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 | d1pyo.1 | Caspase-2 | Caspase-like | Caspase-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 <-- 0.630 --> HitDALI alignment (Z-score: 4.9 Raw score:400.40) d1jmva_ 1 ------------------------MYKHILVAVDL----------SEESPILLKKAVGIA 26 ::::::::::: ::::::::::::::: d1pyo.1 1 lqvkpctpefyqthfqlayrlqsrPRGLALVLSNVhftgekelefRSGGDVDHSTLVTLF 60 d1jmva_ 27 KRHDAKLSII-HVDVnfsdlytglidvnmssmqdristetqkalldlaesvdypisekls 85 :::::::::: :::: d1pyo.1 61 KLLGYDVHVLcDQTA--------------------------------------------- 75 d1jmva_ 86 gsGDLGQVLSDAIEQYD-----vDLLVTGHHQdfWSKL-------msSTRQVMNTIK--- 130 ::::::::::::::: ::::::::: :::: :::::::::: d1pyo.1 76 --QEMQEKLQNFAQLPAhrvtdsCIVALLSHG--VEGAiygvdgkllQLQEVFQLFDnan 131 d1jmva_ 131 --------IDMLVVP--------------------------------------------- 137 ::::::: d1pyo.1 132 cpslqnkpKMFFIQAcrgdetdrgvdqqpkmrlptrsdmicgyaclkgtaamrntkrgsw 191 d1jmva_ 138 ------------------------------------------------------------ 138 d1pyo.1 192 yiealaqvfseracdmhvadmlvkvnalikdregyapgtefhrckemseycstlcrhlyl 251 d1jmva_ 138 ---lrd 140 d1pyo.1 252 fpghpp 257 FAST alignment (Normalized score: 2.64 Raw score:501.10) d1jmva_ 1 MY--------------------------KHILVAVDL----------------SEESPIL 18 ::::::: ::::::: d1pyo.1 1 --LQVKPCTPEFYQTHFQLAYRLQSRPRGLALVLS--NVHFTGEKELEFRSGGDVDHSTL 56 d1jmva_ 19 LKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDY 78 :::::: :::::::: d1pyo.1 57 VTLFKL----LGYDVHVL------------------------------------------ 70 d1jmva_ 79 PISEKLSGSG------DLGQVLSDAIEQY------DVDLLVTG-HHQDFWS--------- 116 :::::::::: :::::::: ::::::: d1pyo.1 71 ----------CDQTAQEMQEKLQNFA---QLPAHRVTDSCIVALLSHGVEGAIYGVDGKL 117 d1jmva_ 117 -KLMSSTRQV-MNTI----KIDMLVVPLRD------------------------------ 140 ::::::::: :::: ::::::::: d1pyo.1 118 LQLQEVFQLFDNANCPSLQNKPKMFFIQ--ACRGDETDRGVDQQPKMRLPTRSDMICGYA 175 d1jmva_ 141 ------------------------------------------------------------ 141 d1pyo.1 176 CLKGTAAMRNTKRGSWYIEALAQVFSERACDMHVADMLVKVNALIKDREGYAPGTEFHRC 235 d1jmva_ 141 ---------------------- 141 d1pyo.1 236 KEMSEYCSTLCRHLYLFPGHPP 257 TMalign alignment (TM-score: 0.49 Raw score:67.98) d1jmva_ 1 --------------------M----YKHILVAVDLS----------E-ESPILLKKAVGI 25 : ::::::::::: : :::::::::::: d1pyo.1 1 LQVKPCTPEFYQTHFQLAYRLQSRPRGLALVLSNVHFTGEKELEFRSGGDVDHSTLVTLF 60 d1jmva_ 26 AKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESVDYPISEKLS 85 :: ::::::::::::: d1pyo.1 61 KL-LGYDVHVLCDQTA-------------------------------------------- 75 d1jmva_ 86 GSGDLGQVLSDAIEQYDV-----DLLVTGHHQDFWSKL-------MSSTRQVMNTIK--- 130 :::::::::::::::: :::::::: :::::: ::::::::::: d1pyo.1 76 --QEMQEKLQNFAQLPAHRVTDSCIVALLSH-GVEGAIYGVDGKL-LQLQEVFQLFDNAN 131 d1jmva_ 131 --------IDMLVVP------------------------------------LRD------ 140 ::::::: ::: d1pyo.1 132 CPSLQNKPKMFFIQACRGDETDRGVDQQPKMRLPTRSDMICGYACLKGTAAMRNTKRGSW 191 d1jmva_ 141 ------------------------------------------------------------ 141 d1pyo.1 192 YIEALAQVFSERACDMHVADMLVKVNALIKDREGYAPGTEFHRCKEMSEYCSTLCRHLYL 251 d1jmva_ 141 ------ 141 d1pyo.1 252 FPGHPP 257 HHsearch alignment (Probability: 0.06 E-value:0.10) d1jmva_ 67 KALLDLAESVDYPISEKLSGSGD-LGQVLSDAIEQ---YDVD--LLVTGHHQDFWSKLMS 120 ::::::::::::::::::::::: ::::::::::: :::: :::::::::::::::: d1pyo.1 54 STLVTLFKLLGYDVHVLCDQTAQEMQEKLQNFAQLPAHRVTDSCIVALLSHGVEGAIYGV 113 d1jmva_ 121 ST 122 :: d1pyo.1 114 DG 115