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 <-- 0.847 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1l5xa_) 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 d1l5xa_ SurE homolog PAE2908 (SurE-​alpha)SurE-​likeSurE-​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 <-- 0.847 --> Hit
DALI alignment (Z-score: 5.3 Raw score:539.50) d1jmva_ 1 myKHILVAV---DLSEESPILLKKAVGIAkrhdaKLSIIHVDV--------nFSDLYTGL 49 ::::::: ::::::::::::::::: ::::::::: :::::::: d1l5xa_ 1 --MKILVTNddgVHSPGLRLLYQFALSLG-----DVDVVAPESpksatglgiTLHKPLRM 53 d1jmva_ 50 IDVnmssmqdristetqkALLDLAesvdypiseKLSGSGDLGQVLSDAIEQY--DVDLLV 107 ::: :::::: ::::::::::::::::::: :::::: d1l5xa_ 54 YEV---------------DLCGFR---------AIATSGTPSDTVYLATFGLgrKYDIVL 89 d1jmva_ 108 T-GHHQ-DFWS-KLMSST-rQVMN---tIKIDMLVVPLRD-------------------- 140 : :::: :::: :::::: :::: :::::::::::: d1l5xa_ 90 SgINLGdNTSLqVILSSGtlGAAFqaalLGIPALAYSAYLenwnellnnkeaveimgavv 149 d1jmva_ 141 ------------------------------------------------------------ 141 d1l5xa_ 150 sstasyvlkngmpqgvdvisvnfprrlgrgvraklvkaaklryaqqvvervdprgvryyw 209 d1jmva_ 141 ------------------------------------------------------------ 141 d1l5xa_ 210 lygrdlapepetdvyvvlkeggiaitpltlnlnavdahrevdmdslnrmveyinaslskl 269 d1jmva_ 141 ------- 141 d1l5xa_ 270 aaalehh 276 FAST alignment (Normalized score: 3.83 Raw score:752.00) d1jmva_ 1 MYKHILVAV---DLSEESPILLKKAVGIAKRHD-AKLSIIHVDVNFSDLY---------- 46 ::::::: ::::::::::::::: :::::::: d1l5xa_ 1 --MKILVTNDDGVHSPGLRLLYQFALS------LGDVDVVAP--------ESPKSATGLG 44 d1jmva_ 47 ------TGLIDVNMSSMQDRISTETQKALLDLAESVDYPI-----SEKLSGSG---DLGQ 92 ::::: :::::::: :::: d1l5xa_ 45 ITLHKPLRMYE-----------------------------VDLCGFRAIATSGTPSDTVY 75 d1jmva_ 93 VLSDAIEQ--YDVDLLVTGHHQDFW---------------SKLMSSTRQVMNTIKIDMLV 135 ::::: :::::::: :::::::::::: ::::::: d1l5xa_ 76 LATFG---LGRKYDIVLS-------GINLGDNTSLQVILSSGTLGAAFQAAL-LGIPALA 124 d1jmva_ 136 VPLRD------------------------------------------------------- 140 ::: d1l5xa_ 125 YSA--YLENWNELLNNKEAVEIMGAVVSSTASYVLKNGMPQGVDVISVNFPRRLGRGVRA 182 d1jmva_ 141 ------------------------------------------------------------ 141 d1l5xa_ 183 KLVKAAKLRYAQQVVERVDPRGVRYYWLYGRDLAPEPETDVYVVLKEGGIAITPLTLNLN 242 d1jmva_ 141 ---------------------------------- 141 d1l5xa_ 243 AVDAHREVDMDSLNRMVEYINASLSKLAAALEHH 276 TMalign alignment (TM-score: 0.60 Raw score:84.01) d1jmva_ 1 MYKHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIHV-----DVNF-SDLYTGLIDVNM 54 :::::::::::: :::::::::::: ::::::::::: :::: :::::: :::: d1l5xa_ 1 -MKILVTNDDGVH-SPGLRLLYQFAL-SLGDVDVVAPESPKSATGLGITLHKPL-RMYE- 55 d1jmva_ 55 SSMQDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQ-Y-D-VDLLVTG-H 110 : ::: : :: ::::::: :: :::::::: : : ::::::: : d1l5xa_ 56 ---------------V--DLC-G-FR-AIATSGT-PS-DTVYLATFGLGRKYDIVLSGIN 93 d1jmva_ 111 -HQDFWSKLMS-S--TRQVMN--TIKIDMLVVPL-RD----------------------- 140 :::::::::: : :::::: ::::::::::: :: d1l5xa_ 94 LGDNTSLQVILSSGTLGAAFQAALLGIPALAYSAYLENWNELLNNKEAVEIMGAVVSSTA 153 d1jmva_ 141 ------------------------------------------------------------ 141 d1l5xa_ 154 SYVLKNGMPQGVDVISVNFPRRLGRGVRAKLVKAAKLRYAQQVVERVDPRGVRYYWLYGR 213 d1jmva_ 141 ------------------------------------------------------------ 141 d1l5xa_ 214 DLAPEPETDVYVVLKEGGIAITPLTLNLNAVDAHREVDMDSLNRMVEYINASLSKLAAAL 273 d1jmva_ 141 --- 141 d1l5xa_ 274 EHH 276 HHsearch alignment (Probability: 0.01 E-value:0.31) d1jmva_ 82 EKLSGSGDLGQVLSDAIE--QYDVDLLVTGHHQDF 114 :::::::::::::::::: ::::::::::::::: d1l5xa_ 62 RAIATSGTPSDTVYLATFGLGRKYDIVLSGINLGD 96