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 <-- 1.159 --> Intermediate <-- 1.020 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1lw7a1) through the intermediate protein (d1ru8a_) by significant SVM score (>0.4).

  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 d1lw7a1 Transcriptional regulator NadR,​ NMN-​adenylyltransferase domainNucleotidylyl transferaseAdenine nucleotide alpha hydrolase-​likeα/β

Supporting Alignments

Query <-- 1.159 --> 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 <-- 1.020 --> Hit
DALI alignment (Z-score: 8.5 Raw score:558.60) d1ru8a_ 1 GLADVAVLYSG---GKDSNYALYWAIKNrFSVKFLVTMVSENEESYMY-------TINAN 50 ::::::::::: :::::::::::::: ::::::::::::::::::: ::::: d1lw7a1 1 EKKVGVIFGKFypvHTGHINMIYEAFSK-VDELHVIVCSDTVRDLKLFydskmkrMPTVQ 59 d1ru8a_ 51 -LTDLQARALG-----IPLVKGFTQGEK------EKEVEDLKRVLS--GLKIQGIVAgas 96 :::::::::: :::::::::::: :::::::::::: ::::::::: d1lw7a1 60 dRLRWMQQIFKyqknqIFIHHLVEDGIPsypngwQSWSEAVKTLFHekHFEPSIVFS--- 116 d1ru8a_ 97 kyqRKRIEKVAKE-LGLEVYTPAWGrdakeymrellnlgfkimvvgvsaygldeswlgri 155 :::::::::: ::::::::::: d1lw7a1 117 --sEPQDKAPYEKyLGLEVSLVDPD----------------------------------- 139 d1ru8a_ 156 ldesaleelitlnekykvhvageggefetfvldmplfkykivvdkakkvwepctssgkli 215 d1lw7a1 140 ------------------------------------------------rtffnvsatkir 151 d1ru8a_ 216 ieeahleskleh 227 d1lw7a1 152 ttpfqywkfipk 163 FAST alignment (Normalized score: 4.95 Raw score:952.50) d1ru8a_ 1 GLADVAVLYS----GGKDSNYALYWAIKNRFSV----KFLVTMVSENEESYMYTINAN-- 50 ::::::::: :::::::::::::: ::::::::: d1lw7a1 1 EKKVGVIFG-KFYPVHTGHINMIYEAFS-----KVDELHVIVCSDT------------VR 42 d1ru8a_ 51 --------------LTDLQARALG-----------IPLVKGFTQG---------EKEKEV 76 :::::::: ::::::: :::::: d1lw7a1 43 DLKLFYDSKMKRMPTVQDRLRW--MQQIFKYQKNQIFIHHLV---EDGIPSYPNGWQSWS 97 d1ru8a_ 77 EDLKRVLSGL--KIQGIVAGASKYQRKRIEKVAKELGLEVYTPAWGRDAKEYMRELLNLG 134 :::::::::: ::::::: ::::::::::: ::::::::::::: d1lw7a1 98 EAVKTLFHEKHFEPSIVFS-SEPQDKAPYEK---YLGLEVSLVDPDR------------- 140 d1ru8a_ 135 FKIMVVGVSAYGLDESWLGRILDESALEELITLNEKYKVHVAGEGGEFETFVLDMPLFKY 194 d1lw7a1 141 ------------------------------------------------------------ 141 d1ru8a_ 195 KIVVDKAKKVWEPCTSSGKLIIEEAHLESKLEH----------------------- 227 d1lw7a1 141 ---------------------------------TFFNVSATKIRTTPFQYWKFIPK 163 TMalign alignment (TM-score: 0.47 Raw score:107.43) d1ru8a_ 1 GLADVAVLYSG--GK-DSNYALYWAIKNRFSVKFLVTMVSENEESY--------MYTINA 49 ::::::::::: :: :::::::::::: ::::::::::::::::: ::::: d1lw7a1 1 EKKVGVIFGKFYPVHTGHINMIYEAFSK-VDELHVIVCSDTVRDLKLFYDSKMK-RMPTV 58 d1ru8a_ 50 -NLTDLQARALG--I---PLVKGFTQ-GEK---E--KEVEDLKRVLS-GLKIQGIVAGAS 96 ::::::::::: : :::::::: ::: : ::::::::::: :::::::::::: d1lw7a1 59 QDRLRWMQQIFKYQKNQIFIHHLVEDGIPSYPNGWQSWSEAVKTLFHEKHFEPSIVFSSE 118 d1ru8a_ 97 KYQRKRIEKVAKELGLEVYTPAWGRDAKEYMRELLNLGFKIMVVGVSAYGLDESWLG-RI 155 :::::::::::: ::::::: : : :: ::: : :::: ::::: :: d1lw7a1 119 PQDKAPYEKYLG----LEVSLVD-P-D--RT-FFN-----V-SATK------IRTTPFQY 157 d1ru8a_ 156 LDESALEELITLNEKYKVHVAGEGGEFETFVLDMPLFKYKIVVDKAKKVWEPCTSSGKLI 215 :: ::: : d1lw7a1 158 WK----------------------------FIP-------K------------------- 163 d1ru8a_ 216 IEEAHLESKLEH 227 d1lw7a1 164 ------------ 164 HHsearch alignment (Probability: 0.01 E-value:0.36) d1ru8a_ 21 WAIKNRFSVKFLVTMVSE 38 :::::::::::::::::: d1lw7a1 24 EAFSKVDELHVIVCSDTV 41