HorA Server Transitive Detail

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


Query <-- 0.937 --> Intermediate <-- 0.929 --> Hit

HHsearch
probability
HHsearch
probability

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1owla2) through the intermediate protein (d1ru8a_) by significant HHsearch probability (>0.9).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ru8a_ Putative N-​type ATP pyrophosphatase PF0828Adenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1owla2 DNA photolyaseCryptochrome/​photolyase,​ N-​terminal domainCryptochrome/​photolyase,​ N-​terminal domainα/β

Supporting Alignments

Query <-- 0.937 --> Intermediate
DALI 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 <-- 0.929 --> Hit
DALI alignment (Z-score: 8.7 Raw score:649.50) d1ru8a_ 1 glADVAVLYSGG--kdsNYALYWAIKNrFSVKFLVTMVS-ENEE-----symyTINANLT 52 :::::::::: :::::::::: ::::::::::: :::: ::::::: d1owla2 1 --APILFWHRRDlrlsdNIGLAAARAQ-SAQLIGLFCLDpQILQsadmaparvAYLQGCL 57 d1ru8a_ 53 DLQARALG---IPLVKGFTqgekeKEVEDLKRVLSGLKIQGIVAGAS-----KYQRKRIE 104 :::::::: :::::::: ::::::::::::::::::::::: :::::::: d1owla2 58 QELQQRYQqagSRLLLLQG-----DPQHLIPQLAQQLQAEAVYWNQDiepygRDRDGQVA 112 d1ru8a_ 105 KVAKELGLEVYTPA---wgRDAKEymrellnlgfkimvvgvsaygldeswlgrildESAL 161 :::::::::::::: ::::: :::: d1owla2 113 AALKTAGIRAVQLWdqllhSPDQI----------------------lsgsgnpysvYGPF 150 d1ru8a_ 162 EELITLNekykvhvageggefetfvlDMPL-fkykivvdkakkvwepctssgkliieeah 220 ::::::: :::: d1owla2 151 WKNWQAQ---------------pkptPVATptelvdlspeqltaiaplllselptlkqlg 195 d1ru8a_ 221 leskleh 227 d1owla2 196 fdwdggf 202 FAST alignment (Normalized score: 4.54 Raw score:972.70) d1ru8a_ 1 GLA-DVAVLYSGGKDS--------NYALYWAIKNRFSV----KFLVTMVSENEESY---- 43 :::::: ::::::::: :::::::::: d1owla2 1 ---APILFWH------RRDLRLSDNIGLAAARA-----QSAQLIGLFCLDPQ----ILQS 42 d1ru8a_ 44 --MYTINANLTDLQARA-------LGIPLVKGFTQGEKE--KEVEDLKRVLSGLKIQGIV 92 ::::::::::::::: :::::::: ::::::::::::::::::: d1owla2 43 ADMAPARVAYLQGCLQELQQRYQQAGSRLLLL-------QGDPQHLIPQLAQQLQAEAVY 95 d1ru8a_ 93 AGA------SKYQRKRIEKVAKELGLEVYTPAWGRDAKEYMRELLNLGFKIMVVGVSAYG 146 :: ::::::::::::::::::::: d1owla2 96 WN-QDIEPYGRDRDGQVAAALKTAGIRAVQ------------------------------ 124 d1ru8a_ 147 LDESWLGRILDESALEELITLNEKYKVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKVWE 206 d1owla2 125 ------------------------------------------------------------ 125 d1ru8a_ 207 PCTSSGKLIIEEAHLESKLEH--------------------------------------- 227 d1owla2 125 ---------------------LWDQLLHSPDQILSGSGNPYSVYGPFWKNWQAQPKPTPV 163 d1ru8a_ 228 --------------------------------------- 228 d1owla2 164 ATPTELVDLSPEQLTAIAPLLLSELPTLKQLGFDWDGGF 202 TMalign alignment (TM-score: 0.44 Raw score:100.23) d1ru8a_ 1 GLADVAVLYSGGKDS--NYALYWAIKNRFSVKFLVTMVSE-NEE-----S--YMYTINAN 50 : :::::::::::: :::::::: :::::::::::::: ::: : :::::: d1owla2 1 A--PILFWHRRDLRLSDNIGLAAAR-AQSAQLIGLFCLDPQILQSADMAPAR--VAYLQG 55 d1ru8a_ 51 LTDLQARAL--G-IPLVKGFTQGEKEKEVEDLKRVLSGLKIQGIVAG-AS----KYQRKR 102 ::::::::: : :::::::: ::::::::::::::::::::: :: :::::: d1owla2 56 CLQELQQRYQQAGSRLLLLQG-----DPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQ 110 d1ru8a_ 103 IEKVAKELGLEVYTPAWGRDAKEYM-----------RELLNLGFKIMVVGVSAYGLDESW 151 ::::::::::::::::: : ::::: d1owla2 111 VAAALKTAGIRAVQLWD-Q-LLHSPDQILSGSGNPY------------------------ 144 d1ru8a_ 152 LGRILDESALEELITLNEKYKV--HV-------AGEGGEFETFVLDMPLFK--------- 193 ::::::: : :::::: d1owla2 145 ---------------SVYGPFWKN-WQAQPKPT------------PVATPTELVDLSPEQ 176 d1ru8a_ 194 ----------------------YKIVVDKAKKVWEPCTSSGKLIIEEAHLESKLEH 227 :::: d1owla2 177 LTAIAPLLLSELPTLKQLGFDW---------------------DGGF--------- 202 HHsearch alignment (Probability: 0.92 E-value:0.00) d1ru8a_ 16 NYALYWAIKNRFSVKFLVTMVSENEESYMYTI--------NANLTDLQARALGIPLVKGF 67 :::::::::::::::::::::::::::::::: :::::::::::::::::::: d1owla2 16 NIGLAAARAQSAQLIGLFCLDPQILQSADMAPARVAYLQGCLQELQQRYQQAGSRLLLLQ 75 d1ru8a_ 68 TQGEKEKEVEDLKRVLSGLKIQGIVAG--ASKYQ---RKRIEKVAKELGLEVY 115 :::::::::::::::::::::: ::::: :::::::::::::::: d1owla2 76 -----GDPQHLIPQLAQQLQAEAVYWNQDIEPYGRDRDGQVAAALKTAGIRAV 123