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 | d2uaga1 | UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase MurD | MurCD N-terminal domain | MurCD N-terminal 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 <-- 1.240 --> HitDALI alignment (Z-score: 5.9 Raw score:361.90) d1jmva_ 1 ---MYKHILVAVdlseeSPILLKKAVGIAKRhDAKLSIIHVdvnfsdlytglidvnmssm 57 ::::::::: :::::::::::::: ::::::::: d2uaga1 1 adyQGKNVVIIG----lGLTGLSCVDFFLAR-GVTPRVMDT------------------- 36 d1jmva_ 58 qdristeTQKAllDLAESVDYPiSEKLSGsgdlgqVLSDAIEqyDVDLLVTGHhqdfwsk 117 :::: ::::::::: :::::: ::::::: ::::::::: d2uaga1 37 -------RMTP--PGLDKLPEA-VERHTG-----sLNDEWLM--AADLIVASP------- 72 d1jmva_ 118 lmsSTRQ-VMNTI---KIDMLVvplrd 140 :::: ::::: :::::: d2uaga1 73 -giALAHpSLSAAadaGIEIVG----- 93 FAST alignment (Normalized score: 3.68 Raw score:420.20) d1jmva_ 1 MY-----KHILVAVDLSEE---SPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDV 52 ::::: ::::::::::::: ::::::::: d2uaga1 1 --ADYQGKNVVI-------IGLGLTGLSCVDFFLA-RGVTPRVMD--------------- 35 d1jmva_ 53 NMSSMQDRISTETQKAL----LDLAESVDYPI----SEKLSGSGDLGQV----LSDAIEQ 100 :::::: :::: :::::: d2uaga1 36 -----------------TRMTPPGLDK-----LPEAVERH---------TGSLNDEWLM- 63 d1jmva_ 101 YDVDLLVTGHHQDFWSKLMSST-------RQVMNT---IKIDMLVVPLRD- 140 ::::::: :::::: :::::: d2uaga1 64 -AADLIVA--------------SPGIALAHPSLSAAADAGIEIV------G 93 TMalign alignment (TM-score: 0.45 Raw score:63.27) d1jmva_ 1 ---MYKHILVAVDLSEESPILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSM 57 ::::::::: : :::::::::::::: ::::::::: d2uaga1 1 ADYQGKNVVIIG-L---GLTGLSCVDFFLAR-GVTPRVMDT------------------- 36 d1jmva_ 58 QDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHH-QDFWS 116 :: :: :::::::::: :::::: ::::::: :::::::::: d2uaga1 37 -------RM-TP-PGLDKLPEAV-ERHTGS-----LNDEWLM--AADLIVASPGI----- 74 d1jmva_ 117 KLMSST--RQ-VMNTIKIDMLVVPLRD 140 : ::: :: ::: ::::::: d2uaga1 75 -A-LAHPSLSAAAD-AGIEIVG----- 93 HHsearch alignment (Probability: 0.01 E-value:0.29) d1jmva_ 21 KAVGIAKRHDAKLSIIH 37 ::::::::::::::::: d2uaga1 19 SCVDFFLARGVTPRVMD 35