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 | d1o5za1 | Folylpolyglutamate synthetase, C-terminal domain | MurD-like peptide ligases, peptide-binding domain | MurD-like peptide ligases, peptide-binding domain | 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 <-- 1.621 --> HitDALI alignment (Z-score: 4.3 Raw score:335.00) d1jmva_ 1 -------------------------------------MYKHILVAVDLSEESPILLKKAV 23 ::::::::::::::::::::::: d1o5za1 1 grfeilekngkmyildgahnphgaeslvrslklyfngEPLSLVIGILDDKNREDILRKYT 60 d1jmva_ 24 GIAkrhdAKLSIIHVDVNfsdlytglidvnmssmqdristeTQKALLDLAESVdYPISEK 83 ::: ::::::::::: :::::::::::: :::::: d1o5za1 61 GIF----ERVIVTRVPSP--------------------rmkDMNSLVDMAKKF-FKNVEV 95 d1jmva_ 84 LSgsgdlgqVLSDAIEQYD-vDLLVTGHhqdfwsklmsstRQVMNTIkidmlvvplrd 140 :: :::::::::: ::::::: ::::::: d1o5za1 96 IE-------DPLEAIESTEraTVVTGSL---------flvGYVREFLttgkineewkl 137 FAST alignment (Normalized score: 2.70 Raw score:374.00) d1jmva_ 1 MY---------KHILVAVDLSEE---SPILLKKAVGIAKR--HDAKLSIIHVDVNFSDLY 46 ::::::: :::::::::::::: ::::::::: d1o5za1 1 --GRFEILEKNGKMYILD-----GAHNPHGAESLVRSLKLYFNGEPLSLVI--------- 44 d1jmva_ 47 TGLIDVNMSSMQDRISTETQK------ALLDLAESVDY----PISEKLSG---------- 86 ::::::: :::::::: d1o5za1 45 ---------------------GILDDKNREDILR----KYTGIFERVIVTRVPSPRMKDM 79 d1jmva_ 87 ----------------SGDLGQVLSDAIEQYDV--DLLVTGHHQDFWSK------LMSST 122 :::::::::: ::::: ::::: d1o5za1 80 NSLVDMAKKFFKNVEVIEDPLEAIES-------TERATVV---------TGSLFLVGYVR 123 d1jmva_ 123 RQVMNTIKIDMLVVPLRD---------- 140 :::: d1o5za1 124 EFLT--------------TGKINEEWKL 137 TMalign alignment (TM-score: 0.40 Raw score:55.48) d1jmva_ 1 ----------MYKHILVAVDLSE--ESPILLKKAVGIAKRHDAKLSIIH----------- 37 :::::::::: :::::::::::::: :::::::: d1o5za1 1 GRFEILEKNG---KMYILDGAHNPHGAESLVRSLKLYFN--GEPLSLVIGILDDKNREDI 55 d1jmva_ 38 -------------VDVNF-----SDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYP 79 ::::: ::::::::::::: d1o5za1 56 LRKYTGIFERVIVTRVPSPRMKD-------------------MNSLVDMAKKFFK----- 91 d1jmva_ 80 ISEKLSGSGDLGQVLSDAIEQYDVDLLVTG-HHQD-FWSKLMSSTRQVM-NT-------I 129 ::::::: ::::::: : :: ::::: :: : :: ::::::: :: d1o5za1 92 --NVEVIED-PLEAIES-T---ER-ATVVTGSL-FL---VG-YVREFLTTGKINEEWKL- 137 d1jmva_ 130 KIDMLVVPLRD 140 d1o5za1 138 ----------- 138 HHsearch alignment (Probability: 0.01 E-value:0.75) d1jmva_ 4 HILVAVDLSEESPILLKKAVGIAKRH-DAKLSIIHVDV 40 :::::::::::::::::::::::::: ::::::::::: d1o5za1 10 GKMYILDGAHNPHGAESLVRSLKLYFNGEPLSLVIGIL 47