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 | d1nn5a_ | 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 <-- 0.869 --> HitDALI alignment (Z-score: 4.0 Raw score:488.00) d1tf7a1 1 ehqaiakmrtmiegfddishgglpiGRSTLVSGTSGTGKTLFSIQFLYNGIieFDEPgvf 60 :::::::::::::::::::::::::: :::: d1nn5a_ 1 -----------------------rrGALIVLEGVDRAGKSTQSRKLVEALC--AAGH--- 32 d1tf7a1 61 vtfeetpqdiiknarsfgwdlaklvdegklfildaspdpegqevvggfdlsalierinya 120 d1nn5a_ 33 ------------------------------------------------------------ 33 d1tf7a1 121 iqkyraRRVSIDsVTSV---FQQY-----------------DASSVVRRELFRLVARLKQ 160 :::::: :::: :::: ::::::::::::::::::: d1nn5a_ 33 ------RAELLR-FPERsteIGKLlssylqkksdvedhsvhLLFSANRWEQVPLIKEKLS 85 d1tf7a1 161 IGATTVMTTerieeygpIARYG---------------veeFVSDN--VVILRNVLE---- 199 ::::::::: ::::: ::::: ::::::::: d1nn5a_ 86 QGVTLVVDR------yaFSGVAftgakenfsldwckqpdvGLPKPdlVLFLQLQLAdaak 139 d1tf7a1 200 -----------------gerrrrtlEILKlrgtshmkgeyPFTITdHGINI--------- 233 :::: ::::: ::::: d1nn5a_ 140 reryengafqeralrcfhqlmkdttLNWK-------mvdaSKSIE-AVHEDirvlsedai 191 d1tf7a1 234 ----fplgamrlt 242 d1nn5a_ 192 atatekplgelwk 204 FAST alignment (Normalized score: 3.97 Raw score:882.30) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPI--GRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPG 58 ::::::::::::::::::::::::::: ::::: d1nn5a_ 1 -------------------------RRGALIVLEGVDRAGKSTQSRKLVEALCA-AGHRA 34 d1tf7a1 59 VFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASP----------------DPEGQ 102 ::::: ::::: d1nn5a_ 35 ELLRF----------------------------------PERSTEIGKLLSSYLQKKSDV 60 d1tf7a1 103 EVV-------GGFDLSALIERINYAIQKYRA--RRVSID-SVTSVFQ------QYDASSV 146 : ::::::::::::::::: :::::: :::::: ::::::: d1nn5a_ 61 E--DHSVHLLFSANRWEQVPLIKEKLS----QGVTLVVDRYAFSGV-AFTGAKENFSLDW 113 d1tf7a1 147 VRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEF--VSDNVVILRNVLEGERRR 204 ::::::: ::::::::: d1nn5a_ 114 CKQPDVG---------------------------------LPKPDLVLFLQ--------- 131 d1tf7a1 205 RTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT---------------------- 242 d1nn5a_ 132 --------------------------------------LQLADAAKRERYENGAFQERAL 153 d1tf7a1 243 --------------------------------------------------- 243 d1nn5a_ 154 RCFHQLMKDTTLNWKMVDASKSIEAVHEDIRVLSEDAIATATEKPLGELWK 204 TMalign alignment (TM-score: 0.43 Raw score:104.44) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVF 60 : : :::::::: ::::::::::::::::::::::::::: d1nn5a_ 1 -----R-R----------------GALIVLEG-VDRAGKSTQSRKLVEALCAAGHRAELL 37 d1tf7a1 61 VTFEETP--QDIIKNARSFGWDLAKLVDEGKLFILDA-SPD----PEGQE--VVGGFDLS 111 :::: :: ::: ::: ::::: ::::::: d1nn5a_ 38 RFPE-RSTE-------------------------IGKLLSSYLQKKSDVEDHSVHLLFS- 70 d1tf7a1 112 ALIERINYAI-QKY-R-ARRVSIDSVTSVF-QQ--Y--DASSVVRRELFRLVARLKQIGA 163 :::::::::: ::: : ::::::::::::: :: : :::::::::: : :::: : d1nn5a_ 71 ANRWEQVPLIKEKLSQGVTLVVDRYAFSGVAFTGAKENFSLDWCKQPD-V--GLPK---P 124 d1tf7a1 164 TTVMTTERIEE--------------YGPIARY-GVEEFV-SDNVVILRNVLEGERRRRTL 207 ::::::::::: :::::: :::::: ::::::::: : d1nn5a_ 125 DLVLFLQLQLADAAKRERYENGAFQ-ERALRCFHQLMKDTTLNWKMVDA--------S-- 173 d1tf7a1 208 EILKLRGTSHMKGEYPFTITDHGINI----------------------FPLGAMRLT 242 :::: ::::: d1nn5a_ 174 ----------------KSIE-AVHEDIRVLSEDAIATATEKPLGELWK--------- 204 HHsearch alignment (Probability: 0.97 E-value:0.00) d1tf7a1 24 PIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEETPQDII 71 :::::::::::::::::::::::: ::::::::::::::::::::::: d1nn5a_ 1 RRGALIVLEGVDRAGKSTQSRKLV-EALCAAGHRAELLRFPERSTEIG 47