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 | d1gpma1 | GMP synthetase, central domain | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1m66a2 | Glycerol-3- phosphate dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
Query <-- 2.152 --> IntermediateDALI alignment (Z-score: 17.0 Raw score:1273.10) query 1 DADEEVYSALVVGLRAYVAkngFRSVLIGLSGGIDSALVAAIACDALGaQNVYGVSMPSK 60 ::::::::::::::::::: :::::::::::::::::::::::::: ::::::::::: d1gpma1 1 WTPAKIIDDAVARIREQVG---DDKVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVDNG 56 query 61 YSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMAsLGLTGLAEENLQSRLRGTTLMAI 119 ::::::::::: :::::::::::::::::::::::: ::::::::::::::::::::::: d1gpma1 57 LLRLNEAEQVLdMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFDEE 115 query 120 SNQE--GHIVLAPGNKSELAVGystlygdsvgAYGPIKDVYKTSIFRLAEWRNraaaerg 177 :::: :::::::::::::::: ::::::::::::::::::::: d1gpma1 116 ALKLedVKWLAQGTIYPDVIES-----aakmgLVEPLKELFKDEVRKIGLELG------- 163 query 178 qtppIPEASITKpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrr 237 :::::::: d1gpma1 164 ----LPYDMLYR------------------------------------------------ 171 query 238 qyppgtkisakgfgkdrrlpitnrwregh 266 d1gpma1 172 -------------------------hpfp 175 FAST alignment (Normalized score: 13.11 Raw score:2830.00) query 1 DADEEVYSALVVGLRAYVAKNGF---RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSM 57 ::::::::::::::::: ::::::::::::::::::::::: :::::::::: d1gpma1 1 WTPAKIIDDAVARIREQ------VGDDKVILGLSGGVDSSVTAMLLHRA-IGKNLTCVFV 53 query 58 PSKYSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTL 116 :::::::::::::: :::::::::::::::::::::::::: :::::::::::::::::: d1gpma1 54 DNGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGE-NDPEAKRKIIGRVFVEVF 112 query 117 MAISNQEG----HIVLAPGNKSELAVGYSTLYGDSVG-------AYGPIKDVYKTSIFRL 165 :::::: ::::::::::::: :::::::::::::::: d1gpma1 113 DEEALK--LEDVKWLAQGTIYPDVI------------ESAAKMGLVEPLKELFKDEVRKI 158 query 166 AEWRNRAAAERGQTP-PIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVK 224 ::: :::::::: d1gpma1 159 GLE------------LGLPYDMLY------------------------------------ 170 query 225 TLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----- 266 d1gpma1 171 ------------------------------------------RHPFP 175 TMalign alignment (TM-score: 0.53 Raw score:140.98) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 ::::::::::::::::::: :: :::::::::::::::::::::::: ::::::::::: d1gpma1 1 WTPAKIIDDAVARIREQVG--DD-KVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVDNG 56 query 61 YSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAI 119 ::::::::::: :::::::::::::::::::::::: ::::::::::::::::::::::: d1gpma1 57 LLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFDEE 115 query 120 SNQEG-H-IVLAPGNKSELAVG---YSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAA 174 ::::: : :::::::::::::: ::::::::::::::::::::::: d1gpma1 116 ALKLEDVKWLAQGTIYPDVIESAAK--------MGLVEPLKELFKDEVRKIGLELG---- 163 query 175 ERGQTPPIPEASITKPDY--PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTA 232 :::::::: :: d1gpma1 164 -------LPYDMLYR-HPFP---------------------------------------- 175 query 233 EYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1gpma1 176 ---------------------------------- 176 HHsearch alignment (Probability: 1.00 E-value:0.00) query 4 EEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSS 63 ::::::::::::::::: ::::::::::::::::::::::::::: :::::::::::: d1gpma1 4 AKIIDDAVARIREQVGD---DKVILGLSGGVDSSVTAMLLHRAIGKN-LTCVFVDNGLLR 59 query 64 DHSKGD-AAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQ 122 :::::: ::::::::::::::::::::::::::::::::: ::::::::::::::::::: d1gpma1 60 LNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGENDPEA-KRKIIGRVFVEVFDEEALK 118 query 123 EGHI-VLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPP 181 :::: :::::::::::::::::::: :::::::::::::::::::: d1gpma1 119 LEDVKWLAQGTIYPDVIESAAKMGL----VEPLKELFKDEVRKIGLELG----------- 163 query 182 IPEASITKPDYP 193 :::::::::::: d1gpma1 164 LPYDMLYRHPFP 175
Intermediate <-- 1.056 --> HitDALI alignment (Z-score: 3.3 Raw score:334.10) d1gpma1 1 wtpakiiddavarirEQVGdDKVILGLSgGVDSSVTAMLLHRAIgKNLTCVFVDngllrl 60 :::: :::::::: ::::::::::::::: ::::::::: d1m66a2 1 ------------kdeLLYL-NKAVVFGS-GAFGTALAMVLSKKC-REVCVWHMN------ 39 d1gpma1 61 neAEQVLDMfGDHF-------------gLNIVHVpaedrflsalagendpeakrkiigrv 107 ::::::: :::: :::::: d1m66a2 40 --EEEVRLV-NEKRenvlflkgvqlasnITFTSD-------------------------- 70 d1gpma1 108 fvevfdeealkLEDVKWLAQG-------------tiypdviesaaKMGLVEP-------- 146 :::::::::: ::::::: d1m66a2 71 -------vekaYNGAEIILFViptqflrgffeksggnliayakekQVPVLVCtkgierst 123 d1gpma1 147 ------------------lKELFKdEVRKIGLE--------------------lglpydm 168 ::::: :::::::: d1m66a2 124 lkfpaeiigeflpspllsvLAGPS-FAIEVATGvftcvsiasadinvarrlqrimstgdr 182 d1gpma1 169 lyrhpfp 175 d1m66a2 183 sfvcwat 189 FAST alignment (Normalized score: 2.63 Raw score:477.60) d1gpma1 1 WTPAKIIDDAVARIREQVGD-------DKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFV 53 ::::: :::::::::::::::::: :::::: d1m66a2 1 --------------------KDELLYLNKAVV-FGSGAFGTALAMVLSKKC---REVCVW 36 d1gpma1 54 DNGLLRL---NEAEQVLDMFGDHFG--------------LNIVHVPAEDRFLSALAGEND 96 : :::::::: :::::: d1m66a2 37 H------MNEEEVRLVNE-------KRENVLFLKGVQLASNITFT--------------- 68 d1gpma1 97 PEAK---------------------RKIIGRVFVEVFDEEALKLEDVK----WLAQGTIY 131 ::::::::::::::::: ::::::: d1m66a2 69 ----SDVEKAYNGAEIILFVIPTQFLRGFFEKSGGNLIAYAK------EKQVPVLVCTK- 117 d1gpma1 132 PDVIESAAKM---------------------GLVEPLKELFKD-----EVRKIGLELGLP 165 :::: :::::: d1m66a2 118 ----------GIERSTLKFPAEIIGEFLPSPLLSV--------LAGPSFAIEVA------ 153 d1gpma1 166 YDMLYRHPFP------------------------------------ 175 d1m66a2 154 ----------TGVFTCVSIASADINVARRLQRIMSTGDRSFVCWAT 189 TMalign alignment (TM-score: 0.42 Raw score:73.10) d1gpma1 1 -WTPAKIIDDAVARIREQVGDDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLR 59 : :: :::::::::::::::::::::::: ::: ::::::: : : d1m66a2 1 K------------D-EL--LYLNKAVVFGSGAFGTALAMVLSK-KCR-EVCVWHM-N-E- 40 d1gpma1 60 LNEAEQVLD-MFG-------DHFGLNIVHVPA-----------------EDRFLSALAGE 94 :::::::: ::: :::::::::::: d1m66a2 41 -EEVRLVNEKRENVLFLKGVQLASNITFTSDVEKAYNGAEIILFVIPTQ----------- 88 d1gpma1 95 NDPEAKRKIIGRVFVEVFDEEALK-LEDVKWLAQGTIYPD-----VIES----------- 137 :::::::::::: :: ::: ::::::::::: :: :: d1m66a2 89 -----FLRGFFEKSGGN-LI-AYAK-EKQVPVLVCTK-GIERSTL--KFPAEIIGEFLPS 137 d1gpma1 138 AAKMGLVEPLKELFKDEVRKIGLELG---------------------------------L 164 :::::: :::: :::::: ::: d1m66a2 138 --PLLSVL--AGPS--FAIEVA-TGVFTCVSIASADINVARRLQRIMSTGDRSFVCWAT- 189 d1gpma1 165 PYDMLYRHPFP 175 d1m66a2 190 ----------- 190 HHsearch alignment (Probability: 0.03 E-value:0.12) d1gpma1 21 DKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDN 55 :::::::::::::::::::: : :::::::::::: d1m66a2 8 NKAVVFGSGAFGTALAMVLS-K-KCREVCVWHMNE 40