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 | d1b8pa1 | Malate dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 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 <-- 1.034 --> HitDALI alignment (Z-score: 6.4 Raw score:471.70) d1jmva_ 1 -MYKHILVAVDLSEESPILLKKAV-GIAKR--HDAKLSIIHVDvnfsdlytglidvnmss 56 ::::::::::::::::::::::: ::::: ::::::::::: d1b8pa1 1 kTPMRVAVTGAAGQICYSLLFRIAnGDMLGkdQPVILQLLEIP----------------- 43 d1jmva_ 57 mqdrisTETQKALLDLAESVD------YPISEKLSgsgdlgqVLSDAIEqyDVDLLVT-G 109 ::::::::::::::: :::::::: ::::::: ::::::: : d1b8pa1 44 -----nEKAQKALQGVMMEIDdcafplLAGMTAHA-------DPMTAFK--DADVALLvG 89 d1jmva_ 110 HHQ--------dfWSKLMSSTRQVMNTIK------IDMLVVP------------------ 137 ::: :::::::::::::::: ::::::: d1b8pa1 90 ARPrgpgmerkdlLEANAQIFTVQGKAIDavasrnIKVLVVGnpantnayiamksapslp 149 d1jmva_ 138 ----lrd 140 d1b8pa1 150 aknftam 156 FAST alignment (Normalized score: 5.08 Raw score:751.30) d1jmva_ 1 MY-KHILVAV--DLSEESPILLKKAVGIAKR-------HDAKLSIIHVDVNFSDLYTGLI 50 ::::::: ::::::::::::: ::::::::::: d1b8pa1 1 --KTPMRVAVTGAAGQICYSLLFRI------ANGDMLGKDQPVILQLLE----------- 41 d1jmva_ 51 DVNMSSMQDRIS-------TETQKALLDLAE-SVDYPISEKLSGSGDL-GQVLSDAIEQY 101 :::::::::::: ::: ::::::::: ::::: : d1b8pa1 42 ------------IPNEKAQKALQGVMMEIDDCAFP-LLAGMTAHA---DPMTAF-----K 80 d1jmva_ 102 DVDLLVTGHHQD--------------FWSKLMSSTRQVMNT------IKIDMLVVPLRD- 140 ::::::: ::::::::::::::: ::::::: d1b8pa1 81 DADVALL-----VGARPRGPGMERKDLLEANAQIFTVQGKAIDAVASRNIKVLV-----V 130 d1jmva_ 141 -------------------------- 141 d1b8pa1 131 GNPANTNAYIAMKSAPSLPAKNFTAM 156 TMalign alignment (TM-score: 0.54 Raw score:75.07) d1jmva_ 1 --MYKHILVAVDLSEESPILLKKA--VGIAKRHDAKLSIIHVDVN----FSDLYTGLIDV 52 ::::::::::::::::::::: ::::::::::::::::::: d1b8pa1 1 KT-PMRVAVTGAAGQICYSLLFRIANGDMLGKDQPVILQLLEIPNEKAQ----------- 48 d1jmva_ 53 NMSSMQDRISTETQKALLDLAESVDYPISEKLSGSGDLGQVLSDAIEQYDVDLLVTGHHQ 112 ::::::::::::::::::::::::: ::::::: ::::::::::: d1b8pa1 49 ----------KALQGVMMEIDDCAFPLLAGMTAHA-----DPMTAFK--DADVALLVGAR 91 d1jmva_ 113 D---------FWSKLMSSTRQVMNTIK------IDMLVVPL------------------- 138 : ::::::::::::::::: :::::::: d1b8pa1 92 PRGPGMERKDLLEANAQIFTVQGKAIDAVASRNIKVLVVGNPANTNAYIAMKSAPSLPAK 151 d1jmva_ 139 -----RD 140 d1b8pa1 152 NFTAM-- 156 HHsearch alignment (Probability: 0.00 E-value:1.40) d1jmva_ 87 SGDLGQVLSDAI 98 :::::::::::: d1b8pa1 130 VGNPANTNAYIA 141