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 | d1gm5a3 | RecG helicase domain | 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 <-- 1.916 --> HitDALI alignment (Z-score: 6.9 Raw score:706.70) d1tf7a1 1 ------------------------------------------------------------ 1 d1gm5a3 1 etlperilekrkllgvkdayygmhfpktfyhlekarerlayeelfvlqlafqkirkerek 60 d1tf7a1 1 -ehqaiakmrtMIEG-------------fddishgGLPI----GRSTLVSGTSGTGKTLF 42 :::: :::: ::::::::::::::::: d1gm5a3 61 hggipkkiegkLAEEfikslpfkltnaqkrahqeiRNDMisekPMNRLLQGDVGSGKTVV 120 d1tf7a1 43 SIQFLYNGIIeFDEPGVFVTFE-eTPQDIIKNA-RSFGWDlaKLVD-------------- 86 :::::::::: ::::::::::: ::::::::: :::::: :::: d1gm5a3 121 AQLAILDNYE-AGFQTAFMVPTsiLAIQHYRRTvESFSKF-nIHVAlligattpsekeki 178 d1tf7a1 87 -------EGKLFILDAspdpegqevvggfdlsaLIERinyaiQKYRARRVSIDSvtSVFQ 139 ::::::::: :::: :::::::::::: :::: d1gm5a3 179 ksglrngQIDVVIGTH---------------alIQED----vHFKNLGLVIIDE--QHRF 217 d1tf7a1 140 qydassvvrrelfrlvaRLKQ---IGATTVMTTERieeygpiARYGV----eEFVSDNVV 192 :::: ::::::::::: ::::: :::::::: d1gm5a3 218 -----------------EALMnkgKMVDTLVMSAT-------PIPRSmalafYGDLDVTV 253 d1tf7a1 193 ILRNVLegerrrrtleilklrgtshmkgeypftitdhginifplgamrlt 242 :::::: d1gm5a3 254 IDEMPP-------------------------------------------- 259 FAST alignment (Normalized score: 4.34 Raw score:1088.00) d1tf7a1 1 EH---------------------------------------------------------- 2 d1gm5a3 1 --ETLPERILEKRKLLGVKDAYYGMHFPKTFYHLEKARERLAYEELFVLQLAFQKIRKER 58 d1tf7a1 3 --QAIAKMRTM---------------------IEGFDDISHGGLPI---------GRSTL 30 :::::: ::::::: ::::: d1gm5a3 59 EKHGGIPK---KIEGKLAEEFIKSLPFKLTNAQKRAHQE-------IRNDMISEKPMNRL 108 d1tf7a1 31 VSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEE---TPQDIIKNARS----FGWDLAK 83 ::::::::::::::::::::: ::::::::::: ::::::::::: :::: d1gm5a3 109 LQGDVGSGKTVVAQLAILDNY-EAGFQTAFMVP--TSILAIQHYRRTVESFSKFNIH--- 162 d1tf7a1 84 LVD-----------------------EGKLFILDASPDPEGQEVVGGFDLSALIERINYA 120 :::::::: d1gm5a3 163 ---VALLIGATTPSEKEKIKSGLRNGQIDVVIGT-------------------------- 193 d1tf7a1 121 IQKY-----------RARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQI-------- 161 :::::::: d1gm5a3 194 ----HALIQEDVHFKNLGLVIID-----------------------------EQHRFEAL 220 d1tf7a1 162 -----GATTVMTTERIEEYGPIARY------GVEE---FVSDNVVILRNVLEGERRRRTL 207 :::::::: :::: ::::::::: d1gm5a3 221 MNKGKMVDTLVMS------------ATPIPRSMALAFYGDLDVTVID------------- 255 d1tf7a1 208 EILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT---- 242 d1gm5a3 256 -----------------------------------EMPP 259 TMalign alignment (TM-score: 0.48 Raw score:116.99) d1tf7a1 1 ----------------------------------------------------------EH 2 :: d1gm5a3 1 ETLPERILEKRKLLGVKDAYYGMHFPKTFYHLEKARERLAYEELFVLQLAFQKIRKEREK 60 d1tf7a1 3 --QAIAKMRT-M--IE--------------GFDDISHGGL--P-IGRSTLVSGTSGTGKT 40 :::::: : :: :::::::::: : :::::::::::::::: d1gm5a3 61 HG--GIPKKIEGKLAEEFIKSLPFKLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKT 118 d1tf7a1 41 LFSIQFLYNGIIEFDEPGVFVTFE-ETPQDIIKNA-RSFGWDLAKLV------------- 85 ::::::::::: :::::::::::: :::::::::: ::::::::::: d1gm5a3 119 VVAQLAILDNY-EAGFQTAFMVPTSILAIQHYRRTVESFSKFNIHVALLIGATTPSEKEK 177 d1tf7a1 86 D-------EGKLFILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVF 138 : ::::::::: ::::: :: ::::::::::: : ::: d1gm5a3 178 IKSGLRNGQIDVVIGTH-----------------ALIQE-DV-HFKNLGLVIID-E-QHR 216 d1tf7a1 139 QQYDASSVVRRELFRLVARLK--QIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRN 196 : : ::: ::::::::::::: ::::::::::::::::::::: d1gm5a3 217 -----------F---E--ALMNKGKMVDTLVMSATP---IPRSMALAFYGDLDVTVIDEM 257 d1tf7a1 197 VLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT 242 :: d1gm5a3 258 ------PP-------------------------------------- 259 HHsearch alignment (Probability: 0.97 E-value:0.00) d1tf7a1 25 IGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTF-EETPQDIIKNARSFGW 79 ::::::::::::::::::::::::: ::::::::::::: :::::::::::::::: d1gm5a3 103 KPMNRLLQGDVGSGKTVVAQLAILD-NYEAGFQTAFMVPTSILAIQHYRRTVESFS 157