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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1jmva_ | Universal stress protein A, UspA | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1u0la2 | Probable GTPase EngC (YjeQ), C-terminal domain | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | α/β |
Query <-- 1.476 --> IntermediateDALI 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 <-- 1.388 --> HitDALI alignment (Z-score: 5.5 Raw score:413.60) d1jmva_ 1 ---------MYKHILVAVDL--SEESPILLKKAVGIAKRHDAKLSIIHVDVNfsdlytgl 49 ::::::::::: :::::::::::::::::::::::::::::: d1u0la2 1 nlltkphvaNVDQVILVVTVkmPETSTYIIDKFLVLAEKNELETVMVINKMD-------- 52 d1jmva_ 50 idvnmssmqdrisTETQKALLDLAESVdypiSEKLSGSGDlgqVLSDAIEQYD---vDLL 106 :::::::::::::: ::::::::: :::::::::: ::: d1u0la2 53 -------lydeddLRKVRELEEIYSGL----YPIVKTSAK-tgMGIEELKEYLkgkiSTM 100 d1jmva_ 107 VTGHhqdfwsklmsstrQVMNT---------------------IKID--MLVVP------ 137 :::: ::::: :::: ::::: d1u0la2 101 AGLS--------gvgksSLLNAinpglklrttttaqllkfdfgGYVVdtPGFANleindi 152 d1jmva_ 138 ---------------------------------------------------------lrd 140 d1u0la2 153 epeelkhyfkefgdkqcffsdcnhvdepecgvkeavengeiaesryenyvkmfyellgrr 212 FAST alignment (Normalized score: 3.57 Raw score:614.40) d1jmva_ 1 M----------YKHILVAVDLSEE------SPILLKKAVGIAKRHDAKLSIIHVDVNFSD 44 ::::::::: ::::::::::::::::::::::: d1u0la2 1 -NLLTKPHVANVDQVILVVT----VKMPETSTYIIDKFLVLAEKNELETVMVI------- 48 d1jmva_ 45 LYTGLIDVNMSSMQDRIS----------TETQKALLDLAESVDYP-ISEKLSGSG----- 88 :::::::::::: ::::::: d1u0la2 49 ------------------NKMDLYDEDDLRKVRELEEIYS-----GLYPIVKT--SAKTG 83 d1jmva_ 89 DLGQVLSDAIEQYDV-----DLLVTGHHQDFWSKLMS----STRQVMNTIKIDMLVVPLR 139 ::::::::: ::::: :::::::: d1u0la2 84 MGIEELKEY------LKGKISTMAG------------LSGVGKSSLLNA----------- 114 d1jmva_ 140 D----------------------------------------------------------- 140 d1u0la2 115 -INPGLKLRTTTTAQLLKFDFGGYVVDTPGFANLEINDIEPEELKHYFKEFGDKQCFFSD 173 d1jmva_ 141 --------------------------------------- 141 d1u0la2 174 CNHVDEPECGVKEAVENGEIAESRYENYVKMFYELLGRR 212 TMalign alignment (TM-score: 0.52 Raw score:72.81) d1jmva_ 1 ---------MYKHILVAVDLS--EESPILLKKAVGIAKRHDAKLSIIHVDVNF-----SD 44 :::::::::::: :::::::::::::::::::::::::::::: d1u0la2 1 NLLTKPHVANVDQVILVVTVKMPETSTYIIDKFLVLAEKNELETVMVINKMDLYDEDD-- 58 d1jmva_ 45 LYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYD-- 102 :::::::::::: ::: ::::::::: ::::::::::: d1u0la2 59 ------------------LRKVRELEEIYS---GLY-PIVKTSAKT-GMGIEELKEYLKG 95 d1jmva_ 103 V-DLLVTGHHQDFWSKLMSSTRQ-VM----NTI---------K-------ID--MLVVPL 138 : :::::::: : :::: :: ::: : :: :::::: d1u0la2 96 KISTMAGLSG------V--GKSSLLNAINPGLKLRTTTTAQLLKFDFGGYVVDTPGFANL 147 d1jmva_ 139 ------------------------------------------------------------ 139 d1u0la2 148 EINDIEPEELKHYFKEFGDKQCFFSDCNHVDEPECGVKEAVENGEIAESRYENYVKMFYE 207 d1jmva_ 139 -----RD 140 d1u0la2 208 LLGRR-- 212 HHsearch alignment (Probability: 0.32 E-value:0.01) d1jmva_ 5 ILVAVDL--SEESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRIS 62 ::::::: ::::::::::::::::::::::::::::: :::: : ::: d1u0la2 14 VILVVTVKMPETSTYIIDKFLVLAEKNELETVMVINKM---DLYD----E-------DDL 59 d1jmva_ 63 TETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQDFWSKLMSST 122 ::::: :::: :::::::::::::::::::::::::::: ::::::::::::: ::: d1u0la2 60 RKVRE-LEEI-YSGLYPIVKTSAKTGMGIEELKEYLKGK--ISTMAGLSGVGKS---SLL 112 d1jmva_ 123 RQVM 126 :::: d1u0la2 113 NAIN 116