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 <-- 0.786 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1lk5a1) 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 d1lk5a1 D-​ribose-​5-​phosphate isomerase (RpiA),​ catalytic domainNagB/​RpiA/​CoA transferase-​likeNagB/​RpiA/​CoA transferase-​likeα/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 <-- 0.786 --> Hit
DALI alignment (Z-score: 3.9 Raw score:269.30) d1ni5a1 1 --------smtlTLNRQLltSRQILVAFSGGLDSTVLLHQLVQWRTENPGVALRAIHvhh 52 :::::: ::::::::::::::::::::::::::::::::::::: d1lk5a1 1 mnveemkkiaakEALKFI--EDDMVIGLGTGSTTAYFIKLLGEKLKRGEISDIVGVP--- 55 d1ni5a1 53 glsanadawVTHCENVCQQWQVPLVVErvqlaqeglgieaqarqaryqafaRTLLpgevL 112 :::::::::::::::::: :::: : d1lk5a1 56 --------tSYQAKLLAIEHDIPIASL------------------------DQVD--aiD 81 d1ni5a1 113 VTAqhlddqcetfllalkrgsgpaglsamaevsefagtrlirpllartrgelvqwarqyd 172 ::: d1lk5a1 82 VAV-----------------------------------------------dgadevdpnl 94 d1ni5a1 173 lrwiedesnqddsydrnflrlrvvpllqqrwphfaeatarsaalcaeqeslldel 227 d1lk5a1 95 nlikgrgaaltmekiieyragtfivlvderklvdyldiadivivgtregvkkler 149 FAST alignment (Normalized score: 3.81 Raw score:700.80) d1ni5a1 1 S------MTLTLNRQLLT-SRQILVAFSGGLDSTVLLHQLVQWRTENPG----VALRAIH 49 ::::::::::: :::::::::::::::::::::::::: ::::::: d1lk5a1 1 -MNVEEMKKIAAKEALKFIEDDMVIGLGTGSTTAYFIKLLGEKLK----RGEISDIVGVP 55 d1ni5a1 50 VHHGLSANADAW-VTHCENVCQQWQVPLVVERVQLAQEGLGI------------------ 90 ::::::::::::::::: d1lk5a1 56 ------------TSYQAKLLAIEHDIPIAS------------LDQVDAIDVAVDGADEVD 91 d1ni5a1 91 -----------EAQARQARYQAFARTLLPG-EVLVTAQHLDDQCETFLLALKRGSGPAGL 138 ::::::::::: ::::::::::: d1lk5a1 92 PNLNLIKGRGAALTMEKIIEYR--------AGTFIVLVDERK------------------ 125 d1ni5a1 139 SAMAEVSEFAGTRLIRPLLARTRGELVQWARQYDLRWIEDESNQDDSYDRNFLRLRVVPL 198 d1lk5a1 126 ------------------------------------------------------------ 126 d1ni5a1 199 LQQRWPHFAEATARSAALCAEQESLLDEL------------------------ 227 d1lk5a1 126 -----------------------------LVDYLDIADIVIVGTREGVKKLER 149 TMalign alignment (TM-score: 0.35 Raw score:79.69) d1ni5a1 1 -------SM-TLTLNRQLLTSR-QILVAFSGGLDSTVLLHQLVQWRTE-NPGVALRAIHV 50 :: ::::: ::: :: ::::::: ::::::::::::::::: ::::::::::: d1lk5a1 1 MNVEEMKKIAAKEAL-KFI-EDDMVIGLGT-GSTTAYFIKLLGEKLKRGEISDIVGVPTS 57 d1ni5a1 51 HHGLSANADAWVTHCENVCQQWQV-PLVVE--------------------RVQLAQEGLG 89 : ::::::::::: ::::: d1lk5a1 58 -----------Y-QAKLLAIEHDIPIASLDQVDAIDVAVDGADEVDPNLN---------- 95 d1ni5a1 90 IEAQ---ARQARYQAFARTLLPGEVLVTAQHLDDQCETFLLALKRGSGPAGLSAMAEVSE 146 :::: ::::::::::: : ::::::::::: :: ::: : d1lk5a1 96 LIKGRGAALTMEKIIEYR-A---GTFIVLVDERK-LV--DYL-----------------D 131 d1ni5a1 147 FAGTRLIRPLLARTRGELVQWARQYDLRWIEDESNQDDSYDRNFLRLRVVPLLQQRWPHF 206 : :::: :::: : d1lk5a1 132 I---ADIV--IVGT--------------------------------------------R- 141 d1ni5a1 207 AE-ATARSAALCA-EQESLLDEL 227 : :: :: : d1lk5a1 142 -EG--VK-KL--ER--------- 149 HHsearch alignment (Probability: 0.01 E-value:0.38) d1ni5a1 9 QLLTSRQILVAFSGGLDSTVLLHQLVQWRTENPGVALRAIHVHHGLSANADAWVTHCENV 68 ::::::: :::::::::::::::::::::::::::::: : :::: ::::: d1lk5a1 17 FIEDDMV--IGLGTGSTTAYFIKLLGEKLKRGEISDIVG--V-----PTSY----QAKLL 63 d1ni5a1 69 CQQWQVPLVV 78 :::::::::: d1lk5a1 64 AIEHDIPIAS 73