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 <-- 1.264 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1qx4a2) 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 d1qx4a2 cytochrome b5 reductaseFerredoxin reductase-​like,​ C-​terminal NADP-​linked domainFerredoxin reductase-​like,​ C-​terminal NADP-​linked domainα/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 <-- 1.264 --> Hit
DALI alignment (Z-score: 5.7 Raw score:444.40) d1ni5a1 1 smtltlnrQLLT------------SRQILVAFSGGldSTVLLHQLVQWRTEN--PGVALR 46 :::: ::::::::::: ::::::::::::::: :::::: d1qx4a2 1 -------gKFAIradkksnpvvrtVKSVGMIAGGT--GITPMLQVIRAVLKDpnDHTVCY 51 d1ni5a1 47 AIHVhhglsanADAWVtHCENVCQQWQ------VPLVV----------ERVQlaqeglgi 90 :::: ::::: :::::::::: ::::: :::: d1qx4a2 52 LLFA-----nqSEKDI-LLRPELEELRnehssrFKLWYtvdkapdawdYSQG-------- 97 d1ni5a1 91 eaqarqaRYQAFART-LLPG--EVLVTAQHLddqcetfllalkrgsgpaglsamaevsEF 147 :::::::: :::: ::::::::: :: d1qx4a2 98 -----fvNEEMIRDHlPPPGeeTLILMCGPP----------------pmiqfaclpnlER 136 d1ni5a1 148 AGT---RLIRPllartrgelvqwarqydlrwiedesnqddsydrnflrlrvvpllqqrwp 204 ::: ::::: d1qx4a2 137 VGHpkeRCFTF------------------------------------------------- 147 d1ni5a1 205 hfaeatarsaalcaeqeslldel 227 d1qx4a2 148 ----------------------- 148 FAST alignment (Normalized score: 3.57 Raw score:652.50) d1ni5a1 1 SMTLTLNRQL---------------LTSRQILVAFSG---GLDSTVLLHQLVQWRTEN-- 40 ::::::::::: ::::::::::::: d1qx4a2 1 ----------GKFAIRADKKSNPVVRTVKSVGMIAG-GTGITPMLQVIRAVLK-----DP 44 d1ni5a1 41 -PGVALRAIHVHHGLSANADA--------WVTHCENVCQQW---QVPLVVERVQLAQEGL 88 :::::::::: ::::::::::: :::::::: d1qx4a2 45 NDHTVCYLLFA----------NQSEKDILLRPELEELRNE-HSSRFKLWYTV-------- 85 d1ni5a1 89 GIEAQARQA--------------RYQAFARTLL---PGEVLVTAQHLDDQCETFLLALKR 131 :::::::::: ::::::: d1qx4a2 86 ---------DKAPDAWDYSQGFVNEEMIRDHLPPPGEETLILM----------------- 119 d1ni5a1 132 GSGPAGLSAMAEVSE----------------FAGTRLIRPLLARTRGELVQWARQYDLRW 175 :::: d1qx4a2 120 ---------------CGPPPMIQFACLPNLERVGH------------------------- 139 d1ni5a1 176 IEDESNQDDSYDRNFLRLRVVPLLQQRWPHFAEATARSAALCAEQESLLDEL-------- 227 d1qx4a2 140 ----------------------------------------------------PKERCFTF 147 TMalign alignment (TM-score: 0.36 Raw score:80.87) d1ni5a1 1 --SMTLTLNRQ-------LLTSR-QILVAFSGGLDSTVLLHQLVQWRTE-NPGVALRAIH 49 :::: ::::: ::::::: ::::::::::::::::: ::::::::: d1qx4a2 1 GK-----FAIRADKKSNPVVRTVKSVGMIAG-GTGITPMLQVIRAVLKDP-NDHTVCYLL 53 d1ni5a1 50 VHHGLSANADAWVTHCENVCQQWQ--VPLVVE----------RVQLAQEGLGIEAQARQA 97 :::: ::::::::::::::::: : :::::: ::: :: d1qx4a2 54 FANQ-SEKDILLRPELEELRNE-HSSRFKLWYTVDKAPDAWDYSQ-----------GF-- 98 d1ni5a1 98 RY-QAFARTLLP-G--EVLVTAQHLDDQ-CET--FLLALKRGSGPAGLSAMA--EVSEFA 148 :: ::::::::: : ::::::: ::: :: :: :::: d1qx4a2 99 VNEEMIRDHLPPPGEETLILMCG--PPPM-IQFA----------------CLPN--LERV 137 d1ni5a1 149 GTRL--IRPLLARTRGELVQWARQYDLRWIEDESNQDDSYDRNFLRLRVVPLLQQRWPHF 206 :::: :::: d1qx4a2 138 GHPKERCFTF-------------------------------------------------- 147 d1ni5a1 207 AEATARSAALCAEQESLLDEL 227 d1qx4a2 148 --------------------- 148 HHsearch alignment (Probability: 0.25 E-value:0.03) d1ni5a1 10 LLTSRQILVAFSGGLDSTVLLHQLVQWRTE-NPGVALRAIHVHHGLSANADAWVTHCENV 68 :::::::::::::::::::::::::::::: :::::::::::::: ::::::::::::: d1qx4a2 14 VVRTVKSVGMIAGGTGITPMLQVIRAVLKDPNDHTVCYLLFANQS--EKDILLRPELEEL 71 d1ni5a1 69 CQQWQVPLVVERV 81 ::::::::::::: d1qx4a2 72 RNEHSSRFKLWYT 84