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: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1jmva_ | Universal stress protein A, UspA | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1ngva_ | Amyloid beta precursor protein-binding protein 1, APPBP1 | Activating enzymes of the ubiquitin-like proteins | Activating enzymes of the ubiquitin-like proteins | α/β |
Query <-- 1.476 --> IntermediateDALI alignment (Z-score: 6.4 Raw score:517.70) query 1 dadeevysalvvglrayvaknGFRSVLIGLSGGIDSALVAAIACDALG--aqNVYGVSMP 58 ::::::::::::::::::::::::::: :::::::: d1jmva_ 1 ---------------------MYKHILVAVDLSEESPILLKKAVGIAKrhdaKLSIIHVD 39 query 59 S------------------kysSDHSKGDAAELARRTG---lNFRTVSIepmfdaymasl 97 : :::::::::::::::: ::::::: d1jmva_ 40 VnfsdlytglidvnmssmqdriSTETQKALLDLAESVDypisEKLSGSG----------- 88 query 98 gltglaeenlqsrLRGTTLMAISNQEGH-IVLAPGNKseLAVG--YSTL----ygdsvgA 150 ::::::::::::::: :::::::: :::: :::: : d1jmva_ 89 -------------DLGQVLSDAIEQYDVdLLVTGHHQ--DFWSklMSSTrqvmntikidM 133 query 151 YGPiKDVYktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtgad 210 ::: :::: d1jmva_ 134 LVV-PLRD---------------------------------------------------- 140 query 211 aivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1jmva_ 141 -------------------------------------------------------- 141 FAST alignment (Normalized score: 4.82 Raw score:930.50) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQ------NVYG 54 ::::::::::::::::::::::::: :::: d1jmva_ 1 ---------------------MYKHILVAVDLSEESPILLKKAVGI----AKRHDAKLSI 35 query 55 VSMPSKYSS-----------------------DHSKGDAAELAR--RTGL-NFRTVSIEP 88 :::: :::::::::::: :::: ::::: d1jmva_ 36 IHVD-----VNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSG---- 86 query 89 MFDAYMASLGLTGLAEENLQSR--LRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY- 144 :::::::::::::: :::::::: d1jmva_ 87 ----------------------SGDLGQVLSDAIEQYDVDLLVTGHH------------Q 112 query 145 ------------GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDY 192 :::::: d1jmva_ 113 DFWSKLMSSTRQVMNTIK------------------------------------------ 130 query 193 PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGK 252 d1jmva_ 131 ------------------------------------------------------------ 131 query 253 DRRLPITNRWREGH---------- 266 d1jmva_ 131 --------------IDMLVVPLRD 140 TMalign alignment (TM-score: 0.33 Raw score:88.21) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALG--AQNVYGVSMP 58 ::::::::::::::::::::::::::: :::::::::: d1jmva_ 1 ---------------------MYKHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIHVD 39 query 59 SK---------------------YSSDHSKGDAAELARRT--GLNFRTVSIEPMFDAYMA 95 :: :: :::::::::::: ::::::::: d1jmva_ 40 VNFSDLYTGLIDVNMSSMQDRIS--TE-TQKALLDLAESVDYPISEKLSGS--------- 87 query 96 SLGLTGLAEENLQSRLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG---- 149 : ::::::::::::::: ::::::: ::::::::: ::: :: d1jmva_ 88 ------------G--DLGQVLSDAIEQYDVDLLVTGHH-QDFWSKLMS--STRQVMNTIK 130 query 150 --AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDT 207 ::: :: : :: d1jmva_ 131 IDMLV-VP-L-RD----------------------------------------------- 140 query 208 GADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1jmva_ 141 ----------------------------------------------------------- 141 HHsearch alignment (Probability: 0.05 E-value:0.16) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :::::::::::::::::::::::::::::::::::::::::::::: ::::: :::::: d1jmva_ 56 SMQDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQY-DVDLL--VTGHHQ 112 query 61 YSSDHSKGDAAELARRTGLNFRTVSIEP 88 :::::::::::::::::::::::::::: d1jmva_ 113 DFWSKLMSSTRQVMNTIKIDMLVVPLRD 140
Intermediate <-- 0.862 --> HitDALI alignment (Z-score: 6.3 Raw score:495.40) d1jmva_ 1 -----------------------myKHILVAVdlseeSPILLKKAVGIAKRHDAKLSIIH 37 ::::::: ::::::::::::::::::::::: d1ngva_ 1 kllkeqkydrqlrlwgdhgqealesAHVCLIN----aTATGTEILKNLVLPGIGSFTIID 56 d1jmva_ 38 VDvnfsdlytglidvnmssmqdrisTETQkALLDLAESVD-----YPISeKLSG-sgDLG 91 :: :::: :::::::::: :::: :::: ::: d1ngva_ 57 GN------qvsgedagnnfflqrssIGKN-RAEAAMEFLQelnsdVSGS-FVEEspeNLL 108 d1jmva_ 92 QvlSDAIEqyDVDLLVTGHhqdfwskLMSSTRQVMNTI---KIDMLVVPLRD-------- 140 : ::::: ::::::::: :::::::::::: ::::::::::: d1ngva_ 109 DndPSFFC--RFTVVVATQ------lPESTSLRLADVLwnsQIPLLICRTYGlvgymrii 160 d1jmva_ 141 ------------------------------------------------------------ 141 d1ngva_ 161 ikehpvieshpdnaledlrldkpfpelrehfqsydldhmekkdhshtpwiviiakylaqw 220 d1jmva_ 141 ------------------------------------------------------------ 141 d1ngva_ 221 ysetngripktykekedfrdlirqgilknengapedeenfeeaiknvntalnttqipssi 280 d1jmva_ 141 ------------------------------------------------------------ 141 d1ngva_ 281 edifnddrcinitkqtpsfwilaralkefvakegqgnlpvrgtipdmiadsgkyiklqnv 340 d1jmva_ 141 ------------------------------------------------------------ 141 d1ngva_ 341 yrekakkdaaavgnhvakllqsigqapesisekelkllcsnsaflrvvrcrslaeeygld 400 d1jmva_ 141 ------------------------------------------------------------ 141 d1ngva_ 401 tinkdeiissmdnpdneivlylmlravdrfhkqqgrypgvsnyqveedigklkscltgfl 460 d1jmva_ 141 ------------------------------------------------------------ 141 d1ngva_ 461 qeyglsvmvkddyvhefcrygaaephtiaaflggaaaqevikiitkqfvifnntyiysgm 520 d1jmva_ 141 --------- 141 d1ngva_ 521 sqtsatfql 529 FAST alignment (Normalized score: 2.56 Raw score:695.30) d1jmva_ 1 MY-------------------------KHILVAVDLSEESPILLKKAVGIAKRHDAK--- 32 ::::: :::::::::::::::: d1ngva_ 1 --KLLKEQKYDRQLRLWGDHGQEALESAHVCL-INATATGTEILKNLVL--------PGI 49 d1jmva_ 33 LSIIHVDVNFSDLYTGLIDVNMSSMQDRI----------------------STETQKALL 70 :::::: ::::::::: d1ngva_ 50 GSFTII-----------------------DGNQVSGEDAGNNFFLQRSSIGKNRAEAAME 86 d1jmva_ 71 DLAESVDYPI----SEKLSGSGD---------LGQVLSDAIEQYDVDLLVTGHHQDFWSK 117 :::: ::::::: :::::: ::::::: ::::::: d1ngva_ 87 FLQE------LNSDVSGSFVE--ESPENLLDNDPSFFC------RFTVVVA--TQLPEST 130 d1jmva_ 118 LMSSTRQVMNTIKIDMLVVPLRD------------------------------------- 140 :::::::::: :::::::::: d1ngva_ 131 SLRLADVLWN-SQIPLLICRT--YGLVGYMRIIIKEHPVIESHPDNALEDLRLDKPFPEL 187 d1jmva_ 141 ------------------------------------------------------------ 141 d1ngva_ 188 REHFQSYDLDHMEKKDHSHTPWIVIIAKYLAQWYSETNGRIPKTYKEKEDFRDLIRQGIL 247 d1jmva_ 141 ------------------------------------------------------------ 141 d1ngva_ 248 KNENGAPEDEENFEEAIKNVNTALNTTQIPSSIEDIFNDDRCINITKQTPSFWILARALK 307 d1jmva_ 141 ------------------------------------------------------------ 141 d1ngva_ 308 EFVAKEGQGNLPVRGTIPDMIADSGKYIKLQNVYREKAKKDAAAVGNHVAKLLQSIGQAP 367 d1jmva_ 141 ------------------------------------------------------------ 141 d1ngva_ 368 ESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAV 427 d1jmva_ 141 ------------------------------------------------------------ 141 d1ngva_ 428 DRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVHEFCRYGAAEPHT 487 d1jmva_ 141 ------------------------------------------ 141 d1ngva_ 488 IAAFLGGAAAQEVIKIITKQFVIFNNTYIYSGMSQTSATFQL 529 TMalign alignment (TM-score: 0.53 Raw score:74.69) d1jmva_ 1 ---------------------MY-KHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIHV 38 :: ::::::::::::::::::: :: :: ::::::::: d1ngva_ 1 KLLKEQKYDRQLRLWGDHGQEALESAHVCLINATATGTEILKN-LV-LP--GIGSFTIID 56 d1jmva_ 39 DV------------------NFSDLYTGLIDVNMSSMQDRISTET-QKALLDLAESVDYP 79 :: ::: :::::::::::::: d1ngva_ 57 GNQVSGEDAGNNFFLQRSSI----------------------GKNRAEAAMEFLQELNSD 94 d1jmva_ 80 ISEKLSGSG-DLGQ-VLSDAIEQYDVDLLVTGHHQDFWSKLMSSTRQVMNTI--K-IDML 134 ::::::::: :::: ::::::: :::::::::: :: :::::::::: : :::: d1ngva_ 95 VSGSFVEESPENLLDNDPSFFC--RFTVVVATQL-----PE-STSLRLADVLWNSQIPLL 146 d1jmva_ 135 VVPL-------------------------------------------------------- 138 :::: d1ngva_ 147 ICRTYGLVGYMRIIIKEHPVIESHPDNALEDLRLDKPFPELREHFQSYDLDHMEKKDHSH 206 d1jmva_ 139 ------------------------------------------------------------ 139 d1ngva_ 207 TPWIVIIAKYLAQWYSETNGRIPKTYKEKEDFRDLIRQGILKNENGAPEDEENFEEAIKN 266 d1jmva_ 139 ------------------------------------------------------------ 139 d1ngva_ 267 VNTALNTTQIPSSIEDIFNDDRCINITKQTPSFWILARALKEFVAKEGQGNLPVRGTIPD 326 d1jmva_ 139 ------------------------------------------------------------ 139 d1ngva_ 327 MIADSGKYIKLQNVYREKAKKDAAAVGNHVAKLLQSIGQAPESISEKELKLLCSNSAFLR 386 d1jmva_ 139 ------------------------------------------------------------ 139 d1ngva_ 387 VVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAVDRFHKQQGRYPGVSNYQVE 446 d1jmva_ 139 -------------------------------------RD--------------------- 140 :: d1ngva_ 447 EDIGKLKSCLTGFLQEYGLSVMVKDDYVHEFCRYGAAEPHTIAAFLGGAAAQEVIKIITK 506 d1jmva_ 141 ----------------------- 141 d1ngva_ 507 QFVIFNNTYIYSGMSQTSATFQL 529 HHsearch alignment (Probability: 0.01 E-value:0.67) d1jmva_ 101 YDVDLLV 107 ::::::: d1ngva_ 141 SQIPLLI 147