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 | d1q0ua_ | Probable DEAD box RNA helicase YqfR | 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 <-- 0.607 --> HitDALI alignment (Z-score: 5.0 Raw score:566.40) d1tf7a1 1 ehqaiakmrtmiEGFDD----------------------ishgGLPIGRSTLVSGTSGTG 38 ::::: ::::::::::::::::: d1q0ua_ 1 ----------tqFTRFPfqpfiieaiktlrfykpteiqeriipGALRGESMVGQSQTGTG 50 d1tf7a1 39 KTLFSIQFLYNGIIEFD--ePGVFVTFE-ETPQDIIKNARSFGW-----dlAKLV----- 85 ::::::::::::::::: :::::::: ::::::::::::::: :::: d1q0ua_ 51 KTHAYLLPIMEKIKPERaevQAVITAPTrELATQIYHETLKITKfcpkdrmIVARcligg 110 d1tf7a1 86 -----------dEGKLFILDAspdpegqevvggfdlsaLIER--inYAIQkyRARRVSID 132 ::::::::: :::: :::: :::::::: d1q0ua_ 111 tdkqkaleklnvQPHIVIGTP--------------griNDFIreqaLDVH--TAHILVVD 154 d1tf7a1 133 SVTS-VFQQydassvvrrelfrlvarlkqIGATTVMTTErieeygpiARYGVEEFVS--- 188 :::: :::: :::::::::: :::::::::: d1q0ua_ 155 EADLmLDMG-------fitdvdqiaarmpKDLQMLVFSA--------TIPEKLKPFLkky 199 d1tf7a1 189 ---DNVVILRnvlegerrrrtleilklrgtshmkgeypftitdhginifplgamrlt 242 ::::::: d1q0ua_ 200 menPTFVHVL----------------------------------------------- 209 FAST alignment (Normalized score: 4.49 Raw score:1009.00) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHGGLP------------------------------------ 24 d1q0ua_ 1 ------------------------TQFTRFPFQPFIIEAIKTLRFYKPTEIQERIIPGAL 36 d1tf7a1 25 IGRSTLVSGTSGT---GKTLFSIQFLYNG-IIEFDE--PGVFVTFEE---TPQDIIKNAR 75 :::::::::: ::::::::::::: ::::: ::::::: :::::::::: d1q0ua_ 37 RGESMVGQSQ---TGTGKTHAYLLPIMEKIKPERA-EVQAVITAP--TRELATQIYHETL 90 d1tf7a1 76 SFGWDLAKLVDE--------------------------------GKLFILDASPDPEGQE 103 : :::::: d1q0ua_ 91 K-----------ITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIG---------- 129 d1tf7a1 104 VVGGFDLSALIERINYAIQKY-----------------RARRVSIDSVTSVFQQYDASSV 146 ::::::::::::::: d1q0ua_ 130 ---------------------TPGRINDFIREQALDVHTAHILVVDEADLMLD------- 161 d1tf7a1 147 VRRE------LFRLVARLKQ--IGATTVMTTERIEEYGPIA--RYGVEEFVS-------D 189 ::::::: ::::::::: :::::::: : d1q0ua_ 162 ----MGFITDVDQIAAR---MPKDLQMLVFS----------ATIPEKLKPF-LKKYMENP 203 d1tf7a1 190 NVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT-- 242 :::: d1q0ua_ 204 TFVH-------------------------------------------------VL 209 TMalign alignment (TM-score: 0.44 Raw score:106.88) d1tf7a1 1 -----EHQAIAKMRTMI--------------------EGFDDISHGGLPIGRSTLVSGTS 35 ::: ::::::: :::: ::::::: d1q0ua_ 1 TQFTR---------FPFQPFIIEAIKTLRFYKPTEIQERIIPGA-LRGE----SMVGQSQ 46 d1tf7a1 36 GT-GKTLFSIQFLYNGIIEFDEP---GVFVTF----EET--PQDIIKNARSFGWDLAKLV 85 :: :::::::::::::: :::: :::::: ::: :::::: :::::: d1q0ua_ 47 TGTGKTHAYLLPIMEKI--KPERAEVQAVITAPTRELATQIYHETLK-------ITKFCP 97 d1tf7a1 86 DEGKLFILDASPDPE-GQ--------------EVVGGFDLSALI-ERINYAIQKYRARRV 129 ::::::::::::::: :: :::::::::: ::::: :: ::: d1q0ua_ 98 KDRMIVARCLIGGTDKQKALEKLNVQPHIVIG--TPGRINDFIREQALDV-HT----AHI 150 d1tf7a1 130 SIDSVT-SVFQQYDASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVS 188 :::::: ::::: : :: :::::::::::: : ::::::::: :::::::::::: d1q0ua_ 151 LVVDEADLMLDM-G---FI-TDVDQIAARMPK-D-LQMLVFSAT----IPEKLKPFLKKY 199 d1tf7a1 189 DN-VVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT 242 :: ::::::: d1q0ua_ 200 MENPTFVHVL--------------------------------------------- 209 HHsearch alignment (Probability: 0.97 E-value:0.00) d1tf7a1 23 LPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEF--DEPGVFVTFEE-TPQDIIKNARSFGW 79 :::::::::::::::::::::::::::::::: ::::::::::: :::::::::::::: d1q0ua_ 35 ALRGESMVGQSQTGTGKTHAYLLPIMEKIKPERAEVQAVITAPTRELATQIYHETLKITK 94 d1tf7a1 80 DLAKLVDEGKLF------ILDASPDPEGQEVVGGFDLSALIERINYA-IQKYRARRVSID 132 :::::::::::: ::::::::::::::::::::::::::::: :::::::::::: d1q0ua_ 95 FCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIREQALDVHTAHILVVD 154 d1tf7a1 133 SVTSVFQQYDASSVVRRELFRLVARLKQIGATTVMTTER 171 ::::::::: :::::::::::::::::: :::::: d1q0ua_ 155 EADLMLDMG-----FITDVDQIAARMPKDLQM-LVFSAT 187