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 | d1b0ua_ | ATP-binding subunit of the histidine permease | 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 <-- 1.886 --> HitDALI alignment (Z-score: 7.4 Raw score:800.60) d1tf7a1 1 ehqaiAKMRtMIEG--------fddishgGLPIGRSTLVSGTSGTGKTLFSIQFLY---- 48 :::: :::: ::::::::::::::::::::::::::: d1b0ua_ 1 -----NKLH-VIDLhkrygghevlkgvslQARAGDVISIIGSSGSGKSTFLRCINFlekp 54 d1tf7a1 49 -------------------------ngiIEFDE--PGVFVTFEetpqdiiknarsfgwdl 81 ::::: :::::::: d1b0ua_ 55 segaiivngqninlvrdkdgqlkvadknQLRLLrtRLTMVFQH----------------- 97 d1tf7a1 82 aklvdegklfildASPDPE----------------------------------------- 100 :::::: d1b0ua_ 98 -------------FNLWSHmtvlenvmeapiqvlglskhdareralkylakvgideraqg 144 d1tf7a1 101 --gQEVVGGFDLSALIERINYAIqkyrARRVSIDSVTSVfQQYDassVVRRELFRLVARL 158 :::::::::::::::::::: :::::::::::: :::: ::::::::::::: d1b0ua_ 145 kypVHLSGGQQQRVSIARALAME----PDVLLFDEPTSA-LDPE---LVGEVLRIMQQLA 196 d1tf7a1 159 KQiGATTVMTTErieeygpiarYGVE-EFVSDNVVILRNvlegerrrRTLEILKLR-gts 216 :: ::::::::: :::: :::::::::::: ::::::::: d1b0ua_ 197 EE-GKTMVVVTH----------EMGFaRHVSSHVIFLHQ--------GKIEEEGDPeqvf 237 d1tf7a1 217 hMKGEypftitdhginifplgamrlt 242 :::: d1b0ua_ 238 gNPQS------prlqqflkgslkkle 257 FAST alignment (Normalized score: 4.71 Raw score:1173.00) d1tf7a1 1 EHQAIAKMRTMIEGFDDISHG------------------GLPIGRSTLVSGTSGTGKTLF 42 ::::: ::::::::::::::::::::: d1b0ua_ 1 -----NKLHV-----------IDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTF 44 d1tf7a1 43 SIQFLYNGIIEFDE-----------------------------------------PGVFV 61 :::: ::::: d1b0ua_ 45 LRCI----------NFLEKPSEGAIIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMV 94 d1tf7a1 62 TFEETPQDIIKNARSFGWDLAKLVDEGKLFILDA----SPDPEGQEVVGG---------- 107 :::: d1b0ua_ 95 ----------------------------------FQHFNLWS--------HMTVLENVME 112 d1tf7a1 108 --------------------------------------FDLSALIERINYAIQKYRARRV 129 ::::::::::::: :::::::: d1b0ua_ 113 APIQVLGLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARA-LAMEPDVL 171 d1tf7a1 130 SIDSVTSVFQQY---DASSVVRRELFRLVARLKQIGATTVMTTERIEEYGPIARYGVE-E 185 ::::: ::::::::::::: ::::::::::::: :::::: : d1b0ua_ 172 LFDEP-------TSALDPELVGEVLRIM-QQLAEEGKTMVVV----------THEMGFAR 213 d1tf7a1 186 FVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGAMRLT--- 242 ::::::::: d1b0ua_ 214 HVSSHVIFL------------------------------------------------HQG 225 d1tf7a1 243 -------------------------------- 243 d1b0ua_ 226 KIEEEGDPEQVFGNPQSPRLQQFLKGSLKKLE 257 TMalign alignment (TM-score: 0.50 Raw score:120.49) d1tf7a1 1 EHQAIAKMRTMIE------------GFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLY 48 ::::::: ::: : ::::::::::::::::::::::::::: d1b0ua_ 1 ------NKLHVIDLHKRYGGHEVLKGVS--L--QARAGDVISIIGSSGSGKSTFLRCINF 50 d1tf7a1 49 --------NGIIEFDEP------GVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLF--I 92 ::: ::::: ::::::::::::::::: : d1b0ua_ 51 LEKPSEGAIIV-NGQNINLVRDK-----------------DGQLKVADKNQLRLLRTRLT 92 d1tf7a1 93 LD---ASPDP--------------------------------------------EGQEVV 105 :: ::::: :::::: d1b0ua_ 93 MVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDARERALKYLAKVGIDERAQGKYPVHLSG 152 d1tf7a1 106 GGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRRELFRLVARLKQIGATT 165 ::::: :::::::::: ::::::::::: ::::: ::::::::::::::: :::: d1b0ua_ 153 GQQQR-VSIARALAME----PDVLLFDEPTS--ALDPE--LVGEVLRIMQQLAEE-GKTM 202 d1tf7a1 166 VMTTERIEEYGPIARYGVEEFVSD-NVVILRNVLEGERRRRTLEILKLRG----TSHMKG 220 :::: : ::::::::: ::::::: ::::::::::: :: d1b0ua_ 203 VVVT---------H-EMGFARHVSSHVIFLHQ-------GKIEEEGDPEQVFGN----PQ 241 d1tf7a1 221 EYP-------------FTITDHGINIFPLGAMRLT 242 ::: d1b0ua_ 242 SPRLQQFLKGSLKKLE------------------- 257 HHsearch alignment (Probability: 0.98 E-value:0.00) d1tf7a1 14 GFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTFEE-T------ 66 ::::::: ::::::::::::::::::::::::: : :::::::::::::::: : d1b0ua_ 17 VLKGVSL-QARAGDVISIIGSSGSGKSTFLRCI-N-FLEKPSEGAIIVNGQNINLVRDKD 73 d1tf7a1 67 -------PQDIIKNARSFGWDLAKLVDEGKL--------------------------FIL 93 :::::::::::::::::::::::: ::: d1b0ua_ 74 GQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVLGLSKHDARERALKYL 133 d1tf7a1 94 DASPDPEGQ--EVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRREL 151 ::::::::: ::::::::::::::::::::::::::::::::::: ::::::::: d1b0ua_ 134 AKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTSA-----LDPELVGEV 188 d1tf7a1 152 FRLVARLKQIGATTVMTTERIEEYGPIARYGVEEFVSDNVVILRN 196 ::::::::::::::::::::::: ::::::::::::: d1b0ua_ 189 LRIMQQLAEEGKTMVVVTHEMGF---------ARHVSSHVIFLHQ 224