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 | d1nqua_ | Lumazine synthase | Lumazine synthase | Lumazine synthase | 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 <-- 1.428 --> HitDALI alignment (Z-score: 5.5 Raw score:417.30) d1jmva_ 1 ----------MYKHILVAVDL--SEESPILLKKAVGIAKRHDA---KLSIIHVDvnfsdl 45 ::::::::::: :::::::::::::::::::: :::::::: d1nqua_ 1 mqiyegkltaEGLRFGIVASRfnHALVDRLVEGAIDCIVRHGGreeDITLVRVP------ 54 d1jmva_ 46 ytglidvnmssmqdristetqkalldlaesvdypiseklsgsgdLGQVLSDAIEQYDVDL 105 :::::::::::::::: d1nqua_ 55 ----------------------------------------gsweIPVAAGELARKEDIDA 74 d1jmva_ 106 LVTGHHQD------FWSKLMSSTRQVMNTI---KIDMLVVPL------------------ 138 :::::::: :::::::::::::::: ::::::::: d1nqua_ 75 VIAIGVLIrgatphFDYIASEVSKGLANLSlelRKPITFGVItadtleqaieragtkhgn 134 d1jmva_ 139 ------------------rd 140 d1nqua_ 135 kgweaalsaiemanlfkslr 154 FAST alignment (Normalized score: 5.57 Raw score:818.20) d1jmva_ 1 MY------------KHILVAVDL--SEESPILLKKAVGIAKRHDA---KLSIIHVDVNFS 43 ::::::::: :::::::::::::::::::: ::::::: d1nqua_ 1 --MQIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRV----- 53 d1jmva_ 44 DLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLSGSG----DLGQVLSDAIE 99 :::::::::: d1nqua_ 54 ---------------------------------------------PGSWEIPVAAGELA- 67 d1jmva_ 100 Q--YDVDLLVTGHHQD---------FWSKLMSSTRQVMN---TIKIDMLVVPLRD----- 140 :::::::::: :::::::::::::: ::::::::: d1nqua_ 68 -RKEDIDAVIAIG---VLIRGATPHFDYIASEVSKGLANLSLELRKPITFG----VITAD 119 d1jmva_ 141 ----------------------------------- 141 d1nqua_ 120 TLEQAIERAGTKHGNKGWEAALSAIEMANLFKSLR 154 TMalign alignment (TM-score: 0.37 Raw score:52.03) d1jmva_ 1 ------MY----KHILVAVDL-SEE-SPILLKKAVGIAK-RHDA--KLSII-H--VDV-N 41 :: ::::::::: ::: ::::::::::::: :::: ::::: : ::: d1nqua_ 1 MQIYEGKLTAEGLRFGIVASRFNHALVDRLVEGAIDCIVRHGGREEDITLVRVPGSWEI- 59 d1jmva_ 42 FSDLYTGLI--DV-NM--SSMQDRISTETQKALLDLAESVDYPIS--EKL---------- 84 ::: :: : :: ::: d1nqua_ 60 ------PVAAGELA-RKE-------------------------DIDAVIAIGVLIRGATP 87 d1jmva_ 85 ----SGS-GDLGQVLSDAIE-QYDVDLLVTGHHQDFWSKL-MSSTRQVMNTIKIDMLVVP 137 : :::::::::::: :::::::::::::::: :: :: d1nqua_ 88 HFDY--IASEVSKGLANLSLELRKPITFGVITADTLE-QAI-----------------ER 127 d1jmva_ 138 LR-------------------------D 140 :: d1nqua_ 128 AGTKHGNKGWEAALSAIEMANLFKSLR- 154 HHsearch alignment (Probability: 0.07 E-value:0.07) d1jmva_ 13 EESPILLKKAVGIAKRHDA 31 ::::::::::::::::::: d1nqua_ 25 ALVDRLVEGAIDCIVRHGG 43