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: T542_A.pdb A
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 <-- 2.423 --> IntermediateDALI alignment (Z-score: 17.0 Raw score:1263.90) query 1 slqlrlalnqidstvgdiagnaeailrwtrhsaeqgahlvafpemaltgypvedlalrss 60 d1gpma1 1 ------------------------------------------------------------ 1 query 61 fveasrtalrelaarlaeegfgelpvlvgyldrsesaqpkygqpagaprnaaavlhrgrv 120 d1gpma1 1 ------------------------------------------------------------ 1 query 121 altfakhhlpnygvfdefryfvpgdtmpivrlhgvdialaicedlwqdggrvpaarsaga 180 d1gpma1 1 ------------------------------------------------------------ 1 query 181 glllsvnaspyerdkddtrlelvrkraqeagcttaylamiggqdelvfdgdsivvdrdge 240 d1gpma1 1 ------------------------------------------------------------ 1 query 241 vvarapqfsegcvvldldlpaaeaepptgvvddglridrlviseeplpayeaelaggyad 300 d1gpma1 1 ------------------------------------------------------------ 1 query 301 rlDADEEVYSALVVGLRAYVAkngFRSVLIGLSGGIDSALVAAIACDALGaQNVYGVSMP 360 ::::::::::::::::::: :::::::::::::::::::::::::: ::::::::: d1gpma1 1 --WTPAKIIDDAVARIREQVG---DDKVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVD 54 query 361 SKYSS-DHSKGDAAELARRTGLNFRTVSIEPMFDAYMAsLGLTGLAEENLQSRLRGTTLM 419 ::::: :::::::::::::::::::::::::::::::: ::::::::::::::::::::: d1gpma1 55 NGLLRlNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFD 113 query 420 AISNQE--GHIVLAPGNKSELAVGystlygdsvgAYGPIKDVYKTSIFRLAEWRNraaae 477 :::::: :::::::::::::::: ::::::::::::::::::::: d1gpma1 114 EEALKLedVKWLAQGTIYPDVIES-----aakmgLVEPLKELFKDEVRKIGLELG----- 163 query 478 rgqtppIPEASITKpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeyk 537 :::::::: d1gpma1 164 ------LPYDMLYR---------------------------------------------- 171 query 538 rrqyppgtkisakgfgkdrrlpitnrwregh 568 d1gpma1 172 ---------------------------hpfp 175 FAST alignment (Normalized score: 8.89 Raw score:2802.00) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1gpma1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1gpma1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1gpma1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 d1gpma1 1 ------------------------------------------------------------ 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1gpma1 1 ------------------------------------------------------------ 1 query 301 RLDADEEVYSALVVGLRAYVAKNGF---RSVLIGLSGGIDSALVAAIACDALGAQNVYGV 357 ::::::::::::::::: ::::::::::::::::::::::: :::::::: d1gpma1 1 --WTPAKIIDDAVARIREQ------VGDDKVILGLSGGVDSSVTAMLLHRA-IGKNLTCV 51 query 358 SMPSKYSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGT 416 :::::::::::::::: :::::::::::::::::::::::::: :::::::::::::::: d1gpma1 52 FVDNGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGE-NDPEAKRKIIGRVFVE 110 query 417 TLMAISNQEG----HIVLAPGNKSELAVGYSTLYGDSVG-------AYGPIKDVYKTSIF 465 :::::::: ::::::::::::: :::::::::::::: d1gpma1 111 VFDEEALK--LEDVKWLAQGTIYPDVI------------ESAAKMGLVEPLKELFKDEVR 156 query 466 RLAEWRNRAAAERGQTP-PIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELV 524 ::::: :::::::: d1gpma1 157 KIGLE------------LGLPYDMLY---------------------------------- 170 query 525 VKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----- 568 d1gpma1 171 --------------------------------------------RHPFP 175 TMalign alignment (TM-score: 0.27 Raw score:151.12) query 1 SLQLRLALNQIDSTVGDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSS 60 d1gpma1 1 ------------------------------------------------------------ 1 query 61 FVEASRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRGRV 120 d1gpma1 1 ------------------------------------------------------------ 1 query 121 ALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAARSAGA 180 d1gpma1 1 ------------------------------------------------------------ 1 query 181 GLLLSVNASPYERDKDDTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGE 240 : d1gpma1 1 --------------W--------------------------------------------- 1 query 241 VVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYAD 300 d1gpma1 2 ------------------------------------------------------------ 2 query 301 RLDADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMP 360 :::::::::::::::::: :: :::::::::::::::::::::::: ::::::::: d1gpma1 2 ---TPAKIIDDAVARIREQVG--DD-KVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVD 54 query 361 SKYSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLM 419 ::::::::::::: :::::::::::::::::::::::: ::::::::::::::::::::: d1gpma1 55 NGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFD 113 query 420 AISNQEG-H-IVLAPGNKSELAVG---YSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRA 474 ::::::: : :::::::::::::: ::::::::::::::::::::::: d1gpma1 114 EEALKLEDVKWLAQGTIYPDVIESAAK--------MGLVEPLKELFKDEVRKIGLELG-- 163 query 475 AAERGQTPPIPEASITKPDY--PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVD 532 :::::::: :: d1gpma1 164 ---------LPYDMLYR-HPFP-------------------------------------- 175 query 533 TAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 568 d1gpma1 176 ------------------------------------ 176 HHsearch alignment (Probability: 1.00 E-value:0.00) query 306 EEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSS 365 ::::::::::::::::: :::::::::::::::::::::::::::::::::::::::: d1gpma1 4 AKIIDDAVARIREQVGD---DKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRL 60 query 366 DHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQE 425 ::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::: d1gpma1 61 NEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGEN-DPEAKRKIIGRVFVEVFDEEALKL 119 query 426 GHI-VLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPI 484 ::: :::::::::::::::::::: ::::::::::::::::::: :::::::::::: d1gpma1 120 EDVKWLAQGTIYPDVIESAAKMGL----VEPLKELFKDEVRKIGLEL-GLPYDMLYRHPF 174 query 485 P 485 : d1gpma1 175 P 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