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 <-- 1.911 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1iira_) 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 d1iira_ UDP-​glucosyltransferase GtfBUDP-​Glycosyltransferase/​glycogen phosphorylaseUDP-​Glycosyltransferase/​glycogen phosphorylaseα/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 <-- 1.911 --> Hit
DALI alignment (Z-score: 5.9 Raw score:519.70) d1jmva_ 1 myKHILVAVDLSEE-SPILLKKAVGIAKRhDAKLSIIHvdvnfsdlytglidvnmssmqd 59 :::::::::::: :::::::::::::: :::::::: d1iira_ 1 --MRVLLATCGSRGdTEPLVALAVRVRDL-GADVRMCA---------------------- 35 d1jmva_ 60 ristetqkALLDLAESVDypisEKLSGS-------------------GDLGQVLSDAIEq 100 :::::::::: :::::: :::::::::::: d1iira_ 36 ------ppDCAERLAEVG---vPHVPVGprakpltaedvrrftteaiATQFDEIPAAAE- 85 d1jmva_ 101 yDVDLLVTGHhqdfwskLMSSTRQVMNTI---KIDMLVVPLR------------------ 139 ::::::::: :::::::::::: :::::::::: d1iira_ 86 -GCAAVVTTG-------LLAAAIGVRSVAeklGIPYFYAFHCpsyvpspyyppppidipa 137 d1jmva_ 140 ------------------------------------------------------------ 140 d1iira_ 138 qwernnqsayqryggllnshrdaiglppvediftfgytdhpwvaadpvlaplqptdldav 197 d1jmva_ 140 ------------------------------------------------------------ 140 d1iira_ 198 qtgawilpderplspelaafldagpppvylgfgapadavrvaidairahgrrvilsrgwa 257 d1jmva_ 140 ------------------------------------------------------------ 140 d1iira_ 258 dlvlpddgadcfaigevnhqvlfgrvaavihhggagtthvaaragapqillpqmadqpyy 317 d1jmva_ 140 ------------------------------------------------------------ 140 d1iira_ 318 agrvaelgvgvahdgpiptfdslsaalataltpetharatavagtirtdgaavaarllld 377 d1jmva_ 140 ----d 140 d1iira_ 378 avsre 382 FAST alignment (Normalized score: 4.38 Raw score:1013.00) d1jmva_ 1 MYKHILVAVDLSE-ESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQD 59 ::::::::::: :::::::::::::: :::::::: d1iira_ 1 --MRVLLATCGSRGDTEPLVALAVRVRD-LGADVRMC----------------------- 34 d1jmva_ 60 RISTETQ--KALLDLAESVDYPISEKLSGSG----------------------DLGQVLS 95 :::::::: :::: :::: ::::::: d1iira_ 35 -------APPDCAERLA--EVGV-PHVP---VGPRAKPLTAEDVRRFTTEAIATQFDEIP 81 d1jmva_ 96 DAIEQYDVDLLVTGHHQDFWSK--LMSSTRQVMN---TIKIDMLVVPLRD---------- 140 ::: :::::::: :::::::::: :::::::::: d1iira_ 82 AAA--EGCAAVVT---------TGLLAAAIGVRSVAEKLGIPYFYAF---HCPSYVPSPY 127 d1jmva_ 141 ------------------------------------------------------------ 141 d1iira_ 128 YPPPPIDIPAQWERNNQSAYQRYGGLLNSHRDAIGLPPVEDIFTFGYTDHPWVAADPVLA 187 d1jmva_ 141 ------------------------------------------------------------ 141 d1iira_ 188 PLQPTDLDAVQTGAWILPDERPLSPELAAFLDAGPPPVYLGFGAPADAVRVAIDAIRAHG 247 d1jmva_ 141 ------------------------------------------------------------ 141 d1iira_ 248 RRVILSRGWADLVLPDDGADCFAIGEVNHQVLFGRVAAVIHHGGAGTTHVAARAGAPQIL 307 d1jmva_ 141 ------------------------------------------------------------ 141 d1iira_ 308 LPQMADQPYYAGRVAELGVGVAHDGPIPTFDSLSAALATALTPETHARATAVAGTIRTDG 367 d1jmva_ 141 --------------- 141 d1iira_ 368 AAVAARLLLDAVSRE 382 TMalign alignment (TM-score: 0.48 Raw score:67.33) d1jmva_ 1 MYKHILVAVDLSEE-SPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQD 59 :::::::::::: :::::::::::::: :::::::: d1iira_ 1 --MRVLLATCGSRGDTEPLVALAVRVRDL-GADVRMCA---------------------- 35 d1jmva_ 60 RISTETQKALLDLAESVDYPISEKLS----------------GSG--------------- 88 :::::::::: ::::::::: ::: d1iira_ 36 ------PPDCAERLAE-VGVPHVPVGPRAKPLTAEDVRRFTTEAIATQFDEIPAAAEGCA 88 d1jmva_ 89 --------DLGQVLSDAIEQYDVDLLVTGHHQDFWSKLMS-------------------- 120 :::::::::::::::::::::: : :: ::: d1iira_ 89 AVVTTGLLAAAIGVRSVAEKLGIPYFYAFH-C-PS--YVPSPYYPPPPIDIPAQWERNNQ 144 d1jmva_ 121 ------------------------STRQVMNTIKIDMLVVP------------------- 137 ::::::: : :::::: d1iira_ 145 SAYQRYGGLLNSHRDAIGLPPVEDIFTFGYT-D--HPWVAADPVLAPLQPTDLDAVQTGA 201 d1jmva_ 138 ------------------------------------------------------------ 138 d1iira_ 202 WILPDERPLSPELAAFLDAGPPPVYLGFGAPADAVRVAIDAIRAHGRRVILSRGWADLVL 261 d1jmva_ 138 ------------------------------LRD--------------------------- 140 ::: d1iira_ 262 PDDGADCFAIGEVNHQVLFGRVAAVIHHGGAGTTHVAARAGAPQILLPQMADQPYYAGRV 321 d1jmva_ 141 ------------------------------------------------------------ 141 d1iira_ 322 AELGVGVAHDGPIPTFDSLSAALATALTPETHARATAVAGTIRTDGAAVAARLLLDAVSR 381 d1jmva_ 141 - 141 d1iira_ 382 E 382 HHsearch alignment (Probability: 0.17 E-value:0.16) d1jmva_ 4 HILVAVDLS-EESPILLKKAVGIAKRHDAKLSIIH 37 ::::::::: :::::::::::::::: :::::::: d1iira_ 2 RVLLATCGSRGDTEPLVALAVRVRDL-GADVRMCA 35