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 <-- 1.003 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1jkea_) 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 d1jkea_ D-​Tyr tRNAtyr deacylase,​ DTDDTD-​like (Pfam 02580)DTD-​like (Pfam 02580)α/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 <-- 1.003 --> Hit
DALI alignment (Z-score: 3.9 Raw score:324.60) d1jmva_ 1 ----------------------myKHILVAVDL-----sEESPILLKKAVG--------- 24 ::::::::: :::::::::::: d1jkea_ 1 mialiqrvtrasvtvegevtgeigAGLLVLLGVekdddeQKANRLCERVLGyrifsdaeg 60 d1jmva_ 25 ----IAKRHDAKLSIIHVDV--NFSDlytglidvnmssmqdriSTETQKALLDLAESVD- 77 :::::::::::::::: :::: :::::::::::::::: d1jkea_ 61 kmnlNVQQAGGSVLVVSQFTlaADTE-----rgmrpsfskgasPDRAEALYDYFVERCRq 115 d1jmva_ 78 --YPISEKLSGsgdlgqvlsDAIEqydvdllvtghhqdfwsklmsstrqvmntikIDMLV 135 ::::::::: :::: ::::: d1jkea_ 116 qeMNTQTGRFA------admQVSL---------------------------vndgPVTFW 142 d1jmva_ 136 VPLrd 140 ::: d1jkea_ 143 LQV-- 145 FAST alignment (Normalized score: 2.64 Raw score:376.50) d1jmva_ 1 MY------------------------KHILVAVDLSEE-SPILLKKAVGIAK-------- 27 :::::::::::: ::::::::::::: d1jkea_ 1 --MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDA 58 d1jmva_ 28 ---------RHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRIS---------------- 62 ::::::::::: d1jkea_ 59 EGKMNLNVQQAGGSVLVVSQ------------------------FTLAADTERGMRPSFS 94 d1jmva_ 63 -----TETQKALLDLAES-VDYPISEKLS------GSGDLGQVLSDAIEQYDVDLLVTGH 110 ::::::::::::: ::::: :::: d1jkea_ 95 KGASPDRAEALYDYFVERCRQQEM-----NTQTGRFAAD--------------------- 128 d1jmva_ 111 HQDFWSKLMSSTRQVMNTIK---------IDMLVVPLRD-- 140 :::::: d1jkea_ 129 --------------------MQVSLVNDGPVTFWL----QV 145 TMalign alignment (TM-score: 0.45 Raw score:62.82) d1jmva_ 1 ------MY----------------KHILVAVDL---SE--ESPILLKKAVG--------- 24 :: ::::::::: :: ::::::::::: d1jkea_ 1 MIALIQRVTRASVTVEGEVTGEIGAGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAEG 60 d1jmva_ 25 ----IAKRHDAKLSIIHVDV--N------FS-------DLYTGLIDVNMSSMQDRISTE- 64 :::::::::::::::: : :: :: d1jkea_ 61 KMNLNVQQAGGSVLVVSQFTLAADTERGMRPSFSKGAS-------------------PDR 101 d1jmva_ 65 TQKALLDLAESV--DYPISEKL-SGSGDLGQVLSDAIEQYDVDLLVTGHHQDFWSKLMSS 121 :::::::::::: :::::::: :::: : :: : :::: d1jkea_ 102 AEALYDYFVERCRQQEMNTQTGRFAAD----M--QV-S--LVND---------------- 136 d1jmva_ 122 TRQVMNTIKIDMLVVPLRD 140 ::::::::: d1jkea_ 137 --------GPVTFWLQV-- 145 HHsearch alignment (Probability: 0.01 E-value:0.39) d1jmva_ 31 AKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISE 82 :::::::::::::::::::::::::::::::::::::::::::::::::::: d1jkea_ 71 GSVLVVSQFTLAADTERGMRPSFSKGASPDRAEALYDYFVERCRQQEMNTQT 122