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 | d8abpa_ | L-arabinose-binding protein | Periplasmic binding protein-like I | Periplasmic binding protein-like I | 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 <-- 0.750 --> HitDALI alignment (Z-score: 2.9 Raw score:325.30) d1ii7a_ 1 -MKFAHLAD---------------ihlgyeqfhkpqreeeFAEAFKNALEIAVQENVDFI 44 :::::::: :::::::::::::::::::: d8abpa_ 1 nLKLGFLVKqpeepwfqtewkfadkagkdlgfevikiavpDGEKTLNAIDSLAASGAKGF 60 d1ii7a_ 45 LIagDLFHssrpspgtlKKAIALLQIPKEHSIPVFAIEgnhdrtqrgpsvlnLLEDfglV 104 :: :::: ::::::::::::::::::::: :::: : d8abpa_ 61 VI--CTPD--------pKLGSAIVAKARGYDMKVIAVD-----dqfvnakgkPMDT---V 102 d1ii7a_ 105 YVIGM------------------------------------------------------- 109 ::::: d8abpa_ 103 PLVMLaatkigerqgqelykemqkrgwdvkesavmaitaneldtarrrttgsmdalkaag 162 d1ii7a_ 110 ------------------------------------------------------------ 110 d8abpa_ 163 fpekqiyqvptksndipgafdaansmlvqhpevkhwlivgmndstvlggvrategqgfka 222 d1ii7a_ 110 ----------------------rkekveneyltserlgngeylvkgVYKDLEIH--gMKY 145 :::::::: ::: d8abpa_ 223 adiigigingvdavselskaqatgfygsllpspdvhgykssemlynWVAKDVEPpkfTEV 282 d1ii7a_ 146 MSsawfeankeilkrlfrptdnailmlhqgvrevseargedyfeiglgdlpegylyyalg 205 :: d8abpa_ 283 TD---------------------------------------------------------- 284 d1ii7a_ 206 hihkryetsysgspvvypgslerwdfgdyevryewdgikfkerygvnkgfyivedfkprf 265 d8abpa_ 285 ------------------------------------------------------------ 285 d1ii7a_ 266 veikvrpfidvkikgseeeirkaikrliplipknayvrlnigwrkpfdlteikellnvey 325 d8abpa_ 285 -----------------------------------------------vvlitrdnfkeel 297 d1ii7a_ 326 lkidtwri 333 d8abpa_ 298 ekkglggk 305 FAST alignment (Normalized score: 1.79 Raw score:569.20) d1ii7a_ 1 -MKFAHLADIHLGYEQFHKPQREEE---------------------------------FA 26 :::::: :: d8abpa_ 1 NLKLGFL------------------VKQPEEPWFQTEWKFADKAGKDLGFEVIKIAVPDG 42 d1ii7a_ 27 EAFKNALEIAVQENVDFILIAGDLFHSSRPSPG---TLKKAIALLQIPKEHSIPVFAIEG 83 :::::::::::::::::::: :::::::::::::::::::::: d8abpa_ 43 EKTLNAIDSLAASGAKGFVI-------------CTPDPKLGSAIVAKARGYDMKVIAV-- 87 d1ii7a_ 84 NHDRTQRGPSVLNLLEDFG-------------LVYVIGMRKEKVENEYLTSERLGNGEYL 130 :::::: d8abpa_ 88 -------------------DDQFVNAKGKPMDTVPLVM---------------------- 106 d1ii7a_ 131 VKG--------------------------------------------------------- 133 d8abpa_ 107 ---LAATKIGERQGQELYKEMQKRGWDVKESAVMAITANELDTARRRTTGSMDALKAAGF 163 d1ii7a_ 134 ------------------------------------------------------------ 134 d8abpa_ 164 PEKQIYQVPTKSNDIPGAFDAANSMLVQHPEVKHWLIVGMNDSTVLGGVRATEGQGFKAA 223 d1ii7a_ 134 ---------------------------------------------VYKDLEIHGMKYMSS 148 ::::: d8abpa_ 224 DIIGIGINGVDAVSELSKAQATGFYGSLLPSPDVHGYKSSEMLYNWVAKD---------- 273 d1ii7a_ 149 AWFEA-------------------NKEILKRLFRPTDNAILMLHQGVREVSEARGEDYFE 189 ::::::: d8abpa_ 274 -----VEPPKFTEVTDVVLITRDNFKEELEK----------------------------- 299 d1ii7a_ 190 IGLGDLPEGYLYYALGHIHKRYETSYSGSPVVYPGSLERWDFGDYEVRYEWDGIKFKERY 249 d8abpa_ 300 ------------------------------------------------------------ 300 d1ii7a_ 250 GVNKGFYIVEDFKPRFVEIKVRPFIDVKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWR 309 d8abpa_ 300 ------------------------------------------------------------ 300 d1ii7a_ 310 KPFDLTEIKELLNVEYLKIDTWRI------ 333 d8abpa_ 300 ------------------------KGLGGK 305 TMalign alignment (TM-score: 0.30 Raw score:101.07) d1ii7a_ 1 ------------MKFAHLADIHL-GYEQFHKPQR-------------------------- 21 :::: ::::::::: d8abpa_ 1 NLKLGFLVKQPE-------EPWFQ-TEWKFADKAGKDLGFEVIKIAVPDGEKTLNAIDSL 52 d1ii7a_ 22 ---------------------------------EEEFAEAFKNALEIAVQENVDFILIAG 48 d8abpa_ 53 AASGAKGFVICTPDPKLGSAIVAKARGYDMKVI--------------------------- 85 d1ii7a_ 49 DLFHSSRP----------SPGTLKKAIALLQ-IPK-EHSIPVF----------------A 80 :::::: ::::: ::: ::: :: :::: : d8abpa_ 86 --AVDDQFVNAKGKPMDTVPLVM-LAA-TKIG-ERQ---GQELYKEMQKRGWDVKESAVM 137 d1ii7a_ 81 IEGNHDRTQRGPSVLNLLEDFGLVYVI-GMRKEKVENEYLTSERLGNGEYLVKGVYKDLE 139 ::: :: : ::::::::: :::: ::::::::: ::: d8abpa_ 138 AIT---AN-E-LDTARRRTT---GSMDA------LKAAGFPEK-------QIY------- 169 d1ii7a_ 140 IHGMKYMS---SAWFEANKEILKRLFRPTDNAILML----HQGVREVSEARGEDYFEIGL 192 :::::: ::::: ::::::::::::::::::: :::: ::::: d8abpa_ 170 --QVPTKSNDIPGAFD-AANSMLVQHPEVKHWLIVGMNDSTVLG-----------GVRAT 215 d1ii7a_ 193 GDLPEG-YLYYALGH---IHKRYE-TSYSGSPVVYPGSLERWD----------------- 230 :::::: :::::::: :::::: ::: ::::::::::::: d8abpa_ 216 EGQGFKAADIIGIGINGVDAVSELSKAQ--ATGFYGSLLPSPDVHGYKSSEMLYNWVAKD 273 d1ii7a_ 231 ------------FGDYEVRYEWDGIKFKERYGVNKGFYIVEDFKPRFV-EI--KVRPFID 275 :::: :::: :: ::::::: d8abpa_ 274 VEPPKFTEVTDV-----------------------VLIT-----RDNFKEELEKKGLGGK 305 d1ii7a_ 276 VKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYLKIDTWRI 333 d8abpa_ 306 ---------------------------------------------------------- 306 HHsearch alignment (Probability: 0.49 E-value:0.00) d1ii7a_ 30 KNALEIAVQENVDFILIAGDLFHSSRPSPGTLKKAIALLQIPKEHSIPVFAIEGNHD 86 ::::::::::::::::::::::: :::::::::::::::::::::::: d8abpa_ 46 LNAIDSLAASGAKGFVICTPDPK----------LGSAIVAKARGYDMKVIAVDDQFV 92