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 | d1j23a_ | Putative ATP-dependent RNA helicase Hef, nuclease domain | Restriction endonuclease-like | Restriction endonuclease-like | 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 <-- 0.990 --> HitDALI alignment (Z-score: 2.3 Raw score:296.60) d1tf7a1 1 ehqaiakmrtmiegfddishgglpigrstlvsgtsgtgktlfsiqflyngiiefdepgvf 60 d1j23a_ 1 --------------------------------------------------------vkvv 4 d1tf7a1 61 vtfeetpQDIIKNARSFGWDLAKlvDEGK---------lFILDASpdpegqevvgGFDL- 110 :::::::::::::::: :::: :::::: :::: d1j23a_ 5 vdsrelrSEVVKRLKLLGVKLEV--KTLDvgdyiisedvAIERKS------andlIQSIi 56 d1tf7a1 111 -SALIERINYAIQKYRARRVSIDSvtSVFQQYDassVVRRELFRLVARL-KQIGATTVMT 168 ::::::::::::::::::::::: ::::::: ::::::::::::: :::::::::: d1j23a_ 57 dGGLFDQVKRLKEAYSRPIMIVEG--SLYGIRN---VHPNAIRGAIAAVtVDFGVPIIFS 111 d1tf7a1 169 Terieeygpiarygveefvsdnvvilrnvlegerrrrtleilklrgtshmkgeypftitd 228 : d1j23a_ 112 S-----------------------------------------------tpeetaqyifli 124 d1tf7a1 229 hGINIfplgamrlt 242 :::: d1j23a_ 125 aKREQ-------ee 131 FAST alignment (Normalized score: 2.71 Raw score:481.70) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVF 60 d1j23a_ 1 ------------------------------------------------------------ 1 d1tf7a1 61 VTFEETP-----------QDIIKNARSFGWDLAKLVDE--------------GKLFILDA 95 ::::::::::::: ::::::: d1j23a_ 1 -------VKVVVDSRELRSEVVKRLKLLGVK-------LEVKTLDVGDYIISEDVAIER- 45 d1tf7a1 96 SPDPEGQEVVGGFD-----------LSALIERINYAIQKYRA--RRVSI-DSVTSVFQQY 141 ::::::::::::::: ::::: ::::: ::: d1j23a_ 46 --------------KSANDLIQSIIDGGLFDQVKRLKEAY--SRPIMIVEGSLYG--IRN 87 d1tf7a1 142 DASSVVRRELFRLVAR-LKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEG 200 : ::::::::::: :::::::::: d1j23a_ 88 V----HPNAIRGAIAAVTVDFGVPIIF--------------------------------- 110 d1tf7a1 201 ERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT------------------ 242 d1j23a_ 111 ------------------------------------------SSTPEETAQYIFLIAKRE 128 d1tf7a1 243 --- 243 d1j23a_ 129 QEE 131 TMalign alignment (TM-score: 0.30 Raw score:71.90) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVF 60 : : :::: d1j23a_ 1 -----------------------------------------------V---K----VVVD 6 d1tf7a1 61 -VTFEETPQ-D-IIKNARSFGWDLAKLVDEG-KLFI---------LDASPDPEG-QEVV- 105 ::: : :::::::::::: : :::: ::: :::::: : :: d1j23a_ 7 S-----RELRSEVVKRLKLLGVKL-E-VKTLD-VGDYIISEDVAIERKSAN--DL--IQS 54 d1tf7a1 106 GGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQY-DASSVVRRELFRLVARLKQIGAT 164 ::: ::::::::::::: :::::::::::: :::: :::::::::::::::::: : d1j23a_ 55 IID--GGLFDQVKRLKEA-YSRPIMIVEGSL-YGIRNVHPNAIRGAIAAVTVDFG---V- 106 d1tf7a1 165 TVMTTE------RIEEYGPIARYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHM 218 :::::: d1j23a_ 107 PIIFSSTPEETA------------------------------------------------ 118 d1tf7a1 219 KGEYPFTI--TDHGI-------NIFPLGAMRLT 242 : ::: d1j23a_ 119 -------QYI--FLIAKREQEE----------- 131 HHsearch alignment (Probability: 0.07 E-value:0.09) d1tf7a1 59 VFVTFEETPQDIIKNARSFGWDLAK-LVDEGKLFILD-AS-PDPEGQEVVGGFDLSALIE 115 ::::::::::::::::::::::::: ::::::::::: :: ::::::::::::::::::: d1j23a_ 3 VVVDSRELRSEVVKRLKLLGVKLEVKTLDVGDYIISEDVAIERKSANDLIQSIIDGGLFD 62 d1tf7a1 116 RINYAIQKYRARRVSID-SVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEE 174 ::::::::::::::::: ::::::: ::::: ::::::::::::::::::::::::: d1j23a_ 63 QVKRLKEAYSRPIMIVEGSLYGIRN--VHPNA---IRGAIAAVTVDFGVPIIFSSTPEET 117