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 | d1nlfa_ | Hexameric replicative helicase repA | 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 <-- 2.143 --> HitDALI alignment (Z-score: 16.4 Raw score:1567.70) d1tf7a1 1 --------------EHQAIAKMRtmiegfddishGGLPIGRSTLVSGTSGTGKTLFSIQF 46 ::::::::: :::::::::::::::::::::::::: d1nlfa_ 1 athkpinileafaaAPPPLDYVL-----------PNMVAGTVGALVSPGGAGKSMLALQL 49 d1tf7a1 47 LYNGIIE---------FDEPGVFVTFEETPQDIIKNARSFG-----wdlAKLVdeGKLFI 92 ::::::: ::::::::::::::::::::::::: :::: ::::: d1nlfa_ 50 AAQIAGGpdllevgelPTGPVIYLPAEDPPTAIHHRLHALGahlsaeerQAVA--DGLLI 107 d1tf7a1 93 LDASPDpegqevvggfDLSA--LIERINYAIQkyRARRVSIDSVTSVFQQY-DASSVVRR 149 :::::: :::: :::::::::: ::::::::::::::::: :::::::: d1nlfa_ 108 QPLIGS--------lpNIMApeWFDGLKRAAE--GRRLMVLDTLRRFHIEEeNASGPMAQ 157 d1tf7a1 150 ELFRLVARLKQIGATTVMTTERieeygpiarygVEEFVSDNVVILRNVLE---------G 200 :::::::::::::::::::::: ::::::::::::::::: : d1nlfa_ 158 VIGRMEAIAADTGCSIVFLHHA-----------VLVDNIRWQSYLSSMTSaeaeewgvdD 206 d1tf7a1 201 ERR--RRTLEILKLRGTSHMKgEYPFTITD-HGINIFPLgaMRLT------ 242 ::: :::::::::::::::: :::::::: :::::::: :::: d1nlfa_ 207 DQRrfFVRFGVSKANYGAPFA-DRWFRRHDgGVLKPAVL--ERQRkskgvp 254 FAST alignment (Normalized score: 11.56 Raw score:2867.00) d1tf7a1 1 --------------EHQAIAKMRTMIEGFDDISHG---GLPIGRSTLVSGTSGTGKTLFS 43 ::::::: :::::::::::::::::::::: d1nlfa_ 1 ATHKPINILEAFAAAPPPLDY--------------VLPNMVAGTVGALVSPGGAGKSMLA 46 d1tf7a1 44 IQFLYNGII-----------EFDEPGVFVTFEETPQDIIKNARSFGWDLAKLVDE----- 87 ::::::: :::::::::::::::::::::::: d1nlfa_ 47 LQLAAQI--AGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHA-----------LGAHL 93 d1tf7a1 88 ---------GKLFILDASPDPEGQEVVGGFD--------LSALIERINYAIQKYRARRVS 130 :::::::: ::::::::::::: :::::: d1nlfa_ 94 SAEERQAVADGLLIQPL--------------IGSLPNIMAPEWFDGLKRAAE--GRRLMV 137 d1tf7a1 131 IDSVTSVFQQYDASSV-VRRELFRLVARLKQ----IGATTVMTTERIEEYGPIARYGVEE 185 ::::::: ::::: :::::::::::::: ::::::::: ::::: d1nlfa_ 138 LDTLRRF--HIEEE--NASGPMAQVIGRMEAIAADTGCSIVFLH-----------HAVLV 182 d1tf7a1 186 FVSDNVVILRNVLEGER----------------RRRTLEILKLRGTSHMKGEYPFTITDH 229 :::::::::::: :::::::::::::: ::::::::::: d1nlfa_ 183 DNIRWQSYLSSM-----TSAEAEEWGVDDDQRRFFVRFGVSKANYGA-PFADRWFRRHD- 235 d1tf7a1 230 GINIFPLGAMRLT------------------- 242 d1nlfa_ 236 -------------GGVLKPAVLERQRKSKGVP 254 TMalign alignment (TM-score: 0.68 Raw score:164.05) d1tf7a1 1 ----------E----HQAIAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQF 46 : :::::::: : ::::::::::::::::::::::::: d1nlfa_ 1 ATHKPINILEAFAAAPPPLDYVL---------P--NMVAGTVGALVSPGGAGKSMLALQL 49 d1tf7a1 47 LYNGIIE---------FDEPGVFVTFEETPQDIIKNARSFGW-D----LAKLVDEGKLFI 92 ::::::: :::::::::::::::::::::::::: : :::::::::: d1nlfa_ 50 AAQIAGGPDLLEVGELPTGPVIYLPAEDPPTAIHHRLHALGAHLSAEE--RQAVADGLLI 107 d1tf7a1 93 LDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYD-ASS-VVRRE 150 :::::: : ::::: :::::::::::: :::::::::::::: ::: ::: ::::: d1nlfa_ 108 QPLIGS--L--PNIMA--PEWFDGLKRAAE--GRRLMVLDTLRRFH-IEEENASGPMAQV 158 d1tf7a1 151 LFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRNVLEG--------E- 201 ::::::::::::::::::::: :::::::::::::::::: : d1nlfa_ 159 IGRMEAIAADTGCSIVFLHHA-----------VLVDNIRWQSYLSSMTSAEAEEWGVDDD 207 d1tf7a1 202 -RR-RRTLEILKLRGTSHMKGEYPFTITD-HGINIFPLG---------AMRLT 242 :: :::::::::::::::: :::::::: ::::::::: d1nlfa_ 208 QRRFFVRFGVSKANYGAPFA-DRWFRRHDGGVLKPAVLERQRKSKGVP----- 254 HHsearch alignment (Probability: 1.00 E-value:0.00) d1tf7a1 5 IAKMRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEF---------D 55 :::::::::::::::: ::::::::::::::::::::::::::::::::: : d1nlfa_ 9 LEAFAAAPPPLDYVLP-NMVAGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPT 67 d1tf7a1 56 EPGVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLFILDASPDPEGQEVVGGFDLSALIE 115 :::::::::::::::::::::::::::::::::::::::: : :::::::::::: d1nlfa_ 68 GPVIYLPAEDPPTAIHHRLHALGAHLSAEERQAVADGLLI------Q-PLIGSLPNIMAP 120 d1tf7a1 116 RINYAI--QKYRARRVSIDSVTSVFQQYD-ASSVVRRELFRLVARLKQIGATTVMTTERI 172 :::::: ::::::::::::::::::::: :::::::::::::::::::::::::::::: d1nlfa_ 121 EWFDGLKRAAEGRRLMVLDTLRRFHIEEENASGPMAQVIGRMEAIAADTGCSIVFLHHAV 180 d1tf7a1 173 EEYGPIARYGVEEFVSD-NVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGI 231 ::::: ::::::::::: ::::::::::::::::::::::::::::: :::::::::::: d1nlfa_ 181 LVDNI-RWQSYLSSMTSAEAEEWGVDDDQRRFFVRFGVSKANYGAPF-ADRWFRRHDGGV 238 d1tf7a1 232 NI 233 :: d1nlfa_ 239 LK 240