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 | d1iqpa2 | Replication factor C | 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 <-- 2.427 --> HitDALI alignment (Z-score: 7.3 Raw score:670.80) d1tf7a1 1 ---------------------ehqaiakmrtmIEGFDD-isHGGLPigrSTLVSGTSGTG 38 :::::: ::::: ::::::::::: d1iqpa2 1 seeirevkvlekpwvekyrpqrlddivgqehiVKRLKHyvkTGSMP---HLLFAGPPGVG 57 d1tf7a1 39 KTLFSIQFLYNGIiEFDE--PGVFVTFEetpqdiiknarsfgwdlaklvdegklfildas 96 ::::::::::::: :::: :::::::: d1iqpa2 58 KTTAALALARELF-GENWrhNFLELNAS-------------------------------- 84 d1tf7a1 97 pdpegqevvgGFDLSALIERINYAIQKYR-----aRRVSIDSVTSVfqqydassvVRREL 151 ::::::::::::::::::: ::::::::::: ::::: d1iqpa2 85 ---------dERGINVIREKVKEFARTKPiggasfKIIFLDEADAL---------TQDAQ 126 d1tf7a1 152 FRLVARLKQIG--ATTVMTTErieeygpIARYgvEEFVS--DNVVILRNVLE-------- 199 ::::::::::: :::::::: :::: ::::: ::::::::::: d1iqpa2 127 QALRRTMEMFSsnVRFILSCN-------YSSK-iIEPIQsrCAIFRFRPLRDediakrlr 178 d1tf7a1 200 --------------------GERRRrtleilklrgtshmkgeypftitdhginifplgam 239 ::::: d1iqpa2 179 yiaeneglelteeglqailyIAEGD----------mrrainilqaaaaldkkitdenvfm 228 d1tf7a1 240 rlt 242 d1iqpa2 229 vas 231 FAST alignment (Normalized score: 4.98 Raw score:1178.00) d1tf7a1 1 EHQAIAKMRTM----------------------------IEGFDDISHGGLPI------- 25 ::::::: d1iqpa2 1 -----------SEEIREVKVLEKPWVEKYRPQRLDDIVGQEHIVKR-------LKHYVKT 42 d1tf7a1 26 --GRSTLVSGTSGTGKTLFSIQFLYNGIIEFDE-------PGVFVTFEETPQDIIKNARS 76 ::::::::::::::::::::::::: ::::::: d1iqpa2 43 GSMPHLLFAGPPGVGKTTAALALAREL------FGENWRHNFLELNA------------- 83 d1tf7a1 77 FGWDLAKLVDEGKLFILDASPDPEGQEVV-GGFDLSALIERINYAIQKYRA--------R 127 :::::::::::::::::: : d1iqpa2 84 -----------------------------SDERGINVIREKVKEFART---KPIGGASFK 111 d1tf7a1 128 RVSIDSVTSVFQQYDASSV-VRRELFRLVARLKQI---GATTVMTTERIEEYGPIA---- 179 ::::::::: :::::::::::::: :::::::: d1iqpa2 112 IIFLDEADA----------LTQDAQQALRRTMEM-FSSNVRFILSC----------NYSS 150 d1tf7a1 180 -RYGVEEFVSDNVVILRNVLEGERRRRTLEILKLRGTSHMKGEYPFTITDHGINIFPLGA 238 :::::::: :::::: d1iqpa2 151 KIIEPIQSR-CAIFRF-------------------------------------------- 165 d1tf7a1 239 MRLT-------------------------------------------------------- 242 d1iqpa2 166 ----RPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALDKKI 221 d1tf7a1 243 ---------- 243 d1iqpa2 222 TDENVFMVAS 231 TMalign alignment (TM-score: 0.44 Raw score:107.57) d1tf7a1 1 --------------------EHQAIAKMRTMIE-----G-FDDISHGGL-P-IGRSTLVS 32 :::: : ::::::::: : :::::::: d1iqpa2 1 SEEIREVKVLEKPWVEKYRP---------QRLDDIVGQEHIVKRLKHYVKTGSMPHLLFA 51 d1tf7a1 33 GTSGTGKTLFSIQFLYNGIIEFDEP-GVFVTFEETPQDIIKNARSFGWDLAKLVDEGKLF 91 :::::::::::::::::::: ::: ::::::: d1iqpa2 52 GPPGVGKTTAALALARELFG--ENWRHNFLELN--------------------------- 82 d1tf7a1 92 ILDASPDPEGQEVVGGFDLSALIERINYAIQKYRARRVSIDSVTSVFQQYDASSVVRREL 151 ::: :::::: :: ::::::::::::::::::::::::: :: ::: :::::: d1iqpa2 83 ---ASD---ERGINV-IR--EKVKEFARTKPIGGASFKIIFLDEA-DA--LTQ-DAQQAL 129 d1tf7a1 152 FRLVARLKQIGATTVMTTERIEEYGPIARYGVE-EFVSDNVVILRNVLEGERRRRTLEIL 210 :::::::::: : ::::::: ::: :::: :::::::::::: ::: d1iqpa2 130 RRTMEMFSSN-V-RFILSCN-----YSS-KIIEPIQSRCAIFRFRP------LRD----- 170 d1tf7a1 211 KLRGTSHMKGEYPFT-ITD-H--------------------------------------- 229 ::: ::: : d1iqpa2 171 ------------EDIAKRLRYIAENEGLELTEEGLQAILYIAEGDMRRAINILQAAAALD 218 d1tf7a1 230 -------------GINIFPLGAMRLT 242 d1iqpa2 219 KKITDENVFMVAS------------- 231 HHsearch alignment (Probability: 0.96 E-value:0.00) d1tf7a1 13 EGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFLYNGII-EFDEPGVFVTFE 64 :::::::::: :::::::::::::::::::::::::::: :::::::::::: d1iqpa2 34 KRLKHYVKTG--SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNAS 84