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 <-- 1.476 --> Intermediate <-- 0.998 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1nf9a_) through the intermediate protein (d1jmva_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jmva_ Universal stress protein A,​ UspAAdenine nucleotide alpha hydrolases-​likeAdenine nucleotide alpha hydrolase-​likeα/β
Hit d1nf9a_ Phenazine biosynthesis protein PhzDIsochorismatase-​like hydrolasesIsochorismatase-​like hydrolasesα/β

Supporting Alignments

Query <-- 1.476 --> Intermediate
DALI alignment (Z-score: 6.4 Raw score:517.70) query 1 dadeevysalvvglrayvaknGFRSVLIGLSGGIDSALVAAIACDALG--aqNVYGVSMP 58 ::::::::::::::::::::::::::: :::::::: d1jmva_ 1 ---------------------MYKHILVAVDLSEESPILLKKAVGIAKrhdaKLSIIHVD 39 query 59 S------------------kysSDHSKGDAAELARRTG---lNFRTVSIepmfdaymasl 97 : :::::::::::::::: ::::::: d1jmva_ 40 VnfsdlytglidvnmssmqdriSTETQKALLDLAESVDypisEKLSGSG----------- 88 query 98 gltglaeenlqsrLRGTTLMAISNQEGH-IVLAPGNKseLAVG--YSTL----ygdsvgA 150 ::::::::::::::: :::::::: :::: :::: : d1jmva_ 89 -------------DLGQVLSDAIEQYDVdLLVTGHHQ--DFWSklMSSTrqvmntikidM 133 query 151 YGPiKDVYktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtgad 210 ::: :::: d1jmva_ 134 LVV-PLRD---------------------------------------------------- 140 query 211 aivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1jmva_ 141 -------------------------------------------------------- 141 FAST alignment (Normalized score: 4.82 Raw score:930.50) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQ------NVYG 54 ::::::::::::::::::::::::: :::: d1jmva_ 1 ---------------------MYKHILVAVDLSEESPILLKKAVGI----AKRHDAKLSI 35 query 55 VSMPSKYSS-----------------------DHSKGDAAELAR--RTGL-NFRTVSIEP 88 :::: :::::::::::: :::: ::::: d1jmva_ 36 IHVD-----VNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSG---- 86 query 89 MFDAYMASLGLTGLAEENLQSR--LRGTTLMAISNQEG-HIVLAPGNKSELAVGYSTLY- 144 :::::::::::::: :::::::: d1jmva_ 87 ----------------------SGDLGQVLSDAIEQYDVDLLVTGHH------------Q 112 query 145 ------------GDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDY 192 :::::: d1jmva_ 113 DFWSKLMSSTRQVMNTIK------------------------------------------ 130 query 193 PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGK 252 d1jmva_ 131 ------------------------------------------------------------ 131 query 253 DRRLPITNRWREGH---------- 266 d1jmva_ 131 --------------IDMLVVPLRD 140 TMalign alignment (TM-score: 0.33 Raw score:88.21) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALG--AQNVYGVSMP 58 ::::::::::::::::::::::::::: :::::::::: d1jmva_ 1 ---------------------MYKHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIHVD 39 query 59 SK---------------------YSSDHSKGDAAELARRT--GLNFRTVSIEPMFDAYMA 95 :: :: :::::::::::: ::::::::: d1jmva_ 40 VNFSDLYTGLIDVNMSSMQDRIS--TE-TQKALLDLAESVDYPISEKLSGS--------- 87 query 96 SLGLTGLAEENLQSRLRGTTLMAISNQEGH-IVLAPGNKSELAVGYSTLYGDS-VG---- 149 : ::::::::::::::: ::::::: ::::::::: ::: :: d1jmva_ 88 ------------G--DLGQVLSDAIEQYDVDLLVTGHH-QDFWSKLMS--STRQVMNTIK 130 query 150 --AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDT 207 ::: :: : :: d1jmva_ 131 IDMLV-VP-L-RD----------------------------------------------- 140 query 208 GADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1jmva_ 141 ----------------------------------------------------------- 141 HHsearch alignment (Probability: 0.05 E-value:0.16) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :::::::::::::::::::::::::::::::::::::::::::::: ::::: :::::: d1jmva_ 56 SMQDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQY-DVDLL--VTGHHQ 112 query 61 YSSDHSKGDAAELARRTGLNFRTVSIEP 88 :::::::::::::::::::::::::::: d1jmva_ 113 DFWSKLMSSTRQVMNTIKIDMLVVPLRD 140
Intermediate <-- 0.998 --> Hit
DALI alignment (Z-score: 4.1 Raw score:395.70) d1jmva_ 1 ---------------------------mYKHILVAVD-----------------lsEESP 16 ::::::::: :::: d1nf9a_ 1 msgipeitayplptaqqlpanlarwslePRRAVLLVHdmqryflrplpeslraglvANAA 60 d1jmva_ 17 ILLKKAVGIAkrhdakLSIIHVDVN----fsdlytglidvnmssmqdriSTET--qkALL 70 :::::::::: ::::::::: :::: ::: d1nf9a_ 61 RLRRWCVEQG------VQIAYTAQPgsmteeqrgllkdfwgpgmraspaDREVveelAPG 114 d1jmva_ 71 DlaesvdypisEKLSGSG---DLGQ--VLSDAIEQYDVDLLVTGHHQDFwsklMSSTRQV 125 : ::::::: :::: :::::::::::::::::::::: ::::::: d1nf9a_ 115 P----------DDWLLTKwrySAFFhsDLLQRMRAAGRDQLVLCGVYAH-vgvLISTVDA 163 d1jmva_ 126 MNtIKIDMLVVPL------------------------------rd 140 :: :::::::::: d1nf9a_ 164 YS-NDIQPFLVADaiadfseahhrmaleyaasrcamvvttdevle 207 FAST alignment (Normalized score: 4.26 Raw score:725.90) d1jmva_ 1 ---------------------------MYKHILVAVDL-------------------SEE 14 ::::::::: ::: d1nf9a_ 1 MSGIPEITAYPLPTAQQLPANLARWSLEPRRAVLLV--HDMQRYFLRPLPESLRAGLVAN 58 d1jmva_ 15 SPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAE 74 :::::::::: :::::::::: d1nf9a_ 59 AARLRRWCVE------QGVQIAYTAQ---------------------------------- 78 d1jmva_ 75 SVDYPIS-------------------------------------EKLSGSGDLG------ 91 ::::: d1nf9a_ 79 -------PGSMTEEQRGLLKDFWGPGMRASPADREVVEELAPGPDDWLL-----TKWRYS 126 d1jmva_ 92 ----QVLSDAIEQYDVDLLVTGHHQDFW-SKLMSSTRQVMNTIKIDMLVVPLRD------ 140 :::::::::::::::::: :::: :::::::::::: :::::::: d1nf9a_ 127 AFFHSDLLQRMRAAGRDQLVLC--GVYAHVGVLISTVDAYS-NDIQPFLV----ADAIAD 179 d1jmva_ 141 ---------------------------- 141 d1nf9a_ 180 FSEAHHRMALEYAASRCAMVVTTDEVLE 207 TMalign alignment (TM-score: 0.52 Raw score:72.40) d1jmva_ 1 ----------------------------MYKHILVAVDL----S-------E--ESPILL 19 ::::::::::: : : :::::: d1nf9a_ 1 MSGIPEITAYPLPTAQQLPANLARWSLEPRRAVLLVHDMQRYFLRPLPESLRAGLVANAA 60 d1jmva_ 20 KKAVGIAKRHDAKLSIIHVD------VNFSDLY---------TGLIDVNMSSMQDRIST- 63 ::::::::: :::::::::: :::: ::: d1nf9a_ 61 RLRRWCVEQ-GVQIAYTAQPGSMTEE---QRGLLKDFWGPGM--------------RASP 102 d1jmva_ 64 ETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYD--V-D-LLVTGHH-QDFWSKL 118 ::: ::::::: : :::::::::::::::: :::::::: : : ::::::: : :: d1nf9a_ 103 ADR-EVVEELA-P-GPDDWLLTKWRYSAFF-HSDLLQRMRAAGRDQLVLCGVY-A---HV 154 d1jmva_ 119 --MSST-RQVMNTIKIDMLVVPLR-D----------------------------- 140 :: ::::::::::::::::: : d1nf9a_ 155 GV--LISTVDAYSNDIQPFLVADAIADFSEAHHRMALEYAASRCAMVVTTDEVLE 207 HHsearch alignment (Probability: 0.23 E-value:0.05) d1jmva_ 93 VLSDAIEQYDVDLLVT 108 :::::::::::::::: d1nf9a_ 132 DLLQRMRAAGRDQLVL 147