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 | d1jwqa_ | N-acetylmuramoyl-L-alanine amidase CwlV | Zn-dependent exopeptidases | Phosphorylase/hydrolase-like | 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 <-- 1.534 --> HitDALI alignment (Z-score: 4.3 Raw score:378.80) d1jmva_ 1 myKHILVAVD----------------lSEES-PILLKKAVGIAKRHDAKLSIIHvdvnfs 43 :::::::: :::: :::::::::::::::::::::: d1jwqa_ 1 -mKVVVIDAGhgakdsgavgisrknyeKTFNlAMALKVESILKQNPKLEVVLTR------ 53 d1jmva_ 44 dlytglidvnmssmqdristetqkalldlaesvdypiseklsgSGDLgQVLSDAIEQYDV 103 :::: :::::::::::: d1jwqa_ 54 ---------------------------------------sddtFLEL-KQRVKVAENLKA 73 d1jmva_ 104 DLLVTGHHQDF------------------------------------wsklMSSTrQVMN 127 ::::::::::: :::: :::: d1jwqa_ 74 NVFVSIHANSSgssasngtetyyqrsaskafanvmhkyfapatgltdrgirYGNF-HVIR 132 d1jmva_ 128 TIKIDMLVVPLR----------------------------------d 140 :::::::::::: d1jwqa_ 133 ETTMPAVLLEVGylsnakeeatlfdedfqnrvaqgiadgiteyldvk 179 FAST alignment (Normalized score: 4.41 Raw score:698.50) d1jmva_ 1 MY-KHILVAVDLS----------------EESPILLKKAVGIAKRH-----DAKLSIIHV 38 ::::::: :::::::::::::::: :::::: d1jwqa_ 1 --MKVVVIDA---GHGAKDSGAVGISRKNYEKTFNLAMALKVESI-LKQNPKLEVVL--- 51 d1jmva_ 39 DVNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSGSGD--------L 90 : d1jwqa_ 52 ---------------------------------------------------TRSDDTFLE 60 d1jmva_ 91 GQVLSDAIEQYDVDLLVTGHHQDFWSKLMSST---------------------------- 122 :::::::::::::::::::::: d1jwqa_ 61 LKQRVKVAENLKANVFVSIHAN----------SSGSSASNGTETYYQRSASKAFANVMHK 110 d1jmva_ 123 -----------------RQVMNTIKIDMLVVPLRD------------------------- 140 :::::::::::::::: d1jwqa_ 111 YFAPATGLTDRGIRYGNFHVIRETTMPAVLLEV--GYLSNAKEEATLFDEDFQNRVAQGI 168 d1jmva_ 141 ----------- 141 d1jwqa_ 169 ADGITEYLDVK 179 TMalign alignment (TM-score: 0.45 Raw score:62.63) d1jmva_ 1 MYKHILVAVDL---S---------EESPILLKKAVGIAKRHD-----AKLSIIHVDVNFS 43 ::::::::::: : :::::::::::::::::: :::::: d1jwqa_ 1 MKVVVIDAGHGAKDSGAVGISRKNYEKTFNLAMALKVESILKQNPKLEVVLTR------- 53 d1jmva_ 44 DLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSGSGDLGQV-LSDAIEQYD 102 :::: ::: : : ::::::::: d1jwqa_ 54 --------------------------SDDT----------FLE---L--KQRVKVAENLK 72 d1jmva_ 103 V-DLLVTGHHQDF---W-----SKL----------------------------MSSTRQV 125 : ::::::::::: : : :: :::: d1jwqa_ 73 ANVFVSIHANSSGSSASNGTET--YYQRSASKAFANVMHKYFAPATGLTDRGIRY-GNFH 129 d1jmva_ 126 -MNTI-KIDMLVVPL-R-----D--------------------------- 140 :::: ::::::::: : : d1jwqa_ 130 VIRETTMPAVLLEVGYLSNAKEEATLFDEDFQNRVAQGIADGITEYLDVK 179 HHsearch alignment (Probability: 0.12 E-value:0.08) d1jmva_ 62 STETQKALLDLAESV-DYPISEKLSGSG---DLGQVLSDAIEQYDVDLLVT 108 ::::::::::::::: :::::: :::: :::::::::::::::::::: d1jwqa_ 30 NLAMALKVESILKQNPKLEVVL--TRSDDTFLELKQRVKVAENLKANVFVS 78