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 | d1g99a2 | Acetate kinase | Actin-like ATPase domain | Ribonuclease H-like motif | 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 <-- 0.668 --> HitDALI alignment (Z-score: 2.3 Raw score:280.90) d1jmva_ 1 -------------mykhilvavdLSEESPILLKKAVGIAKRHdAKLSiihvdvnfsdlyt 47 ::::::::::::::::::: :::: d1g99a2 1 pyaymyalpydlyekhgvrkygfHGTSHKYVAERAALMLGKPaEETK------------- 47 d1jmva_ 48 glidvnmssmqdristetqkalldlaesvdypISEKLSGS-------------------- 87 :::::::: d1g99a2 48 ---------------iitchlgngssitavegGKSVETSMgftpleglamgtrcgsidpa 92 d1jmva_ 88 ----------------------------------------------------------gD 89 : d1g99a2 93 ivpflmekeglttreidtlmnkksgvlgvsglsndfrdldeaaskgnrkaelaleifayK 152 d1jmva_ 90 LGQVLSDAIEQY-DVDLLVTGHHqdfwsKLMSSTRQVMN---tIKID------------- 132 :::::::::::: :::::::::: ::::::::::: :::: d1g99a2 153 VKKFIGEYSAVLnGADAVVFTAG--igeNSASIRKRILTgldgIGIKiddeknkirgqei 210 d1jmva_ 133 ----------MLVVPLR--------------d 140 ::::::: d1g99a2 211 distpdakvrVFVIPTNeelaiaretkeivet 242 FAST alignment (Normalized score: 2.51 Raw score:461.20) d1jmva_ 1 MYKHILVAVDLSEE-----------------------SPILLKKAVGIAKR------HDA 31 :::::::::::::: ::: d1g99a2 1 --------------PYAYMYALPYDLYEKHGVRKYGFHGTSHKYVAERAALMLGKPAEET 46 d1jmva_ 32 KLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVD------------YP 79 :::::: :: d1g99a2 47 KIITCH----------------------------------------LGNGSSITAVEGGK 66 d1jmva_ 80 ISEKLSGSG--------------------------------------------------- 88 :::: d1g99a2 67 SVET-----SMGFTPLEGLAMGTRCGSIDPAIVPFLMEKEGLTTREIDTLMNKKSGVLGV 121 d1jmva_ 89 --------------------------DLGQVLSDAIEQ-----YDVDLLVTGHHQDFWSK 117 :::::::::::: :::::::: d1g99a2 122 SGLSNDFRDLDEAASKGNRKAELALEIFAYKVKKFIGEYSAVLNGADAVVF--------- 172 d1jmva_ 118 -------LMSSTRQVMNTI---------------------------KIDMLVVPLRD--- 140 ::::::::::: ::::::::: d1g99a2 173 TAGIGENSASIRKRILTG-LDGIGIKIDDEKNKIRGQEIDISTPDAKVRVFVIPT--NEE 229 d1jmva_ 141 ------------- 141 d1g99a2 230 LAIARETKEIVET 242 TMalign alignment (TM-score: 0.46 Raw score:64.43) d1jmva_ 1 ---------------------MYKHILVAVDLSEESPILLKKAVG-IAKRHDAKLSIIHV 38 :::::::::::::::: :::::::::::::: d1g99a2 1 PYAYMYALPYDLYEKHGVRKY--------GFHGTSHKYVAERAALMLGKPAEETKIITCH 52 d1jmva_ 39 ---DVNFSDLYTGLIDVNMSSMQDRISTET-QKALLDLAESVDYPISEKLSG-------S 87 :: : :: : ::::::::: : d1g99a2 53 LGNGS------------------------SI---TA--V----EGGKSVETSMGFTPLEG 79 d1jmva_ 88 G----------------------------------------------------------- 88 : d1g99a2 80 LAMGTRCGSIDPAIVPFLMEKEGLTTREIDTLMNKKSGVLGVSGLSNDFRDLDEAASKGN 139 d1jmva_ 89 ------------DLGQVLSDAIEQ--YDVDLLVTGHHQDFWSKLMSSTRQVMNTIK---I 131 :::::::::: : ::::::::::::::: ::::::::::::: : d1g99a2 140 RKAELALEIFAYKVKKFIGEYS-AVLNGADAVVFTAGIGEN--SASIRKRILTGLDGIGI 196 d1jmva_ 132 -----------------------DMLVVPLR-D------------- 140 :::::::: : d1g99a2 197 KIDDEKNKIRGQEIDISTPDAKVRVFVIPTNEELAIARETKEIVET 242 HHsearch alignment (Probability: 0.05 E-value:0.01) d1jmva_ 127 NTIKIDMLVVPLRD 140 :::::::::::::: d1g99a2 215 PDAKVRVFVIPTNE 228