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 <-- 1.085 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1enya_) 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 d1enya_ Enoyl-​ACP reductaseNAD(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 <-- 1.085 --> Hit
DALI alignment (Z-score: 5.6 Raw score:544.80) d1jmva_ 1 ----MYKHILVAVDLSEESpILLKKAVGIAKRhDAKLSIIHVDvnfsdlytglidvnmss 56 ::::::::::::::: :::::::::::: :::::::::: d1enya_ 1 agllDGKRILVSGIITDSS-IAFHIARVAQEQ-GAQLVLTGFD----------------- 41 d1jmva_ 57 mqdristeTQKALLDLAESVDYPIsEKLSGS---gDLGQVLSDAIEQY-----DVDLLVT 108 :::::::::::::::: :::::: ::::::::::::: ::::::: d1enya_ 42 --------RLRLIQRITDRLPAKA-PLLELDvqneEHLASLAGRVTEAigagnKLDGVVH 92 d1jmva_ 109 GHHQD-------------------FWSKL-MSSTRQVMNTIK------IDMLVVP----- 137 ::::: ::::: :::::::::::: ::::::: d1enya_ 93 SIGFMpqtgmginpffdapyadvsKGIHIsAYSYASMAKALLpimnpgGSIVGMDfdpsr 152 d1jmva_ 138 ------------------------------------------------------------ 138 d1enya_ 153 ampaynwmtvaksalesvnrfvareagkygvrsnlvaagpirtlamsaivggalgeeaga 212 d1jmva_ 138 -----------------------------------------------------lrd 140 d1enya_ 213 qiqlleegwdqrapigwnmkdatpvaktvcallsdwlpattgdiiyadggahtqll 268 FAST alignment (Normalized score: 4.72 Raw score:915.00) d1jmva_ 1 MY------KHILVAVDLSEES-------PILLKKAVGIAKRHDAKLSIIHVDVNFSDLYT 47 ::::: :::::::::::: ::::::::: d1enya_ 1 --AGLLDGKRILV--------SGIITDSSIAFHIARVAQE-QGAQLVLTG---------- 39 d1jmva_ 48 GLIDVNMSSMQDRISTE--TQKALLDLAESVDYPISEKLSGSG-----DLGQVLSDAIEQ 100 ::::::::::::::: :::::: :::::::::::: d1enya_ 40 -----------------FDRLRLIQRITDRLPAK-APLLEL--DVQNEEHLASLAGRVTE 79 d1jmva_ 101 -----YDVDLLVTGHHQD--------------------FWSK----LMSSTRQVMNTIK- 130 ::::::::: :::: ::::::::::: d1enya_ 80 AIGAGNKLDGVVHS----IGFMPQTGMGINPFFDAPYADVSKGIHISAYSYASMAKA--L 133 d1jmva_ 131 -------IDMLVVPLRD------------------------------------------- 140 :::::: d1enya_ 134 LPIMNPGGSIVGM----DFDPSRAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVA 189 d1jmva_ 141 ------------------------------------------------------------ 141 d1enya_ 190 AGPIRTLAMSAIVGGALGEEAGAQIQLLEEGWDQRAPIGWNMKDATPVAKTVCALLSDWL 249 d1jmva_ 141 ------------------- 141 d1enya_ 250 PATTGDIIYADGGAHTQLL 268 TMalign alignment (TM-score: 0.58 Raw score:81.57) d1jmva_ 1 ---M-YKHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSS 56 : :::::::::: :::::::::::::::: :::::::::: d1enya_ 1 AGLLDGKRILVSGII-TDSSIAFHIARVAQEQ-GAQLVLTGFD----------------- 41 d1jmva_ 57 MQDRISTETQKALLDLAESVDYPISEKLSGS--GD-LGQVLSDAIEQ-Y---D-VDLLVT 108 :::::::::::: :::::::::: :: ::::::::::: : : :::::: d1enya_ 42 --------RLRLIQRITDRL-PAKAPLLELDVQNEEHLASLAGRVTEAIGAGNKLDGVVH 92 d1jmva_ 109 GHHQD-----------------F--WSK--LMSSTRQVMNTIK--I----DMLVVP---- 137 ::::: : :: ::::::::::::: : :::::: d1enya_ 93 SIGFMPQTGMGINPFFDAPYADVSK-GIHISAYSYASMAKALLPIMNPGGSIVGMDFDPS 151 d1jmva_ 138 --------------------------------------L--R----D------------- 140 : : : d1enya_ 152 RAMPAYNWMTVAKSALESVNRFVAREAGKYGVRSNLVAAGPIRTLAMSAIVGGALGEEAG 211 d1jmva_ 141 --------------------------------------------------------- 141 d1enya_ 212 AQIQLLEEGWDQRAPIGWNMKDATPVAKTVCALLSDWLPATTGDIIYADGGAHTQLL 268 HHsearch alignment (Probability: 0.07 E-value:0.10) d1jmva_ 22 AVGIAKRHDAKLSIIH 37 ::::::: :::::::: d1enya_ 25 ARVAQEQ-GAQLVLTG 39