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 | d1j7xa_ | Interphotoreceptor retinoid-binding protein IRBP | 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 <-- 0.847 --> HitDALI alignment (Z-score: 3.3 Raw score:435.70) d1ii7a_ 1 ------------------------------------------------------------ 1 d1j7xa_ 1 dpsvthvlhqlcdilannyafseriptllqhlpnldystviseediaaklnyelqslted 60 d1ii7a_ 1 ---------------------------------------------MKFAHLADiHLGYeq 15 :::::::: :::: d1j7xa_ 61 prlvlksktdtlvmpgdsiqaenipedeamlqalvntvfkvsilpGNIGYLRFdQFAD-- 118 d1ii7a_ 16 fhkpQREEEFAEAFK-NALEIAVqeNVDFILIAGdlfhSSRPSpgTLKKAIALLQ----- 69 ::::::::::: ::::::: ::::::::: ::::: :::::::::: d1j7xa_ 119 ---vSVIAKLAPFIVnTVWEPIT--ITENLIIDLrynvGGSST--AVPLLLSYFLdpetk 171 d1ii7a_ 70 --------------------------IPKEhSIPVFAIE---GNHDrtqrgpSVLNLLED 100 :::: :::::::: :::: :::::::: d1j7xa_ 172 ihlftlhnrqqnstdevyshpkvlgkPYGS-KKGVYVLTshqTATA----aeEFAYLMQS 226 d1ii7a_ 101 FGLVYVIGMR-----------------------------------kekveneyLTSErlg 125 :::::::::: :::: d1j7xa_ 227 LSRATIIGEItsgnlmhskvfpfgdtqlsvtvpiinfidsngdywlgggvvpdAIVL-ad 285 d1ii7a_ 126 ngeylvkgVYKDLEihgmkymssawfeankeilkrlfrptdnailmlhqgvrevsearge 185 :::::: d1j7xa_ 286 ealdkakeIIAFHP---------------------------------------------- 299 d1ii7a_ 186 dyfeiglgdlpegylyyalghihkryetsysgspvvypgslerwdfgdyevryewdgikf 245 d1j7xa_ 300 ------------------------------------------------------------ 300 d1ii7a_ 246 kerygvnkgfyivedfkprfveikvrpfidvkikgseeeirkaikrliplipknayvrln 305 d1j7xa_ 300 ------------------------------------------------------------ 300 d1ii7a_ 306 igwrkpfdlteikellnveylkidtwri 333 d1j7xa_ 300 -------------------------pla 302 FAST alignment (Normalized score: 0.85 Raw score:268.90) d1ii7a_ 1 MKFAHLADIHLGYEQFHKPQREEEFAEAFKNALEIAVQENVDFILIAGDLFHSSRPSPGT 60 d1j7xa_ 1 ------------------------------------------------------------ 1 d1ii7a_ 61 LKKAIALLQIPKEHSIPVFAIEGNHDRTQRGPSVLNLLEDFGLVYVIGMRKEKVENEYLT 120 d1j7xa_ 1 ------------------------------------------------------------ 1 d1ii7a_ 121 SERLGNGE---------------------------------------------------- 128 d1j7xa_ 1 --------DPSVTHVLHQLCDILANNYAFSERIPTLLQHLPNLDYSTVISEEDIAAKLNY 52 d1ii7a_ 129 ---------------------------------------------YLVKGVYK-DLEIHG 142 :::::::: :::::: d1j7xa_ 53 ELQSLTEDPRLVLKSKTDTLVMPGDSIQAENIPEDEAMLQALVNTVFKVSILPGNIGYLR 112 d1ii7a_ 143 M-KYMSSAWFEANK--EILKRLFRPTDNAILMLHQGVREVSEARGEDYFEIGLGDL---- 195 : :::::::::: :::::: d1j7xa_ 113 FDQFADVSVIAK--LAPFIVNT----------------------------------VWEP 136 d1ii7a_ 196 PEGYLYYALGHIHKRYETS----------------------------------------- 214 ::::::::: d1j7xa_ 137 ITITENLII----------DLRYNVGGSSTAVPLLLSYFLDPETKIHLFTLHNRQQNSTD 186 d1ii7a_ 215 -------------YSGSPVVYPGS-------------------------LERWDFGD--- 233 ::::::::: :::: d1j7xa_ 187 EVYSHPKVLGKPYGSKKGVYVL--TSHQTATAAEEFAYLMQSLSRATIIGEIT----SGN 240 d1ii7a_ 234 -YEVRYEWD--GIKFKERYGVNKGFYIVEDFKPRFVEIKVRPFIDVKIKGSEEEIRKAIK 290 :::::::: ::::::: d1j7xa_ 241 LMHSKVFPFGDTQLSVTV------------------------------------------ 258 d1ii7a_ 291 RLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYLKIDTWRI----------------- 333 d1j7xa_ 259 -------------------------------------------PIINFIDSNGDYWLGGG 275 d1ii7a_ 334 --------------------------- 334 d1j7xa_ 276 VVPDAIVLADEALDKAKEIIAFHPPLA 302 TMalign alignment (TM-score: 0.30 Raw score:99.67) d1ii7a_ 1 ------------------------------------------------------------ 1 d1j7xa_ 1 DPSVTHVLHQLCDILANNYAFSERIPTLLQHLPNLDYSTVISEEDIAAKLNYELQSLTED 60 d1ii7a_ 1 ----------------MKFAHLADIHLGYEQFHKP-QREEEFAEAFKNALEIAVQENVDF 43 :::::::: ::: ::::::::::: :: :::::::: d1j7xa_ 61 PRLVLKSKTDTLVMPG-------DSIQAENI-PEDEAMLQALVNTVF-KV--SILPGNIG 109 d1ii7a_ 44 ILIAGDLFHSSRPSPGTLKKAIAL-LQIPKEHSIPVFAI--E-GNHDRTQRGPSVLNLLE 99 ::::::: :::::::::::::::: :::::::::::::: : ::: ::: :::::::: d1j7xa_ 110 YLRFDQF-ADVSVIAKLAPFIVNTVWEPITITENLIIDLRYNVGGS-STA--VPLLLSYF 165 d1ii7a_ 100 DFG---LVYV-IGMR-----------KEK---------VENEYLT--------------- 120 ::: : ::: ::: ::::::: d1j7xa_ 166 LDPETK---IH-LFTLHNRQQNSTDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEFA 221 d1ii7a_ 121 ---SERLGNGEYLVKGVYKDLEI-HGMKYMSSAWF----------EANK----------E 156 ::::::: ::: ::::::::::: :::: : d1j7xa_ 222 YLM--------QSLSRAT--IIGEITSGNLMHSKVFPFGDTQLSVTVPIINFIDSNGDYW 271 d1ii7a_ 157 ILKRLFRPTDNAILMLHQGVREVSEARGEDYFEIGLGDLPEGYLYYALGHIHKRYETSYS 216 ::: ::::: : :: d1j7xa_ 272 LGG-GVVPD--A------------------------------IV---------------- 282 d1ii7a_ 217 GSPVVYPGSLERWDFGDYEVRYEWDGIKFKERYGVNKGFYIVEDFK----------PRFV 266 :::: :::::: d1j7xa_ 283 -LADE-----------------------------------ALDKAKEIIAFHPPLA---- 302 d1ii7a_ 267 EIKVRPFIDVKIKGSEEEIRKAIKRLIPLIPKNAYVRLNIGWRKPFDLTEIKELLNVEYL 326 d1j7xa_ 303 ------------------------------------------------------------ 303 d1ii7a_ 327 KIDTWRI 333 d1j7xa_ 303 ------- 303 HHsearch alignment (Probability: 0.03 E-value:0.20) d1ii7a_ 45 LIAGDLFHSSRPSPGTLKKAI--ALLQIPKEHSIPVFAIEGNHDRT 88 ::::::::::: :::::::: :::::::: :::::::::::: d1j7xa_ 32 LPNLDYSTVIS--EEDIAAKLNYELQSLTED---PRLVLKSKTDTL 72