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 <-- 2.482 --> Intermediate <-- 1.209 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1q8fa_) through the intermediate protein (d1ni5a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ni5a1 Putative cell cycle protein MesJ,​ N-​terminal domainAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1q8fa_ Pyrimidine nucleoside hydrolase YeiKNucleoside hydrolaseNucleoside hydrolaseα/β

Supporting Alignments

Query <-- 2.482 --> Intermediate
DALI alignment (Z-score: 13.9 Raw score:1114.50) query 1 dadeevysALVVGLRAYVAknGFRSVLIGLSGGIDSALVAAIACDALG---aQNVYGVSM 57 ::::::::::: ::::::::::::::::::::::::::: :::::::: d1ni5a1 1 --------SMTLTLNRQLL--TSRQILVAFSGGLDSTVLLHQLVQWRTenpgVALRAIHV 50 query 58 PSKYS--SDHSKGDAAELARRTGLNFRTVSIEpmFDAYmaslgltgLAEE-NLQSRLRGT 114 ::::: ::::::::::::::::::::::::: :::: :::: ::::::::: d1ni5a1 51 HHGLSanADAWVTHCENVCQQWQVPLVVERVQ--LAQE--------GLGIeAQARQARYQ 100 query 115 TLMAISNqEGHIVLAPGNKSELAVGY-----------------stlygdsvgAYGPIKDV 157 ::::::: :::::::::::::::::: :::::::: d1ni5a1 101 AFARTLL-PGEVLVTAQHLDDQCETFllalkrgsgpaglsamaevsefagtrLIRPLLAR 159 query 158 YKTSIFRLAEWRNraaaergqtppIPEASitkpdypvldailelyvdrdtgadaivaagy 217 ::::::::::::: ::::: d1ni5a1 160 TRGELVQWARQYD-----------LRWIE------------------------------d 178 query 218 drelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1ni5a1 179 esnqddsydrnflrlrvvpllqqrwphfaeatarsaalcaeqeslldel 227 FAST alignment (Normalized score: 8.92 Raw score:2193.00) query 1 DADEEVYSA-LVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQ-------NV 52 ::::::::: :::::::::::::::::::::::::: :: d1ni5a1 1 ---------SMTLTLNRQL--LTSRQILVAFSGGLDSTVLLHQLVQW----RTENPGVAL 45 query 53 YGVSMPSKYS--SDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAE-----E 105 :::::::::: :::::::::::::::::::::::: :::: : d1ni5a1 46 RAIHVHHGLSANADAWVTHCENVCQQWQVPLVVERV-----QLAQ---------EGLGIE 91 query 106 NLQSRLRGTTLMAISNQ--EGHIVLAPGNKSELAVGYSTLYGDSVG-------------- 149 :::::::::::::: ::::::::::::::: d1ni5a1 92 AQARQARYQAFART---LLPGEVLVTAQHLDDQC------------ETFLLALKRGSGPA 136 query 150 ---------------AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKP---- 190 ::::::::::::::::::: d1ni5a1 137 GLSAMAEVSEFAGTRLIRPLLARTRGELVQWARQ----------------------YDLR 174 query 191 -------------------------------DYPVLDAILELYVDRDTGADAIVAAGYDR 219 :::::::::::::: d1ni5a1 175 WIEDESNQDDSYDRNFLRLRVVPLLQQRWPHFAEATARSAALCAE--------------- 219 query 220 ELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-------- 266 d1ni5a1 220 -----------------------------------------------QESLLDEL 227 TMalign alignment (TM-score: 0.55 Raw score:147.16) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALG--A-QNVYGVSM 57 ::::::::::: : :::::::::::::::::::::::::: : :::::::: d1ni5a1 1 --------SMTLTLNRQLL-T-SRQILVAFSGGLDSTVLLHQLVQWRTENPGVALRAIHV 50 query 58 PSKYS--SDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEE-NLQSRLRGT 114 ::::: ::::::::::::::::::::::::: : : ::: ::: ::::::::: d1ni5a1 51 HHGLSANADAWVTHCENVCQQWQVPLVVERVQ--L---A----QEG-LGIEAQARQARYQ 100 query 115 TLMAISNQEGHIVLAPGNKSELAVG-YS-----------------TLYGDS-V---GAYG 152 :::::: :::::::::::::::::: :: : : :::: d1ni5a1 101 AFARTL-LPGEVLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEV-----SEFAGTRLIR 154 query 153 PIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITK-------------PD-YPVLDAI 198 :::::::::::::::::: : :::::: :: ::::::: d1ni5a1 155 PLLARTRGELVQWARQYD-----------L-RWIEDESNQDDSYDRNFLRLRVVPLLQQR 202 query 199 LELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLP- 257 :::::: : : :::::::::: d1ni5a1 203 WPHFAE-A----------------------T------------------ARSAALCAEQE 221 query 258 ------ITNRWREGH 266 d1ni5a1 222 SLLDEL--------- 227 HHsearch alignment (Probability: 0.96 E-value:0.00) query 24 RSVLIGLSGGIDSALVAAIACDALGAQ---NVYGVSMPSKYSS--DHSKGDAAELARRTG 78 ::::::::::::::::::::::::::: ::::::::::::: ::::::::::::::: d1ni5a1 14 RQILVAFSGGLDSTVLLHQLVQWRTENPGVALRAIHVHHGLSANADAWVTHCENVCQQWQ 73 query 79 LNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQEGHIVLA--------- 129 :::::::::: :::::::::::::::::::::::::::::::: d1ni5a1 74 VPLVVERVQL---------AQEGLGIEAQARQARYQAFARTLLPGEVLVTAQHLDDQCET 124 query 130 --------PGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERG 177 :::::::::::::::::::: ::::::::::::::::::::::::::: d1ni5a1 125 FLLALKRGSGPAGLSAMAEVSEFAGTRL-IRPLLARTRGELVQWARQYDLRWIEDE 179
Intermediate <-- 1.209 --> Hit
DALI alignment (Z-score: 3.7 Raw score:500.20) d1ni5a1 1 smtltlnrqlltsRQILVAFSGGLDSTVLLHQLVQWrtenPGVA-LRAIHVHhglsaNAD 59 ::::::::::::::::::::::: :::: ::::::: ::: d1q8fa_ 1 ------------kRKIILDCDPGHDDAIAIMMAAKH----PAIDlLGITIVA--gnqTLD 42 d1ni5a1 60 AWVTHCENVCQ--QWQVPLVVER-VQLAqegLGIE---------------------aqar 95 ::::::::::: :::::::::: :::: :::: d1q8fa_ 43 KTLINGLNVCQklEINVPVYAGMpQPIM---RQQIvadnihgdtgldgpvfepltrqaes 99 d1ni5a1 96 qarYQAFART---llPGEVLVTAqhlddqcetfllalkrgsgpaglsamaevseFAGT-- 150 ::::::: :::::::: :::: d1q8fa_ 100 thaVKYIIDTlmasdGDITLVPV----------------gplsniavamrmqpaILPKir 143 d1ni5a1 151 RLIRPL-----------------------------------LART-RGELVQ-------- 166 :::::: :::: :::::: d1q8fa_ 144 EIVLMGgaygtgnftpsaefnifadpeaarvvftsgvplvmMGLDlTNQTVCtpdviarm 203 d1ni5a1 167 ---warqYDLRwiedesnqddsydrnflRLRVVP---------llqqrwphfaeatARSA 214 :::: :::::: :::: d1q8fa_ 204 eraggpaGELF-------sdimnftlktQFENYGlaggpvhdatcigylinpdgikTQEM 256 d1ni5a1 215 ---------------alCAEQeSLLD-------------------------el 227 :::: :::: d1q8fa_ 257 yvevdvnsgpcygrtvcDELG-VLGKpantkvgitidtdwfwglveecvrgyi 308 FAST alignment (Normalized score: 3.15 Raw score:833.80) d1ni5a1 1 SMTLTLNRQLLTSRQILVAFSGGLDSTVLLHQLVQWRTENPGVA-LRAIHVHHGLSA--- 56 :::::::::::::::::::::: :::::: ::::: d1q8fa_ 1 ------------KRKIILDCDPGHDDAIAIMMAA----KHPAIDLLGITI-------VAG 37 d1ni5a1 57 --NADAWVTHCENVCQQ--WQVPLVVERVQLAQEGLGIEAQARQ---------------- 96 ::::::::::::::: ::::::: d1q8fa_ 38 NQTLDKTLINGLNVCQKLEINVPVYA------------------GMPQPIMRQQIVADNI 79 d1ni5a1 97 ---------------------ARYQAFARTLL------PGEVLVTAQHLDDQCETFLLAL 129 :::::::: ::::::: d1q8fa_ 80 HGDTGLDGPVFEPLTRQAESTHAVKYIID---TLMASDGDITLVP--------------- 121 d1ni5a1 130 KRGSGPAGLSAMAEVSEFA--------------------GTRLIRPLL------------ 157 :::::: d1q8fa_ 122 -------------------VGPLSNIAVAMRMQPAILPKIREIVL---MGGAYGTGNFTP 159 d1ni5a1 158 ------------------------ARTRGELVQWARQYDLRWIEDESNQDDSYDRNFLRL 193 :::::::: d1q8fa_ 160 SAEFNIFADPEAARVVFTSGVPLVMMGLDLTN---------------------------- 191 d1ni5a1 194 RVVPLLQQRWPHFAEATARSAALCAEQESLLDEL-------------------------- 227 d1q8fa_ 192 ----------------------------------QTVCTPDVIARMERAGGPAGELFSDI 217 d1ni5a1 228 ------------------------------------------------------------ 228 d1q8fa_ 218 MNFTLKTQFENYGLAGGPVHDATCIGYLINPDGIKTQEMYVEVDVNSGPCYGRTVCDELG 277 d1ni5a1 228 ------------------------------- 228 d1q8fa_ 278 VLGKPANTKVGITIDTDWFWGLVEECVRGYI 308 TMalign alignment (TM-score: 0.32 Raw score:73.28) d1ni5a1 1 -----------SM-TLTLNRQLL---TSRQILVAFSGGLDST-VLLHQLVQWRT-ENPGV 43 :: ::::::::: :::::::::: ::::: ::::::::::: ::::: d1q8fa_ 1 KRKIILDCDPGHDDAIAIMMAAKHPAIDLLGITIVA-GNQTLDKTLINGLNVCQKLEINV 59 d1ni5a1 44 ALRAIH-VHHGLSANA---------DAWVTHCENV--------CQQWQVP-LVVE----- 79 :::::: :::: :::: : :::::: :::: d1q8fa_ 60 PVYAGMPQPIM-RQQIVADNIHGDT---------GLDGPVFEP-LTRQAESTHAVKYIID 108 d1ni5a1 80 -----------------RVQLAQEGLGIEAQARQARYQAFARTL--LP--GEVLVTAQHL 118 ::::::::::::: : :::: : d1q8fa_ 109 TLMASDGDITLVPVGPL--------------SNIAVAMRMQPAILP-KIR--EIVL-M-- 148 d1ni5a1 119 DDQCETFLL-----ALK-----------------RGSGPAGLSAMAEVSEFAGTRLIR-P 155 :: : ::: : :::::::: d1q8fa_ 149 -GG-A-YGTGNFTP--SAEFNIFADPEAARVVFT----------------SGVPLVMMG- 186 d1ni5a1 156 L--LA-RT-------------------------RGELVQW-------------------- 167 : :: :: :::::: d1q8fa_ 187 LDLTNQTVCTPDVIARMERAGGPAGELFSDIMN-FTLKTQFENYGLAGGPVHDATCIGYL 245 d1ni5a1 168 -----------------ARQYDLRWIEDESNQDDSYDRNFL---------------RLRV 195 :::::::::: d1q8fa_ 246 INPDGIKTQEMYVEVDV--------------NSGPCYGRTVCDELGVLGKPANTKV---- 287 d1ni5a1 196 VPLLQQRWPHFAEATARSAALC----------------AEQESLLDEL 227 ::::: d1q8fa_ 288 -----------------GITIDTDWFWGLVEECVRGYI---------- 308 HHsearch alignment (Probability: 0.41 E-value:0.01) d1ni5a1 13 SRQILVAFSGGLDSTVLLHQLVQWRTENPGVALRAIHVHHGLSANADAWVTHCENVCQQW 72 ::::::::::::::::::::::: ::::::::::::::::: ::::::::::::::: d1q8fa_ 1 KRKIILDCDPGHDDAIAIMMAAK----HPAIDLLGITIVAGNQT-LDKTLINGLNVCQKL 55 d1ni5a1 73 QVPLVV--ERVQL-----------------------AQEGLGIEAQARQARYQAFARTLL 107 :::::: ::::: :::::::::::::::::::::::: d1q8fa_ 56 EINVPVYAGMPQPIMRQQIVADNIHGDTGLDGPVFEPLTRQAESTHAVKYIIDTLMASDG 115 d1ni5a1 108 PGEVLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEVSEFAGTRLIRPLLART---RGEL 164 ::::::::: :::::::::::::::::::::::::::::::: :::::::: :::: d1q8fa_ 116 DITLVPVGP-LSNIAVAMRMQPAILPKIREIVLMGGAYGTGN---FTPSAEFNIFADPEA 171 d1ni5a1 165 VQWARQYDLRWIEDESNQDDSYDRNFLRLRVVPLLQQRWPHFAEATARSA 214 :::::::::::::::::::: ::::::::::::::::::::::::::: d1q8fa_ 172 ARVVFTSGVPLVMMGLDLTN---QTVCTPDVIARMERAGGPAGELFSDIM 218