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 <-- 1.526 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1xeaa1) 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 d1xeaa1 Putative oxidoreductase VCA1048NAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/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 <-- 1.526 --> Hit
DALI alignment (Z-score: 6.4 Raw score:446.70) d1jmva_ 1 myKHILVAVDLsEESP-ILLKKAVGIakrHDAKLSIIHVdvnfsdlytglidvnmssmqd 59 ::::::::: :::: ::::::::: :::::::::: d1xeaa1 1 -sLKIAMIGLG-DIAQkAYLPVLAQW---PDIELVLCTR--------------------- 34 d1jmva_ 60 risteTQKALLDLAESVdyPISEKLSgsgdlgqVLSDAIeQYDVDLLVTGhhqdfwsklM 119 :::::::::::: ::::::: :::::: :::::::::: : d1xeaa1 35 -----NPKVLGTLATRY--RVSATCT-------DYRDVL-QYGVDAVMIH-------aaT 72 d1jmva_ 120 SSTRQVMNTI---KIDMLVV--------------------------PLRD---------- 140 :::::::::: ::::::: :::: d1xeaa1 73 DVHSTLAAFFlhlGIPTFVDkplaasaqecenlyelaekhhqplyvGFNGfdamvqdwlq 132 d1jmva_ 141 ----------------------------------- 141 d1xeaa1 133 vaaagklpthiiernlashqlaeaicqqitqqvtk 167 FAST alignment (Normalized score: 4.36 Raw score:665.90) d1jmva_ 1 MYKHILVAVDLSEES-PILLKKAVGIAK-RHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQ 58 :::::: ::::::: :::::::: ::::::::: d1xeaa1 1 -SLKIAM-IGLGDIAQKAYLPVLA----QWPDIELVLC---------------------- 32 d1jmva_ 59 DRISTE--TQKALLDLAESVDYPISEKLSGSG---------------------DLGQVLS 95 :::::::::: :::::::: ::::::: d1xeaa1 33 ------TRNPKVLGTLAT--RYRVSATC----TDYRDVLQYGVDAVMIHAATDVHSTLAA 80 d1jmva_ 96 DAIEQYDV--DLLVTGHHQ-----DFWSKLMSSTRQVMNTIKIDMLVVPLRD-------- 140 :::: ::::: ::::::::::::::: :::::::: d1xeaa1 81 FFLH----LGIPTFV----DKPLAASAQECENLYELAEK-HHQPLYVG----FNGFDAMV 127 d1jmva_ 141 ---------------------------------------- 141 d1xeaa1 128 QDWLQVAAAGKLPTHIIERNLASHQLAEAICQQITQQVTK 167 TMalign alignment (TM-score: 0.52 Raw score:72.37) d1jmva_ 1 MYKHILVAVDLSEESP-ILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQD 59 :: :::::: :::::: :::::::: :: :::::::: : d1xeaa1 1 SL-KIAMIG-LGDIAQKAYLPVLAQ-WP--DIELVLCT-R-------------------- 34 d1jmva_ 60 RISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQDFWSKLM 119 :::::::::::: :::::::: :: ::: :::::::::::: : ::: d1xeaa1 35 -----NPKVLGTLATRY--RVSATCTD------YR-DVL-QYGVDAVMIHAA-T---DVH 75 d1jmva_ 120 SSTRQVMNTIKIDMLVVP-------------------------LR--------------- 139 :::::::::::::::::: :: d1xeaa1 76 STLAAFFLHLGIPTFVDKPLAASAQECENLYELAEKHHQPLYVGFNGFDAMVQDWLQVAA 135 d1jmva_ 140 --------------------------------D 140 d1xeaa1 136 AGKLPTHIIERNLASHQLAEAICQQITQQVTK- 167 HHsearch alignment (Probability: 0.04 E-value:0.06) d1jmva_ 67 KALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQDFWSKLMSST 122 :::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1xeaa1 103 ENLYELAEKHHQPLYVGFNGFDAMVQDWLQVAAAGKLPTHIIERNLASHQLAEAIC 158