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 | d1gsia_ | Thymidylate kinase | 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 <-- 0.619 --> HitDALI alignment (Z-score: 3.4 Raw score:431.20) d1tf7a1 1 ehqaiakmrtmiegfddishgglpigRSTLVSGTSGTGKTLFSIQFLYNGIiEFDEpgvf 60 ::::::::::::::::::::::::: :::: d1gsia_ 1 --------------------------MLIAIEGVDGAGKRTLVEKLSGAFR-AAGR---- 29 d1tf7a1 61 vtfeetpqdiiknarsfgwdlaklvdegklfildaspdpegqevvggfdlsalierinya 120 d1gsia_ 30 ------------------------------------------------------------ 30 d1tf7a1 121 iqkyraRRVSIdSVTSV----fQQYD--------------------ASSVVRRELFRLVA 156 ::::: ::::: :::: :::::::::::::: d1gsia_ 30 ------SVATL-AFPRYgqsvaADIAaealhgehgdlassvyamatLFALDRAGAVHTIQ 82 d1tf7a1 157 RLKQIGATTVMTTerieeygpIARY-------------------------gveeFVSDNV 191 ::::::::::::: :::: :::::: d1gsia_ 83 GLCRGYDVVILDR------yvASNAaysaarlhenaagkaaawvqriefarlglPKPDWQ 136 d1tf7a1 192 VILRNVLE--------------------------------gerrrrtleiLKLRgtshmk 219 :::::::: :::: d1gsia_ 137 VLLAVSAElagersrgraqrdpgrardnyerdaelqqrtgavyaelaaqgWGGR-----w 191 d1tf7a1 220 geypFTITdhginifplgamrlt 242 :::: d1gsia_ 192 lvvgADVD------pgrlaatla 208 FAST alignment (Normalized score: 3.70 Raw score:829.20) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVF 60 :::::::::::::::::::::::::: ::::::: d1gsia_ 1 --------------------------MLIAIEGVDGAGKRTLVEKLSGAFRA-AGRSVAT 33 d1tf7a1 61 VTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVV--------------- 105 ::: d1gsia_ 34 LAF------------------------------------------PRYGQSVAADIAAEA 51 d1tf7a1 106 ------------------GGFDLSALIERINYAIQKYRARRVSID-SVTSVFQQYD---- 142 ::::::::::::::::: :::::::: ::::::: d1gsia_ 52 LHGEHGDLASSVYAMATLFALDRAGAVHTIQGLCR--GYDVVILDRYVASNAA---YSAA 106 d1tf7a1 143 ---------ASSVVR-RELFRLVARLKQIGAT------TVMTTERIEEYGPIAR------ 180 :::::: ::::: :::::: d1gsia_ 107 RLHENAAGKAAAWVQRIEFAR-----------LGLPKPDWQVLL----------AVSAEL 145 d1tf7a1 181 ---------------------------------YGVEEFV---SDNVVILRNVLEGERRR 204 :::::: :::::::: d1gsia_ 146 AGERSRGRAQRDPGRARDNYERDAELQQRTGAVYAELAA-QGWGGRWLVVG--------- 195 d1tf7a1 205 RTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT------------- 242 d1gsia_ 196 --------------------------------------ADVDPGRLAATLA 208 TMalign alignment (TM-score: 0.40 Raw score:97.25) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVF 60 ::: ::::::::::::::::::::::::: ::::: d1gsia_ 1 -------------------------MLI-AIEGVDGAGKRTLVEKLSGAFRAAG-RSVAT 33 d1tf7a1 61 VTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDA-SPDP--EG----Q--------E-- 103 ::::::: :: :::: :: : : d1gsia_ 34 LAFPRYG--------------------------QSVAADIAAEALHGEHGDLASSVYAMA 67 d1tf7a1 104 VVGGFDLSALIERINYAIQKYRARRVSIDSV--TSVFQQ--YD-------ASSVVRRELF 152 ::::::::::::::::::: :::::::::: :::::: :: :::::::::: d1gsia_ 68 TLFALDRAGAVHTIQGLCR--GYDVVILDRYVASNAAYSAARLHENAAGKAAAWVQRIEF 125 d1tf7a1 153 RL-VARLKQIGATTVMTTE--R----------------------------IEEYGPIARY 181 :: :::: :::::::: : ::::::::: d1gsia_ 126 ARL-GLPK---PDWQVLLAVSAELAGERSRGRAQRDPGRARDNYERDAELQQRTGAVYA- 180 d1tf7a1 182 GVE-EFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINI------F 234 ::: ::::::::::: : :: :::: d1gsia_ 181 ELAAQGWGGRWLVVG---------A------------------DV----DPGRLAATLA- 208 d1tf7a1 235 PLGAMRLT 242 d1gsia_ 209 -------- 209 HHsearch alignment (Probability: 0.96 E-value:0.00) d1tf7a1 28 STLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEE 65 :::::::::::::::::: ::::::::::::::::::: d1gsia_ 2 LIAIEGVDGAGKRTLVEK-LSGAFRAAGRSVATLAFPR 38