVEKAFKILEFLKLS 141 d1tf7a1 99 PEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARL 158 ::::::::::::::::::::::::::::::::::::::: :::::::::::::::: d1g6ha_ 142 HLYDRKAGELSGGQMKLVEIGRALMTNPKMIVMDEPIAG-----VAPGLAHDIFNHVLEL 196 d1tf7a1 159 KQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRN 196 :::::::::::::::: ::::::::::::: d1g6ha_ 197 KAKGITFLIIEHRLDI---------VLNYIDHLYVMFN 225