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 | d1v4va_ | UDP-N-acetylglucosamine 2-epimerase | UDP-Glycosyltransferase/glycogen phosphorylase | UDP-Glycosyltransferase/glycogen phosphorylase | 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 <-- 0.607 --> HitDALI alignment (Z-score: 6.2 Raw score:582.90) d1gpma1 1 wtpakiiddavarireqvGDDKVILGLSGGVdSSVTAMLLHRAIG----kNLTCVFVDNg 56 ::::::::::::: ::::::::::::: ::::::::: d1v4va_ 1 ------------------GMKRVVLAFGTRP-EATKMAPVYLALRgipglKPLVLLTGQ- 40 d1gpma1 57 llrlnEAEQVLDMFgDHFGLNI-VHVPAEDrfLSALagendpeakRKIIGRVFVEVFDEE 115 ::::::::: ::::::: ::::::: :::: ::::::::::::::: d1v4va_ 41 -----HREQLRQAL-SLFGIQEdRNLDVMQ--ERQA---------LPDLAARILPQAARA 83 d1gpma1 116 ALKLEdVKWLAQGT-----iypdviesaaKMGLVEPL----------------------- 147 ::::: :::::::: :::::::: d1v4va_ 84 LKEMG-ADYVLVHGdtlttfavawaafleGIPVGHVEaglrsgnlkepfpeeanrrltdv 142 d1gpma1 148 -----KELF-------------------kdEVRKIGLELG-------------------- 163 :::: :::::::::: d1v4va_ 143 ltdldFAPTplakanllkegkreegilvtgQTGVDAVLLAaklgrlpeglpegpyvtvtm 202 d1gpma1 164 ----------------------------------------------------------lP 165 : d1v4va_ 203 hrrenwpllsdlaqalkrvaeafphltfvypvhlnpvvreavfpvlkgvrnfvlldpleY 262 d1gpma1 166 YDM--------------------------------------------------------- 168 ::: d1v4va_ 263 GSMaalmraslllvtdsgglqeegaalgvpvvvlrnvterpeglkagilklagtdpegvy 322 d1gpma1 169 --------------------------------------------lyrhpfp 175 d1v4va_ 323 rvvkgllenpeelsrmrkaknpygdgkaglmvargvawrlglgprpedwlp 373 FAST alignment (Normalized score: 2.25 Raw score:574.80) d1gpma1 1 W----------------------------------------------------------- 1 d1v4va_ 1 -GMKRVVLAFGTRPEATKMAPVYLALRGIPGLKPLVLLTGQHREQLRQALSLFGIQEDRN 59 d1gpma1 2 ------------TPAKIIDDAVARIREQVG--DDKVILGLSGGVDSSVTAMLLHRAIGK- 46 ::::::::::::::: :::::: :::::::::::::::: d1v4va_ 60 LDVMQERQALPDLAARILPQAARALKE---MGADYVLV-HGDTLTTFAVAWAAFL----E 111 d1gpma1 47 NLTCVFVDNGLLRL-------------NEAEQVLDMFGDHFGLN---IVHV--------- 81 :::::: ::::::::::: :::: d1v4va_ 112 GIPVGH--------VEAGLRSGNLKEPFPEEANRRLTD------VLTDLDFAPTPLAKAN 157 d1gpma1 82 ---------------PAEDRFLSALAGENDPEAKRKIIGR-------------------- 106 ::::::::: d1v4va_ 158 LLKEGKREEGILVTGQTGVDAVLL----------------AAKLGRLPEGLPEGPYVTVT 201 d1gpma1 107 ------------------------------------------------------------ 107 d1v4va_ 202 MHRRENWPLLSDLAQALKRVAEAFPHLTFVYPVHLNPVVREAVFPVLKGVRNFVLLDPLE 261 d1gpma1 107 ------------------------------------------------------------ 107 d1v4va_ 262 YGSMAALMRASLLLVTDSGGLQEEGAALGVPVVVLRNVTERPEGLKAGILKLAGTDPEGV 321 d1gpma1 107 ---------------------------VFVEVFDEEALKLEDVKWLAQGTIYPDVIESAA 139 :::::::::::: d1v4va_ 322 YRVVKGLLENPEELSRMRKAKNPYGDGKAGLMVARGVAW--------------------- 360 d1gpma1 140 KMGLVEPLKELFKDEVRKIGLELGLPYDMLYRHPFP------------- 175 d1v4va_ 361 ------------------------------------RLGLGPRPEDWLP 373 TMalign alignment (TM-score: 0.53 Raw score:93.06) d1gpma1 1 WTPAKIIDDAVARIREQVGDDKVILGLSGGVDSSVTAMLLHRAIG---KNLTCVFVDNGL 57 ::::::::::::::::::::::::::: :::::::::: d1v4va_ 1 ------------------GMKRVVLAFGTRPEATKMAPVYLALRGIPGLKPLVLLTGQ-- 40 d1gpma1 58 LRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGENDPEAKRKIIGRVFVEVFDEEAL 117 ::::::::: ::::::::::::: ::::: :::::::::::::::::: d1v4va_ 41 ----HREQLRQAL-SLFGIQEDRNLDV--MQERQ--------ALPDLAARILPQAARALK 85 d1gpma1 118 KLEDVKWLAQG----------------------TIYPDVIE------------S----AA 139 ::: ::::::: :::::::: : d1v4va_ 86 EMG-ADYVLVHGDTLTTFAVAWAAFLEGIPVGHVEAGLRSGNLKEPFPEEANRRLTDV-- 142 d1gpma1 140 KMGLVEPLKELF--K-----------------DEVRKIGLELGL---------------- 164 ::::: :::: : :::::::::::: d1v4va_ 143 -LTDLD--FAPTPLAKANLLKEGKREEGILVTGQTGVDAVLLAAKLGRLPEGLPEGPYVT 199 d1gpma1 165 ------------------------------------------------------------ 165 d1v4va_ 200 VTMHRRENWPLLSDLAQALKRVAEAFPHLTFVYPVHLNPVVREAVFPVLKGVRNFVLLDP 259 d1gpma1 165 --PY-D---------------MLYR----------------------------------- 171 :: : :: d1v4va_ 260 LEYGSMAALMRASLLLVTDSG--GLQEEGAALGVPVVVLRNVTERPEGLKAGILKLAGTD 317 d1gpma1 172 --------------------------------------------------------HPFP 175 d1v4va_ 318 PEGVYRVVKGLLENPEELSRMRKAKNPYGDGKAGLMVARGVAWRLGLGPRPEDWLP---- 373 HHsearch alignment (Probability: 0.49 E-value:0.01) d1gpma1 2 TPAKIIDDAVARIREQVGDDK-VILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRL 60 ::::::::::::::::::::: :::::::::::::::::::::: :::::::::::::: d1v4va_ 68 ALPDLAARILPQAARALKEMGADYVLVHGDTLTTFAVAWAAFLE--GIPVGHVEAGLRSG 125 d1gpma1 61 N----EAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGENDPEAKRKIIGRVFVEVFDEEA 116 : ::::::::::::::: :::: :::::::::::::::::::::::::::::::::: d1v4va_ 126 NLKEPFPEEANRRLTDVLTD-LDFA-PTPLAKANLLKEGKREEGILVTGQTGVDAVLLAA 183 d1gpma1 117 LK-------LEDVKWLAQGTIY 131 :: ::::::::::::: d1v4va_ 184 KLGRLPEGLPEGPYVTVTMHRR 205