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 | d1ii7a_ | Mre11 | Metallo-dependent phosphatases | Metallo-dependent phosphatases | α+β |
| Hit | d1fc6a4 | Photosystem II D1 C-terminal processing protease | ClpP/crotonase | ClpP/crotonase | α/β |
Query <-- 1.211 --> IntermediateDALI alignment (Z-score: 7.2 Raw score:832.10) query 1 slqLRLALNQIDS-TVGD------IAGNAEAILRWTRHSAEQGAHLVAFPEMALTgypve 53 :::::::::: :::: ::::::::::::::::::::::::::::::: d1ii7a_ 1 ---MKFAHLADIHlGYEQfhkpqrEEEFAEAFKNALEIAVQENVDFILIAGDLFH----- 52 query 54 dlalrssFVEASRTALRELAARLAeegFGELPVLV---gyLDRSesaqpkygqpaGAPRN 110 ::::::::::::::::: :::::::: :::: ::::: d1ii7a_ 53 ----ssrPSPGTLKKAIALLQIPK---EHSIPVFAiegnhDRTQ-----------RGPSV 94 query 111 AaavlhrgRVALTfakhhlpnygvfdefryfvpgDTMPIVRLHGVDIALAICE----dlw 166 : ::::: ::::::::::::::::::: d1ii7a_ 95 L-nlledfGLVYVigmrkekveneyltserlgngEYLVKGVYKDLEIHGMKYMssawfea 153 query 167 QDGGRVPAARsagaGLLLSV---naspyERDKDDTrleLVRKRAqEAGCT-TAYLAMIgg 222 :::::::::: :::::: ::::::: :::::: ::::: ::::::: d1ii7a_ 154 NKEILKRLFRptdnAILMLHqgvrevseARGEDYF--eIGLGDL-PEGYLyYALGHIH-- 208 query 223 qdelvfDGDSivvdrDGEVVARA--------------------------pqFSEGCVVLD 256 :::: :::::::: ::::::::: d1ii7a_ 209 ------KRYE---tsYSGSPVVYpgslerwdfgdyevryewdgikfkerygVNKGFYIVE 259 query 257 LdlpaaeaepptgvvddglridrlviseeplpayeaeLAGGyadrldadeevysalvvgl 316 : :::: d1ii7a_ 260 D------------------------------------FKPR------------------- 264 query 317 rayvakngfrsvliglsggidsalvaaiacdalgaqnvygvsmpskyssdhskgdaaela 376 d1ii7a_ 265 ------------------------------------------------------------ 265 query 377 rrtglnfrtvsiepmfdaymaslgltglaeenlqsrlrgttlmaisnqeghivlapgnks 436 d1ii7a_ 265 ------------------------------------------------------------ 265 query 437 elavgystlygdsvgaygpikdvyktsifrlaewrnraaaergqtppipeasitkpdypv 496 d1ii7a_ 265 ------------------------------------------------------------ 265 query 497 ldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdr 556 d1ii7a_ 265 ---fveikvrpfidvkikgseeeirkaikrliplipknayvrlnigwrkpfdlteikell 321 query 557 rlpitnrwregh 568 d1ii7a_ 322 nveylkidtwri 333 FAST alignment (Normalized score: 2.90 Raw score:1260.00) query 1 SLQLRLALNQIDSTVG--------------DIAGNAEAILRWTRHSAEQGAHLVAFPEMA 46 :::::: :::::::::::::::::::::::::::::: d1ii7a_ 1 ---MKFAHL-------ADIHLGYEQFHKPQREEEFAEAFKNALEIAVQENVDFILIAGDL 50 query 47 LTGYPVEDLALRSSF------VEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPK 100 ::::::::::::::::: ::::::: d1ii7a_ 51 ---------------FHSSRPSPGTLKKAIALLQIPKE---HSIPVFA------------ 80 query 101 YGQPAGAPRNAAAVLHRGRVALTFAKHHLPNYGVFDEFRYFVPG---------------- 144 d1ii7a_ 81 --------------------------------------------IEGNHDRTQRGPSVLN 96 query 145 -------------------------------DTMPIVRLHGVDIALAICEDLW------- 166 ::::::::::::::::: d1ii7a_ 97 LLEDFGLVYVIGMRKEKVENEYLTSERLGNGEYLVKGVYKDLEIHGMK-----YMSSAWF 151 query 167 --QDGGRVPAARSAGA------GLLLSVNASPYERDKDDT--------------RLELVR 204 :::::::: ::::::::: :::: d1ii7a_ 152 EANKEILKRL------FRPTDNAILMLHQGV---------REVSEARGEDYFEIGLGD-- 194 query 205 KRAQEA----GCTTAYLAMIGGQDELVFD---GDSIVVDRDGEVVARAPQ---------- 247 :::::: :::::: d1ii7a_ 195 ------LPEGYLYYAL-------------GHIHKRYET------------SYSGSPVVYP 223 query 248 ---------------------------FSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRL 280 :::::::: d1ii7a_ 224 GSLERWDFGDYEVRYEWDGIKFKERYGVNKGFYIV------------------------- 258 query 281 VISEEPLPAYEAELAGGYADRLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSAL 340 d1ii7a_ 259 ------------------------------------------------------------ 259 query 341 VAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLG 400 d1ii7a_ 259 ------------------------------------------------------------ 259 query 401 LTGLAEENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVY 460 d1ii7a_ 259 ------------------------------------------------------------ 259 query 461 KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYD 520 d1ii7a_ 259 ------------------------------------------------------------ 259 query 521 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH------------ 568 d1ii7a_ 259 ------------------------------------------------EDFKPRFVEIKV 270 query 569 ------------------------------------------------------------ 569 d1ii7a_ 271 RPFIDVKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYLKIDT 330 query 569 --- 569 d1ii7a_ 331 WRI 333 TMalign alignment (TM-score: 0.35 Raw score:198.57) query 1 SLQLRLALNQIDSTVGD-------IAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVE 53 :::::::::::::: ::::::::::::::::::::::::::::: :: : d1ii7a_ 1 ---MKFAHLADIHLGYEQFHKPQREEEFAEAFKNALEIAVQENVDFILIAGDL-FH--S- 53 query 54 DLALRSSFVEASRTALRELAARLAEEGFGELPVLVGY---LDRSESAQPKYGQPAGAPRN 110 : : ::::::::::::::::: :: :::::::: ::: : :::: d1ii7a_ 54 --S-R--PSPGTLKKAIALLQIPK--EH-SIPVFAIEGNHDRT---------Q---RGPS 93 query 111 AAAVLHRGRVALTFAKH----------------HLPNYGVFDEFRYFVPGDTMPIVRLHG 154 ::::::::::::::::: ::::::::::: d1ii7a_ 94 VLNLLEDFGLVYVIGMRKEKVENEYLTSERLGN----------------GEYLVKGVYKD 137 query 155 VDIALAICEDL--W--QDGGRVPAARSAGAGLLLSVNASP--YERDKDDT-R-LELVRKR 206 ::::::::::: : ::::::::::: :::::::::::: :::::::: : :::::: d1ii7a_ 138 LEIHGMKYMSSAWFEANKEILKRLFRP-TDNAILMLHQGVREVSEARGEDYFE-IGLGDL 195 query 207 AQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVARAPQ------------------- 247 :: :::::::::: :::::::: ::::::::: d1ii7a_ 196 PE--GYLYYALGHI-------HKRYETSY---SGSPVVYPGSLERWDFGDYEVRYEWDGI 243 query 248 -------FSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYA- 299 ::::::::::: ::::: d1ii7a_ 244 KFKERYGVNKGFYIVEDF------------------------------------KPRFVE 267 query 300 --DRLDADEEVYSALVV-GLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYG 356 : ::: : :::: d1ii7a_ 268 IK--------------VR-PFI---------D-----------VKIK------------- 279 query 357 VSMPSKYSSDHSKGDAAELARRTGLN--------------FRTVSIEPMFDAYMASLGLT 402 :::::::::::::::: d1ii7a_ 280 ----------GSEEEIRKAIKRLIPLIPKNAYVRLNIGWR-------------------- 309 query 403 GLAEENLQSRLRGTTLMAISNQ-E-GHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVY 460 :: : :::::::: : :::::::: :: d1ii7a_ 310 -------KP--F--DLTEIKELLNVEYLKIDTW----------RI--------------- 333 query 461 KTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYD 520 d1ii7a_ 334 ------------------------------------------------------------ 334 query 521 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1ii7a_ 334 ------------------------------------------------ 334 HHsearch alignment (Probability: 0.04 E-value:0.06) query 19 AGNAEAILRWTRHSAEQGAHLVAF 42 :::::::::::::::::::::::: d1ii7a_ 23 EEFAEAFKNALEIAVQENVDFILI 46
Intermediate <-- 1.137 --> HitDALI alignment (Z-score: 5.0 Raw score:576.80) d1ii7a_ 1 ------------------------------------------------------------ 1 d1fc6a4 1 vtseqllfleawravdrayvdksfngqswfklretylkkepmdrraqtydairkmlavld 60 d1ii7a_ 1 ---------------------------------------------MKFAHLAdIHLGyeq 15 ::::::: :::: d1fc6a4 61 dpftrflepsrlaalrrgtkvtinpvtfttcsnvaaaalppgaakQQLGYVR-LATF--- 116 d1ii7a_ 16 fhkpqrEEEFAEAFKNALEIAVQENVDFILIAGDlfHSSRPSpGTLKKAIALLQ------ 69 :::::::::::::::::::::::::::: :::::: ::::::::::: d1fc6a4 117 ------NSNTTAAAQQAFTELSKQGVAGLVLDIR-nNGGGLF-PAGVNVARMLVdrgdlv 168 d1ii7a_ 70 ------------------IPKEhsIPVFAIEGNHDRTqrgpSVLNLLEDFGLVYVIgmrk 111 :::: ::::::::::::: ::::::::::::::: d1fc6a4 169 liadsqgirdiysadgnsIDSA--TPLVVLVNRGTAS-aseVLAGALKDSKRGLIA---- 221 d1ii7a_ 112 ekveneyltserlgngeylvkgvykdleihGMKYmssawfeankeilkrlfrptdnailm 171 :::: d1fc6a4 222 ------------------------------GERT---------fgkgliqtvvdlsdgsg 242 d1ii7a_ 172 lhqgvrevseargedyfeiglgdlpegylyYALGhiHKRY--etsysGSPVvypgslerw 229 :::: :::: :::: d1fc6a4 243 vavtvaryqtpagvdinkigvspdvqldpeVLPT--DLEGvcrvlgsDAAP--------- 291 d1ii7a_ 230 dfgdyevryewdgikfkerygvnkgfyivedfkprfveikvrpfidvkikgseeeirkai 289 d1fc6a4 292 ------------------------------------------------------------ 292 d1ii7a_ 290 krliplipknayvrlnigwrkpfdlteikellnveylkidtwri 333 d1fc6a4 292 -----------------------------------------rlf 294 FAST alignment (Normalized score: 2.37 Raw score:740.40) d1ii7a_ 1 ------------------------------------------------------------ 1 d1fc6a4 1 VTSEQLLFLEAWRAVDRAYVDKSFNGQSWFKLRETYLKKEPMDRRAQTYDAIRKMLAVLD 60 d1ii7a_ 1 ---------------------------------------------MKFAHLADIHLGYEQ 15 :::::: d1fc6a4 61 DPFTRFLEPSRLAALRRGTKVTINPVTFTTCSNVAAAALPPGAAKQQLGYV--------- 111 d1ii7a_ 16 FHKPQR-----EEEFAEAFKNALEIAVQENVDFILIAGDLFHSSR-------PSPGTLKK 63 ::::::::::::::::::::::::: :::::::: d1fc6a4 112 ------RLATFNSNTTAAAQQAFTELSKQGVAGLVL---------DIRNNGGGLFPAGVN 156 d1ii7a_ 64 AIALLQIPKE----------------------------HSIPVFAIEGNHDRTQRGP--- 92 :::: ::::::::::: d1fc6a4 157 VARM------LVDRGDLVLIADSQGIRDIYSADGNSIDSATPLVVLVNR--------GTA 202 d1ii7a_ 93 ----SVLNLLEDFGLVYVIGMRKEKVENEYLTSERLGNGEYLVKGVYKDLEIHGMKYMSS 148 :::::::::::::::: d1fc6a4 203 SASEVLAGALKDSKRGLIAG---------------------------------------- 222 d1ii7a_ 149 AWFEANKEILKRLFRPTDNAILMLHQGVREVSEARGEDYFEIGLGDLPEGYLYYALGHIH 208 d1fc6a4 223 ------------------------------------------------------------ 223 d1ii7a_ 209 KRYETSYSGSPVVYPGSLERWDFGDYEVRYEWDGIKFKERYGVNKGFYIVEDFKPRFVEI 268 d1fc6a4 223 ------------------------------------------------------------ 223 d1ii7a_ 269 KVRPFIDVKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYLKI 328 d1fc6a4 223 ------------------------------------------------------------ 223 d1ii7a_ 329 DTWRI------------------------------------------------------- 333 d1fc6a4 223 -----ERTFGKGLIQTVVDLSDGSGVAVTVARYQTPAGVDINKIGVSPDVQLDPEVLPTD 277 d1ii7a_ 334 ----------------- 334 d1fc6a4 278 LEGVCRVLGSDAAPRLF 294 TMalign alignment (TM-score: 0.28 Raw score:94.00) d1ii7a_ 1 ------------------------------------------------------------ 1 d1fc6a4 1 VTSEQLLFLEAWRAVDRAYVDKSFNGQSWFKLRETYLKKEPMDRRAQTYDAIRKMLAVLD 60 d1ii7a_ 1 -------------------MKFAHLADIHLGYEQFHKPQREEEFAEAFKNALEIAVQE-- 39 ::: :: :: :: :: :::: d1fc6a4 61 DPFTRFLEPSRLAALRRGT---------------KVT--IN--PV--TF--TT-CSNVAA 96 d1ii7a_ 40 --------NVDFILIAGDLFHSSRPSPGTLKKAIALLQIPKEHSI-PVFAIEGNHDRTQR 90 ::::::: :::::::: ::::::::::::::::: :::::::::::::: d1fc6a4 97 AALPPGAAKQQLGYV---RLATFNSN--TTAAAQQAFTELSKQGVAGLVLDIRNNGGGLF 151 d1ii7a_ 91 G-PSVLNLLE------------------------DFGL-V-YVI-------------GMR 110 : :::::::: :::: : ::: ::: d1fc6a4 152 PAGVNVARMLVDRGDLVLIADSQGIRDIYSADGNSIDSATPLVVLVNRGTASASEVLAGA 211 d1ii7a_ 111 KEKVENEYLTSERLGNGEYLVKGVYKDLEIHGMKYMSSAW-------------------- 150 : : ::::: ::::::::::: d1fc6a4 212 --------L-K-------DSKRG------LIAGERTFGKGLIQTVVDLSDGSGVAVTVAR 249 d1ii7a_ 151 --------FEANKEILKRLFRPTDNAILMLHQGVREVSEARGEDYFEIGLGDLPEGYLYY 202 ::::: :: :: : : : d1fc6a4 250 YQTPAGVDINKIG-VS--PD-------V------------------------Q------L 269 d1ii7a_ 203 ALGHIHKRYETSYSGSPVVYPGSLERWDFGDYEVRYEWDGIKFKERYGVNKGF--YIVED 260 :: : : ::::: ::: :::: d1fc6a4 270 DP------E---------V-LPTDL-------------------------EGVCRVLGS- 287 d1ii7a_ 261 FKPR---FVEIKVRPFIDVKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEI 317 :::: d1fc6a4 288 DAAPRLF----------------------------------------------------- 294 d1ii7a_ 318 KELLNVEYLKIDTWRI 333 d1fc6a4 295 ---------------- 295 HHsearch alignment (Probability: 0.05 E-value:0.28) d1ii7a_ 28 AFKNALEIAVQENVD 42 ::::::::::::::: d1fc6a4 7 LFLEAWRAVDRAYVD 21