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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1tf7a1 | Circadian clock protein KaiC | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | α/β |
| Hit | d1sxja2 | Replication factor C1 | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | α/β |
Query <-- 0.638 --> IntermediateDALI 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 <-- 2.146 --> HitDALI alignment (Z-score: 7.0 Raw score:711.90) d1tf7a1 1 -ehqaiakmrtMIEGF-----ddishgGLPI--------------------gRSTLVSGT 34 ::::: :::: :::::::: d1sxja2 1 dklwtvkyaptNLQQVcgnkgsvmklkNWLAnwenskknsfkhagkdgsgvfRAAMLYGP 60 d1tf7a1 35 SGTGKTLFSIQFLYNGIiefdEPGVFVTFEetpqdiiknarsfgwdlaklvdegklfild 94 ::::::::::::::::: ::::::::: d1sxja2 61 PGIGKTTAAHLVAQELG----YDILEQNAS------------------------------ 86 d1tf7a1 95 aspdpegqevvGGFDLSALIERINyAIQKYR----------ARRVSIDSVTSVfQQYDas 144 ::::::::::::: :::::: :::::::::::: :::: d1sxja2 87 --------dvrSKTLLNAGVKNALdNMSVVGyfkhqnlngkHFVIIMDEVDGM-SGGD-- 135 d1tf7a1 145 sVVRRELFRLVARLkqiGATTVMTTERieeygpiARYG---VEEFVSdNVVILRNVL--- 198 ::::::::::::: :::::::::: :::: :::::: ::::::::: d1sxja2 136 rGGVGQLAQFCRKT---STPLILICNE-------RNLPkmrPFDRVC-LDIQFRRPDans 184 d1tf7a1 199 ---------------------EGER---RRRTleilklrgtshmkgeypftitdhginif 234 :::: :::: d1sxja2 185 iksrlmtiairekfkldpnviDRLIqttRGDI--rqvinllstistttktinhenineis 242 d1tf7a1 235 plgamrlt 242 d1sxja2 243 kaweknia 250 FAST alignment (Normalized score: 4.11 Raw score:1010.00) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIG---------------------------------- 26 d1sxja2 1 --------------------------DKLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWE 34 d1tf7a1 27 ------------------RSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQ 68 ::::::::::::::::::::::: ::::::::: d1sxja2 35 NSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE----LGYDILEQN------ 84 d1tf7a1 69 DIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGF-----DLSALIERINYAIQK 123 :::::::::::::: d1sxja2 85 ----------------------------------------ASDVRSKTLLNAGVKNALD- 103 d1tf7a1 124 YRA-----------------RRVSIDSVTSVFQQYDASSVVR------RELFRLVARLKQ 160 :::::::::: :::::::::::: d1sxja2 104 ---NMSVVGYFKHQNLNGKHFVIIMDEVDG------------MSGGDRGGVGQLAQFCRK 148 d1tf7a1 161 IGATTVMTTERIEEYGPIAR-------YGVEEFVSDNVVILRNVLEGERRRRTLEILKLR 213 ::::::::: ::::::: :::::: d1sxja2 149 TSTPLILIC-----------NERNLPKMRPFDRV-CLDIQF------------------- 177 d1tf7a1 214 GTSHMKGEYPFTITDHGINIFPLGAMRLT------------------------------- 242 d1sxja2 178 -----------------------------RRPDANSIKSRLMTIAIREKFKLDPNVIDRL 208 d1tf7a1 243 ------------------------------------------ 243 d1sxja2 209 IQTTRGDIRQVINLLSTISTTTKTINHENINEISKAWEKNIA 250 TMalign alignment (TM-score: 0.46 Raw score:111.17) d1tf7a1 1 -----------EHQAIAKMRTMIE-----GFDDISHGGL--PI---G------------- 26 ::: :::::::::: :: : d1sxja2 1 DKLWTVKYAPT----------NLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSG 50 d1tf7a1 27 --RSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDIIKNARSFGWDLAKL 84 ::::::::::::::::::::::::: ::::::::: d1sxja2 51 VFRAAMLYGPPGIGKTTAAHLVAQELG-----YDILEQNAS------------------- 86 d1tf7a1 85 VDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQK-Y---------RARRVSIDSV 134 :: ::::::::::::::::::: : :::::::::: d1sxja2 87 -----------DV-------RSKTLLNAGVKNALDNMSVVGYFKHQNLNGKHFVIIMDEV 128 d1tf7a1 135 TSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVIL 194 :: :::::: ::::::::::::: : ::::::::: :::::::::::::::::: d1sxja2 129 DG-MSGGDR--GGVGQLAQFCRKT--S-TPLILICNE-----RNLPKMRPFDRVCLDIQF 177 d1tf7a1 195 RNV-L--------------------------EGERRRRT--LEILKLRGTSHMKGEYPFT 225 ::: : :::::::: d1sxja2 178 RRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRGDIRQ------------------- 218 d1tf7a1 226 IT------------------------------DHGINIFPLGAMRLT 242 :: d1sxja2 219 VINLLSTISTTTKTINHENINEISKAWEKNIA--------------- 250 HHsearch alignment (Probability: 0.98 E-value:0.00) d1tf7a1 22 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQ--DIIKNARSFGW 79 :::::::::::::::::::::::::: : :::::::::::::::: :::::::: d1sxja2 48 GSGVFRAAMLYGPPGIGKTTAAHLVA-Q---ELGYDILEQNASDVRSKTLLNAGVKN--- 100 d1tf7a1 80 DLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQ 139 ::::::::::::::::::::::::::::::::: d1sxja2 101 ---------------------------ALDNMSVVGYFKHQNLNGKHFVIIMDEVDGMSG 133 d1tf7a1 140 QYDASSVVRRELFRLVARLKQIGATTVMTTERI 172 : :::::::::::::::::::::::::: d1sxja2 134 G------DRGGVGQLAQFCRKTSTPLILICNER 160