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 | d1ru8a_ | Putative N-type ATP pyrophosphatase PF0828 | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1nu0a_ | Hypothetical protein YqgF (RuvX) | Ribonuclease H-like | Ribonuclease H-like motif | α/β |
Query <-- 1.159 --> IntermediateDALI alignment (Z-score: 6.9 Raw score:641.00) query 1 dadeevysalvvglrayvaknGFRSVLIGLSGGIDSALVAAIACDALgaqNVYGVSMPSK 60 :::::::::::::::::::::::::: :::::::::: d1ru8a_ 1 ---------------------GLADVAVLYSGGKDSNYALYWAIKNR-fsVKFLVTMVSE 38 query 61 YS-----sDHSKGdAAELARRTGLNFRTVSIEpmfdaymaslgltglaEENLQSRLRGTT 115 :: ::::: :::::::::::::::::: :::::::::::: d1ru8a_ 39 NEesymytINANL-TDLQARALGIPLVKGFTQ---------------gEKEKEVEDLKRV 82 query 116 LMAIsnqEGHIVLAPGnkselavGYSTlyGDSVG------AYGPIKDVYKTSIFRLAEWR 169 :::: ::::::::: :::: ::::: :::::::::::::::::::: d1ru8a_ 83 LSGL---KIQGIVAGA------sKYQRkrIEKVAkelgleVYTPAWGRDAKEYMRELLNL 133 query 170 N------------------------------------raaaergqtppipEASItkpdyp 193 : :::: d1ru8a_ 134 GfkimvvgvsaygldeswlgrildesaleelitlnekykvhvageggefeTFVL------ 187 query 194 vldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkd 253 d1ru8a_ 188 ---------------------------------dmplfkykivvdkakkvwepctssgkl 214 query 254 rrlpitnrwregh 266 d1ru8a_ 215 iieeahleskleh 227 FAST alignment (Normalized score: 5.12 Raw score:1259.00) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQN-----VYGV 55 :::::::::::::::::::::::: :::: d1ru8a_ 1 ---------------------GLADVAVLYSGGKDSNYALYWAIK------NRFSVKFLV 33 query 56 SMPSKYSSDHS--------KGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLA---E 104 ::::::: ::::::::::::::::::: : d1ru8a_ 34 TMVSENE----ESYMYTINANLTDLQARALGIPLVKGF------------------TQGE 71 query 105 ENLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLY-----GDSVG---------- 149 :::::::::::::: ::: ::::: :::: d1ru8a_ 72 KEKEVEDLKRVLSG--LKI-QGIVA---------------GASKYQRKR-IEKVAKELGL 112 query 150 -AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKP------------------ 190 ::::::::::::::::::: d1ru8a_ 113 EVYTPAWGRDAKEYMRELLN----------------------LGFKIMVVGVSAYGLDES 150 query 191 ------------DYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQ 238 :::::::: d1ru8a_ 151 WLGRILDESALEELITLNEK---------------------------------------- 170 query 239 YPPGTKISAKGFGKDRRLPITNRWREGH-------------------------------- 266 d1ru8a_ 171 ----------------------------YKVHVAGEGGEFETFVLDMPLFKYKIVVDKAK 202 query 267 ------------------------- 267 d1ru8a_ 203 KVWEPCTSSGKLIIEEAHLESKLEH 227 TMalign alignment (TM-score: 0.41 Raw score:109.76) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 ::::::::::::::::::::::::::: ::::::::::: d1ru8a_ 1 ---------------------GLADVAVLYSGGKDSNYALYWAIKNRF-SVKFLVTMVSE 38 query 61 YS-S---DHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTL 116 :: : :::::::::::::::::::::::: : : ::::::::::: d1ru8a_ 39 NEESYMYTINANLTDLQARALGIPLVKGFTQ--G-------------E-KEKEVEDLKRV 82 query 117 MAISNQEGHIVLAPGNKSELAVGYSTL-YGDSV-G------AYGPIKDVYKTSIFRLAEW 168 :::: ::::::::: :: : :: :::: : ::::::::::::::::::: d1ru8a_ 83 LSGL--KIQGIVAGA---SK--Y--QRK-RIEKVAKELGLEVYTPAWGRDAKEYMRELLN 132 query 169 RNRAAAERGQTPPIPEASITK---P-DY----------------PVLDAILELYVDRDTG 208 : : : : :::: : :: ::::: d1ru8a_ 133 L-G----------F-K-IMVVGVSAYGLDESWLGRILDESALEELITLN----------- 168 query 209 ADAIVAAGYDRELV---------------------------------------------- 222 ::: :: d1ru8a_ 169 -------EKY--KVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKVWEPCTSSGKLIIEEA 219 query 223 --------VKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1ru8a_ 220 HLESKLEH-------------------------------------------- 227 HHsearch alignment (Probability: 0.94 E-value:0.00) query 22 GFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHS----KGDAAELARRT 77 ::::::::::::::::::::::::: ::::::::::::::::::: ::::::::::: d1ru8a_ 1 GLADVAVLYSGGKDSNYALYWAIKN-RFSVKFLVTMVSENEESYMYTINANLTDLQARAL 59 query 78 GLNFRTVSIEPMFDAYMASL 97 :::::::::::::::::::: d1ru8a_ 60 GIPLVKGFTQGEKEKEVEDL 79
Intermediate <-- 1.041 --> HitDALI alignment (Z-score: 3.3 Raw score:234.60) d1ru8a_ 1 GLADVAVLYsggkdsnyalywaiknrfsvkflvtmvseneesymytinanltdlqaraLG 60 ::::::::: :: d1nu0a_ 1 MSGTLMAFD----------------------------------fgtksigvavgqritGT 26 d1ru8a_ 61 IPLVKGFtQGEK-EKEVEDLKRVLSGLKIQGIVAG-----------aSKYQRKRIEKVAK 108 ::::::: :::: :::::::::::::::::::::: ::::::::::::: d1nu0a_ 27 ARPLPAI-KAQDgTPDWNIIERLLKEWQPDEIIVGlplnmdgteqplTARARKFANRIHG 85 d1ru8a_ 109 ELGLEVYTPAWGrdakeymrellnlgfkimvvgvsaygldeswlgrildesaleelitln 168 :::::::::::: d1nu0a_ 86 RFGVEVKLHDER------------------------------------------------ 97 d1ru8a_ 169 ekykvhvageggefetfvldmplfkykivvdkakkvwepctssgkliieeahleskleh 227 d1nu0a_ 98 -------------------------lstveaggyralnkgkvdsasaviilesymeqgy 131 FAST alignment (Normalized score: 2.60 Raw score:448.30) d1ru8a_ 1 GLADVAVLYSGGKDSNYALYWAIKNRFSVKFLVTMVSENEESYMYTINANLTDLQARALG 60 :::::::: d1nu0a_ 1 MSGTLMAF---------------------------------------------------- 8 d1ru8a_ 61 ----------------IPLVKG-FTQGEKEK-----EVEDLKRVLSGLKIQGIVAGA--- 95 :::::: :::: :::::::::::::::::::: d1nu0a_ 9 DFGTKSIGVAVGQRITGTARPLPAIKA----QDGTPDWNIIERLLKEWQPDEIIVG-LPL 63 d1ru8a_ 96 ---------SKYQRKRIEKVAKELGLEVYTPAWGRDAKEYMRELLNLGFKIMVVGVSAYG 146 ::::::::::::::::::::::: d1nu0a_ 64 NMDGTEQPLTARARKFANRIHGRFGVEVKLHD---------------------------- 95 d1ru8a_ 147 LDESWLGRILDESALEELITLNEKYKVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKVWE 206 d1nu0a_ 96 ------------------------------------------------------------ 96 d1ru8a_ 207 PCTSSGKLIIEEAHLESKLEH------------------------------------ 227 d1nu0a_ 96 ---------------------ERLSTVEAGGYRALNKGKVDSASAVIILESYMEQGY 131 TMalign alignment (TM-score: 0.28 Raw score:62.60) d1ru8a_ 1 GLADVAVLYSG----G----------------KD------S-N-YALYWAIKNRFSVKFL 32 : ::::::::: : :: : : :::::::: :::::: d1nu0a_ 1 M-SGTLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIERLLKE--WQPDEI 57 d1ru8a_ 33 VTMVSEN----EESYMYTINANL-TDLQARALGIPLVKGFTQGEKE-------------- 73 ::::::: ::::: : :::: :::::::::::::::::::::: d1nu0a_ 58 IVGLPLNMDGTEQPLT-A-RARKFANRIHGRFGVEVKLHDERLSTVEAGGYRALNKGKVD 115 d1ru8a_ 74 --KE--VEDLKRVLS-GLKIQGIVAGASKYQRKRIEKVAKELGLEVYTPAWGRDAKEYMR 128 : : ::::::: :: d1nu0a_ 116 SA-SAVI-ILESYMEQGY------------------------------------------ 131 d1ru8a_ 129 ELLNLGFKIMVVGVSAYGLDESWLGRILDESALEELITLNEKYKVHVAGEGGEFETFVLD 188 d1nu0a_ 132 ------------------------------------------------------------ 132 d1ru8a_ 189 MPLFKYKIVVDKAKKVWEPCTSSGKLIIEEAHLESKLEH 227 d1nu0a_ 132 --------------------------------------- 132 HHsearch alignment (Probability: 0.25 E-value:0.02) d1ru8a_ 61 IPLVKGFTQGEKEKEVEDLKRVLSGLKIQGIVAGA-------S----KYQRKRIEKVAKE 109 ::::::::: ::::::::::::::::::::::::: : ::::::::::::: d1nu0a_ 28 RPLPAIKAQ-DGTPDWNIIERLLKEWQPDEIIVGLPLNMDGTEQPLTARARKFANRIHGR 86 d1ru8a_ 110 LGLEVYTPAWGRDAKEYM 127 :::::: :::::::::: d1nu0a_ 87 FGVEVK--LHDERLSTVE 102