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 | d1emsa2 | NIT-FHIT fusion protein, N-terminal domain | Carbon-nitrogen hydrolase | Carbon-nitrogen hydrolase | α+β |
| Hit | d1tf7a2 | Circadian clock protein KaiC | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | α/β |
Query <-- 1.501 --> IntermediateDALI alignment (Z-score: 25.8 Raw score:2601.40) query 1 --SLQLRLALNQIDSTvGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGyPVED-LAL 57 :::::::::::::: :::::::::::::::::::::::::::::::::: :::: ::: d1emsa2 1 maTGRHFIAVCQMTSD-NDLEKNFQAAKNMIERAGEKKCEMVFLPECFDFI-GLNKnEQI 58 query 58 RssFVEASR-TALRELAARLAeegFGELPVLV-GYLDRSEsaqpkygqPAGA-PRNAAAV 114 : :::::: ::::::::::: :::::::: ::::::: :::: ::::::: d1emsa2 59 D--LAMATDcEYMEKYRELAR---KHNIWLSLgGLHHKDP--------SDAAhPWNTHLI 105 query 115 LH-RGRVALTFAKHHLPNY-----gvFDEFRYFVPG-DTMPIVRLHGVDIALAICEDLWQ 167 :: :::::::::::::::: :::::::::: ::::::::::::::::::::::: d1emsa2 106 IDsDGVTRAEYNKLHLFDLeipgkvrLMESEFSKAGtEMIPPVDTPIGRLGLSICYDVRF 165 query 168 DGgRVPAARSAGAGLLLSVNASPYErdkdDTRLELVRKRAQEAGCTTAYLAMIGG-QDEL 226 :: :::::::::::::::::::::: :::::::::::::::::::::::::: :::: d1emsa2 166 PE-LSLWNRKRGAQLLSFPSAFTLN-tglAHWETLLRARAIENQCYVVAAAQTGAhNPKR 223 query 227 VFDGDSIVVDRDGEVVARAPQfSEGCVVLDLDLPaaeaepptgvvddglridrlviseep 286 ::::::::::::::::::::: :::::::::::: d1emsa2 224 QSYGHSMVVDPWGAVVAQCSE-RVDMCFAEIDLS-------------------------- 256 query 287 lpayeaelaggyadrldadeevysalvvglrayvakngfrsvliglsggidsalvaaiac 346 d1emsa2 257 ------------------------------------------------------------ 257 query 347 dalgaqnvygvsmpskyssdhskgdaaelarrtglnfrtvsiepmfdaymaslgltglae 406 d1emsa2 257 ------------------------------------------------------------ 257 query 407 enlqsrlrgttlmaisnqeghivlapgnkselavgystlygdsvgaygpikdvyktsifr 466 d1emsa2 257 ------------------------------------------------------------ 257 query 467 laewrnraaaergqtppipeasitkpdypvldailelyvdrdtgadaivaagydrelvvk 526 d1emsa2 257 ------------------------------------------------------------ 257 query 527 tlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 568 d1emsa2 257 ---------------------------yvdtlremqpvfshr 271 FAST alignment (Normalized score: 13.47 Raw score:5286.00) query 1 --SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLAL- 57 ::::::::::::: ::::::::::::::::::::::::::::::::: d1emsa2 1 MATGRHFIAVCQMTS-DNDLEKNFQAAKNMIERAGEKKCEMVFLPECFD----------F 49 query 58 -------RSSFVEASR-TALRELAARLAEEGFGELPVLV-GYLDRSESAQPKYGQPA--- 105 ::::::::: :::::::::::: ::::::: ::::::: d1emsa2 50 IGLNKNEQIDLAMATDCEYMEKYRELARK---HNIWLSLGGLHHKDP----------SDA 96 query 106 GAPRNAAAVL-HRGRVALTFAKHHLPNYGV---------FDEFRYFVPGDTM-PIVRLHG 154 :::::::::: ::::::::::::::: ::::::::::::: ::::: d1emsa2 97 AHPWNTHLIIDSDGVTRAEYNKLHLF----DLEIPGKVRLMESEFSKAGTEMIPPVDT-- 150 query 155 --VDIALAICEDLWQDGGRVPAARSAGAGLLLSVNASPYERDKD-----DTRLELVRKRA 207 :::::::::::::: ::::::::::::::::::::: ::::::::::: d1emsa2 151 PIGRLGLSICYDVRFP-ELSLWNRKRGAQLLSFPSAFT------LNTGLAHWETLLRARA 203 query 208 QEAGCTTAYLAMIGG-QDELVFDGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEP 266 ::::::::::::::: :::::::::::::::::::::::: ::::::::::: d1emsa2 204 IENQCYVVAAAQTGAHNPKRQSYGHSMVVDPWGAVVAQCS-ERVDMCFAEID-------- 254 query 267 PTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNGFR 326 d1emsa2 255 ------------------------------------------------------------ 255 query 327 SVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTV 386 d1emsa2 255 ------------------------------------------------------------ 255 query 387 SIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLY 446 d1emsa2 255 ------------------------------------------------------------ 255 query 447 GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVD 506 d1emsa2 255 ------------------------------------------------------------ 255 query 507 RDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWRE 566 d1emsa2 255 ------------------------------------------------------------ 255 query 567 GH----------------- 568 d1emsa2 255 --LSYVDTLREMQPVFSHR 271 TMalign alignment (TM-score: 0.40 Raw score:226.65) query 1 --SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALR 58 :::::::::::::: :::::::::::::::::::::::::::::::::: :::::::: d1emsa2 1 MATGRHFIAVCQMTSD-NDLEKNFQAAKNMIERAGEKKCEMVFLPECFDFI-GLNKNEQI 58 query 59 SSFVEASRTALRELAARLAEEGFGELPVLV-GYLDRSESAQPKYGQPAG-APRNAAAVLH 116 ::::::::::::::::::: :: :::::: :::::::: :: :::::::::: d1emsa2 59 -DLAMATDCEYMEKYRELAR-KH-NIWLSLGGLHHKDPS--------DAAHPWNTHLIID 107 query 117 -RGRVALTFAKHHLPNY-----GVFDEFRYFVPG-DTMPIVRLHGVDIALAICEDLWQDG 169 :::::::::::::::: :::::::::::: ::::::::::::::::::::::::: d1emsa2 108 SDGVTRAEYNKLHLFDLEIPGKVRLMESEFSKAGTEMIPPVDTPIGRLGLSICYDVRFPE 167 query 170 GRVPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQ-DELVF 228 : ::::::::::::::::::::::: :::::::::::::::::::::::::::: ::::: d1emsa2 168 L-SLWNRKRGAQLLSFPSAFTLNTG-LAHWETLLRARAIENQCYVVAAAQTGAHNPKRQS 225 query 229 DGDSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAE------------AEPPTGVVDDGLR 276 :::::::::::::::::: :::::::::::::::: d1emsa2 226 YGHSMVVDPWGAVVAQCS-ERVDMCFAEIDLSYVDTLREMQPVFSHR------------- 271 query 277 IDRLVISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGI 336 d1emsa2 272 ------------------------------------------------------------ 272 query 337 DSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYM 396 d1emsa2 272 ------------------------------------------------------------ 272 query 397 ASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPI 456 d1emsa2 272 ------------------------------------------------------------ 272 query 457 KDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVA 516 d1emsa2 272 ------------------------------------------------------------ 272 query 517 AGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1emsa2 272 ---------------------------------------------------- 272 HHsearch alignment (Probability: 1.00 E-value:0.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 :::::::::::::: ::::::::::::::::::::::::::::::::::::::::::::: d1emsa2 3 TGRHFIAVCQMTSD-NDLEKNFQAAKNMIERAGEKKCEMVFLPECFDFIGLNKNEQIDLA 61 query 61 FVE--ASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVL-HR 117 ::: :::::::::::: ::::::::::::::: ::::::::::::: :: d1emsa2 62 MATDCEYMEKYRELARK------HNIWLSLGGLHHKDP------SDAAHPWNTHLIIDSD 109 query 118 GRVALTFAKHHL-----PNYGVFDEFRYFVPGDTM-PIVRLHGVDIALAICEDLWQDGGR 171 :::::::::::: :::::::::::::::::: :::::::::::::::::::::: : d1emsa2 110 GVTRAEYNKLHLFDLEIPGKVRLMESEFSKAGTEMIPPVDTPIGRLGLSICYDVRFPE-L 168 query 172 VPAARSAGAGLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGG-QDELVFDG 230 ::::::::::::::::::::::: ::::::::::::::::::::::::::: :::::::: d1emsa2 169 SLWNRKRGAQLLSFPSAFTLNTG-LAHWETLLRARAIENQCYVVAAAQTGAHNPKRQSYG 227 query 231 DSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGL 275 ::::::::::::::::: ::::::::::::::::::::::::::: d1emsa2 228 HSMVVDPWGAVVAQCSE-RVDMCFAEIDLSYVDTLREMQPVFSHR 271
Intermediate <-- 0.989 --> HitDALI alignment (Z-score: 2.6 Raw score:402.00) d1emsa2 1 -------------------------------------------------maTGRHFIAVC 11 ::::::::: d1tf7a2 1 qrssnvrvssgvvrldemcgggffkdsiilatgatgtgktllvsrfvenacANKERAILF 60 d1emsa2 12 Q--------------------------------MTSD-nDLEKNFQAAKNMIERageKKC 38 : :::: ::::::::::::::: ::: d1tf7a2 61 AyeesraqllrnayswgmdfeemerqnllkivcAYPEsaGLEDHLQIIKSEIND---FKP 117 d1emsa2 39 EMVFLPEC-fDFIGlnkneqidLAMATDcEYMEKYRELARKHNIWLSLGGlhhkdpsdaa 97 :::::::: :::: :::::: ::::::::::::::::::::: d1tf7a2 118 ARIAIDSLsaLARG-------vSNNAFR-QFVIGVTGYAKQEEITGLFTN--tsdqfmga 167 d1emsa2 98 HPWNthliidsdgVTRAEYNKLHlfdleipgkvrlmesefskagtEMIPpvdtpigrlgl 157 :::: :::::::::: :::: d1tf7a2 168 HSIT---dshistITDTIILLQY-------------veirgemsrAINV------fkmrg 205 d1emsa2 158 sicydvrfpELSL--WNRKrgaqllsfpsaftlntglahwetllraraienqcyvvaaaq 215 :::: :::: d1tf7a2 206 swhdkaireFMISdkGPDI----------------------------------------- 224 d1emsa2 216 tgahnpkrqsyghsmvvdpwgavvaqcservdmcfaeidlsyvdtlremqpvfshr 271 d1tf7a2 225 --------------------------------------kdsfrnferiisgsptri 242 FAST alignment (Normalized score: 1.78 Raw score:455.20) d1emsa2 1 MA--TGRHFI--------------------AVCQMTSDNDLEKNFQAAKNMIERAGEKKC 38 :::::: :::::: d1tf7a2 1 --QRSSNVRVSSGVVRLDEMCGGGFFKDSIILATGA------------------------ 34 d1emsa2 39 EMVFLPECFDFIGLN-------------------------------KNEQIDLAMATDCE 67 :::::::::: d1tf7a2 35 ---------------TGTGKTLLVSRFVENACANKERAILFAYEESRAQLLRNAYS---- 75 d1emsa2 68 YMEKYRELARKHNIWLSLGGLHHKDPSDAAHPWNTHLIIDSDGVT-------------RA 114 :: d1tf7a2 76 ---------------------------------------------WGMDFEEMERQNLLK 90 d1emsa2 115 EYNKLHLFDLEIPGKVRLMESEFSKAGTEMIPPVDTPIGRLGLSICYDVR---------- 164 :: d1tf7a2 91 IV------------------------------------------------CAYPESAGLE 102 d1emsa2 165 -FPELSLWNRK-RGAQLLSFPSAFTLNTG-----------LAHWETLLRARAI---ENQC 208 :::::::::: :::::::: ::::::::::::: :::: d1tf7a2 103 DHLQIIKSEINDFKPARIAI---------DSLSALARGVSNNAFRQFVIGVTGYAKQEEI 153 d1emsa2 209 YVVAAAQTGAHNPKRQSYGHSMVVDPWG---------------AVVAQCSERVDMCFAEI 253 ::::::::: :::::: d1tf7a2 154 TGLFTNTSD-------------------QFMGAHSITDSHISTITDTII----------- 183 d1emsa2 254 DLSYVDTLREMQPVFSHR------------------------------------------ 271 d1tf7a2 184 ------------------LLQYVEIRGEMSRAINVFKMRGSWHDKAIREFMISDKGPDIK 225 d1emsa2 272 ----------------- 272 d1tf7a2 226 DSFRNFERIISGSPTRI 242 TMalign alignment (TM-score: 0.37 Raw score:99.82) d1emsa2 1 -MATGRHFIAVCQMTSDNDLEKNFQAAKNMIERAGE--KKCE-M---VFL------PECF 47 ::::::::: ::::::: :::: : ::: :::: d1tf7a2 1 QRSSNVRVSS-------------------GVVRLDEMCGGGFFKDSIILATGATGTGKTL 41 d1emsa2 48 D-FIGLNKNEQIDLAMATDCEYMEKYRELARKHNIW-LSLGG-LHHKDP----------- 93 : : ::::::::::: ::::: :::::: d1tf7a2 42 LV--------------------S--RFVENACANKERAILFAYEESRAQLLRNAYSWGMD 79 d1emsa2 94 SDAAHPWNTHL--IID-SDGVTRAEYNKLHLFDLEIPGKVRLMESEFSKAGT----EM-- 144 : :: ::::::::::: ::: :: d1tf7a2 80 ----------FEE-MER-QNLLKIVCAYP--------------------ESAGLEDHLQI 107 d1emsa2 145 IP-PV---DTPIGRLGLSICY-DV----R--FPELSLWNRKRGAQ---LLSFPSAF-TLN 189 :: :: :::: ::::::: :: : :::::::::::::: :::::::: ::: d1tf7a2 108 IKSEINDFKPAR--IAIDSLSALARGVSNNAFRQFVIGVTGYAKQEEITGLFTNTSDQFM 165 d1emsa2 190 TGLAHWET-LLRARAIENQCYVVAAAQTGAH----NPKRQSYGHSMVVDPWGAVVAQCSE 244 : :::::: :::::: :::::: :::: :::::::::::: :::::::: d1tf7a2 166 G-AHSITDSHISTIT-----DTIILL-QYVEIRGE----MSRAINVFKMRG-SWHDKAIR 213 d1emsa2 245 RV-------DMC-----------------FAEIDLSYVDTLREMQPVFSHR 271 :: ::: d1tf7a2 214 EFMISDKGPDIKDSFRNFERIISGSPTRI---------------------- 242 HHsearch alignment (Probability: 0.35 E-value:0.01) d1emsa2 68 YMEKYRELARKHNIWLSL 85 :::::::::::::::::: d1tf7a2 140 FVIGVTGYAKQEEITGLF 157