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 <-- 0.695 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1u0ta_) 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 d1u0ta_ Inorganic polyphosphate/​ATP-​NAD kinase PpnKNAD kinase (Pfam 01513)NAD kinase (Pfam 01513)multi

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 <-- 0.695 --> Hit
DALI alignment (Z-score: 2.4 Raw score:232.20) d1jmva_ 1 myKHILVAVDLSEESPI-LLKKAVGIAKRHDAKLSIIHvdvnfsdlytglidvnmssmqd 59 ::::::::::::::: :::::::::::::::::::: d1u0ta_ 1 --RSVLLVVHTGRDEATeTARRVEKVLGDNKIALRVLS---------------------- 36 d1jmva_ 60 ristetqkalldlaesvdypiseklsgsgdlgqvlsdaieqydVDLLVTGHHqdfwsklm 119 ::::::::: d1u0ta_ 37 -------------------------------------------CELVLVLGG----dgtf 49 d1jmva_ 120 sstrQVMNTIKIDMLVVPLRD--------------------------------------- 140 ::::::::::::::::: d1u0ta_ 50 lraaELARNASIPVLGVNLGRigflaeaeaeaidavlehvvaqdyrvedrltldvvvrqg 109 d1jmva_ 141 ------------------------------------------------------------ 141 d1u0ta_ 110 grivnrgwalnevslekgprlgvlgvvveidgrpvsafgcdgvlvstptgstayafsagg 169 d1jmva_ 141 ------------------------------------------------------------ 141 d1u0ta_ 170 pvlwpdleailvvpnnahalfgrpmvtspeatiaieieadghdalvfcdgrremlipags 229 d1jmva_ 141 -------------------------------------- 141 d1u0ta_ 230 rlevtrcvtsvkwarldsapftdrlvrkfrlpvtgwrg 267 FAST alignment (Normalized score: 1.58 Raw score:305.20) d1jmva_ 1 -----------------------------------MYKHILVAVDLSEE--SPILLKKAV 23 ::::::: ::::::::: d1u0ta_ 1 RSVLLVVHTGRDEATETARRVEKVLGDNKIALRVLSCELVLV-------LGGDGTFLRAA 53 d1jmva_ 24 GIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEK 83 :::::::::::::: d1u0ta_ 54 ELARNASIPVLGVN---------------------------------------------- 67 d1jmva_ 84 LSGSGD-------------LGQVLSDAIEQYDVDLLVTGHHQDFWSKLMSSTRQVMNTIK 130 :::::::::: d1u0ta_ 68 ------LGRIGFLAEAEAEAIDAVLEHVV------------------------------- 90 d1jmva_ 131 IDMLVVPLRD-------------------------------------------------- 140 d1u0ta_ 91 ----------AQDYRVEDRLTLDVVVRQGGRIVNRGWALNEVSLEKGPRLGVLGVVVEID 140 d1jmva_ 141 ------------------------------------------------------------ 141 d1u0ta_ 141 GRPVSAFGCDGVLVSTPTGSTAYAFSAGGPVLWPDLEAILVVPNNAHALFGRPMVTSPEA 200 d1jmva_ 141 ------------------------------------------------------------ 141 d1u0ta_ 201 TIAIEIEADGHDALVFCDGRREMLIPAGSRLEVTRCVTSVKWARLDSAPFTDRLVRKFRL 260 d1jmva_ 141 ------- 141 d1u0ta_ 261 PVTGWRG 267 TMalign alignment (TM-score: 0.36 Raw score:50.51) d1jmva_ 1 MYKHILVAVDLSEESPI-LLKKAVGIAKRHDAKLSIIH----------VDVNFSDLYTGL 49 ::::::::::::::: :::::::::::::::::::: d1u0ta_ 1 --RSVLLVVHTGRDEATETARRVEKVLGDNKIALRVLSCELVLVLGGD------------ 46 d1jmva_ 50 IDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTG 109 ::::::::::::::::::::: d1u0ta_ 47 ---------------------------------------GTFLRAAELARNASIPVLGVN 67 d1jmva_ 110 HHQDFWSKLMSSTR---------------------------------------------- 123 :: : :::::: d1u0ta_ 68 LG-R----IGFLAEAEAEAIDAVLEHVVAQDYRVEDRLTLDVVVRQGGRIVNRGWALNEV 122 d1jmva_ 124 -----------------------------------QV--------------MN------- 127 :: : d1u0ta_ 123 SLEKGPRLGVLGVVVEIDGRPVSAFGCDGVLVSTPTGSTAYAFSAGGPVLW-PDLEAILV 181 d1jmva_ 128 ----------------------------------------------------------TI 129 :: d1u0ta_ 182 VPNNAHALFGRPMVTSPEATIAIEIEADGHDALVFCDGRREMLIPAGSRLEVTRCVTSVK 241 d1jmva_ 130 KIDM----------------------LVVPLRD 140 :::: d1u0ta_ 242 WARLDSAPFTDRLVRKFRLPVTGWRG------- 267 HHsearch alignment (Probability: 0.07 E-value:0.05) d1jmva_ 3 KHILVAVD-LSEESPILLKKAVGIAKRHDAKLSII 36 :::::::: :::::::::::::::::::::::::: d1u0ta_ 1 RSVLLVVHTGRDEATETARRVEKVLGDNKIALRVL 35