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 <-- 0.760 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1j09a2) 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 d1j09a2 Glutamyl-​tRNA synthetase (GluRS)Nucleotidylyl transferaseAdenine nucleotide alpha hydrolase-​likeα/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 <-- 0.760 --> Hit
DALI alignment (Z-score: 7.3 Raw score:620.30) d1jmva_ 1 mYKHILVAVD----lSEESPILLKKAVGIAKRHDAKLSIIHVDVNfsdlytglidvnmss 56 ::::::::: :::::::::::::::::::::::::::::: d1j09a2 1 -MVVTRIAPSptgdpHVGTAYIALFNYAWARRNGGRFIVRIEDTD--------------- 44 d1jmva_ 57 mqdriSTETQKALLDLAESVDYPISEK---------LSGS-------------------- 87 :::::::::::::::::::::: :::: d1j09a2 45 -raryVPGAEERILAALKWLGLSYDEGpdvggphgpYRQSerlplyqkyaeellkrgway 103 d1jmva_ 88 ------------------------------------------------------------ 88 d1j09a2 104 rafetpeeleqirkekggydgrarnippeeaeerarrgephvirlkvprpgttevkdelr 163 d1jmva_ 88 ---------------------GDLGQVLSDAIEQYDVDLLVTGHHqdfwskLMSSTRQVM 126 :::::::::::::::::::::::: ::::::::: d1j09a2 164 gvvvydnqeipdvvllksdgyPTYHLANVVDDHLMGVTDVIRAEE------WLVSTPIHV 217 d1jmva_ 127 NTI------KIDMLVVPLRD---------------------------------------- 140 ::: ::::::::::: d1j09a2 218 LLYrafgweAPRFYHMPLLRnpdktkiskrkshtsldwykaegflpealrnylclmgfsm 277 d1jmva_ 141 ---------------------------- 141 d1j09a2 278 pdgreiftleefiqaftwervslggpvf 305 FAST alignment (Normalized score: 5.79 Raw score:1196.00) d1jmva_ 1 MYKHILVAVD----LSEESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSS 56 ::::::::: :::::::::::::::::::::::::::: d1j09a2 1 -MVVTRIAPSPTGDPHVGTAYIALFNYAWARRNGGRFIVRIE------------------ 41 d1jmva_ 57 MQDRIS--------TETQKALLDLAESVDYPISEKLSGS--------------------- 87 :::::::::::::::::::: d1j09a2 42 ------DTDRARYVPGAEERILAALKWLGLSYDE-----GPDVGGPHGPYRQSERLPLYQ 90 d1jmva_ 88 ------------------------------------------------------------ 88 d1j09a2 91 KYAEELLKRGWAYRAFETPEELEQIRKEKGGYDGRARNIPPEEAEERARRGEPHVIRLKV 150 d1jmva_ 88 ----------------------------------GDLGQVLSDAIEQYDVDLLVTGHHQD 113 ::::::::::::::::::::: d1j09a2 151 PRPGTTEVKDELRGVVVYDNQEIPDVVLLKSDGYPTYHLANVVDDHLMGVTDVIR----- 205 d1jmva_ 114 FWSK---LMSSTRQVMNTI-------KIDMLVVPLRD----------------------- 140 ::::::::::: :::::::: d1j09a2 206 ----AEEWLVSTPIHVLL-YRAFGWEAPRFYHMP---LLRNPDKTKISKRKSHTSLDWYK 257 d1jmva_ 141 ------------------------------------------------ 141 d1j09a2 258 AEGFLPEALRNYLCLMGFSMPDGREIFTLEEFIQAFTWERVSLGGPVF 305 TMalign alignment (TM-score: 0.62 Raw score:87.46) d1jmva_ 1 MYKHILVAVD----LSEESPILLKKAVGIAKRHDAKLSIIHVDVNF---SDLYTGLIDVN 53 ::::::::: :::::::::::::::::::::::::::::::: d1j09a2 1 -MVVTRIAPSPTGDPHVGTAYIALFNYAWARRNGGRFIVRIEDTDRARY----------- 48 d1jmva_ 54 MSSMQDRISTETQKALLDLAESVDYPISEK---------LSGS----------------- 87 :::::::::::::::::::::: :::: d1j09a2 49 --------VPGAEERILAALKWLGLSYDEGPDVGGPHGPYRQSERLPLYQKYAEELLKRG 100 d1jmva_ 88 ------------------------------------------------------------ 88 d1j09a2 101 WAYRAFETPEELEQIRKEKGGYDGRARNIPPEEAEERARRGEPHVIRLKVPRPGTTEVKD 160 d1jmva_ 88 ------------------------GDLGQVLSDAIEQYDVDLLVTGHHQDFWSKLMSSTR 123 :::::::::::::::::::::::: ::: ::: d1j09a2 161 ELRGVVVYDNQEIPDVVLLKSDGYPTYHLANVVDDHLMGVTDVIRAEE-----WLV-STP 214 d1jmva_ 124 QVMNTI------KIDMLVVPLRD------------------------------------- 140 :::::: ::::::::::: d1j09a2 215 IHVLLYRAFGWEAPRFYHMPLLRNPDKTKISKRKSHTSLDWYKAEGFLPEALRNYLCLMG 274 d1jmva_ 141 ------------------------------- 141 d1j09a2 275 FSMPDGREIFTLEEFIQAFTWERVSLGGPVF 305 HHsearch alignment (Probability: 0.00 E-value:0.68) d1jmva_ 16 PILLKKAVGIAKRHDAKLSI 35 :::::::::::::::::::: d1j09a2 19 AYIALFNYAWARRNGGRFIV 38