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 | d1qyra_ | High level kasugamycin resistance protein KsgA | S-adenosyl-L-methionine-dependent methyltransferases | S-adenosyl-L-methionine-dependent methyltransferases | 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 <-- 0.593 --> HitDALI alignment (Z-score: 4.3 Raw score:401.10) d1gpma1 1 ---wtPAKIIDDAVARIreQVGD-DKVILGLsggvdsSVTAMLLHRAIgKNLTCVFVdng 56 :::::::::::: :::: ::::::: ::::::::::: :::::::: d1qyra_ 1 qnflnDQFVIDSIVSAI--NPQKgQAMVEIG---pglAALTEPVGERL-DQLTVIEL--- 51 d1gpma1 57 llrlneAEQVLDMFgDHFG-----LNIVHVpaedrflsalagendpeakrkiigrvfvEV 111 :::::::: :::: :::::: :: d1qyra_ 52 ------DRDLAARL-QTHPflgpkLTIYQQ--------------------------daMT 78 d1gpma1 112 FDeeALKLE----DVKWLAQGT--------iypdviesaaKMGLVE-------------- 145 :: ::::: ::::::::: :::::: d1qyra_ 79 FN--FGELAekmgQPLRVFGNLpynistplmfhlfsytdaIADMHFmlqkevvnrlvagp 136 d1gpma1 146 -------------------plkELFKDEVR------------------------------ 156 :::::::: d1qyra_ 137 nskaygrlsvmaqyycnvipvlEVPPSAFTpppkvdsavvrlvphatmphpvkdvrvlsr 196 d1gpma1 157 -------------------------------------kiglelglpydmlyrhpfp 175 d1qyra_ 197 itteafnqrrktirnslgnlfsvevltgmgidpamraenisvaqycqmanylaena 252 FAST alignment (Normalized score: 1.21 Raw score:253.30) d1gpma1 1 WT-----PAKIIDDAVARIREQVGD---------------------------DKVILGLS 28 ::::::::::: ::::::: d1qyra_ 1 --QNFLNDQFVIDSIVSA-------INPQKGQAMVEIGPGLAALTEPVGERLDQLTVIE- 50 d1gpma1 29 -GGVDSSVTAMLLHRA----IGKNLTCVFVDNGLLRLNEAEQVLDMFGDHFGLNIVHVPA 83 ::::::::: :::::::: d1qyra_ 51 LDRDLAARLQ------THPFLGPKLTIY-------------------------------- 72 d1gpma1 84 EDRFLSALAGENDPEAKRKIIGRV--FVEVFDE-EALKLEDV--------KWLAQGT--- 129 :::: :::: :::: d1qyra_ 73 ------------------------QQDAMT---FNFGE----LAEKMGQPLRVF---GNL 98 d1gpma1 130 --------------------------IYPDVIESAAKMGLVEPLKELFKDEVRKIGLELG 163 :::::::: d1qyra_ 99 PYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRL-------------------------- 132 d1gpma1 164 LPYDMLYRHPFP------------------------------------------------ 175 d1qyra_ 133 ------------VAGPNSKAYGRLSVMAQYYCNVIPVLEVPPSAFTPPPKVDSAVVRLVP 180 d1gpma1 176 ------------------------------------------------------------ 176 d1qyra_ 181 HATMPHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQ 240 d1gpma1 176 ------------ 176 d1qyra_ 241 YCQMANYLAENA 252 TMalign alignment (TM-score: 0.46 Raw score:80.57) d1gpma1 1 -----WTPAKIIDDAVARIREQVGD-DKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVD 54 ::::::::::::: ::: ::::::::: : ::::::::: ::::::::: : d1qyra_ 1 QNFLN--DQFVIDSIVSAIN--PQKGQAMVEIGPG-L--AALTEPVGE-RLDQLTVIE-L 51 d1gpma1 55 NGLLRLNEAEQVLDMFGDHF-GL--NIVHVPAEDRFLSALAGENDPEAKRKIIGRVFVEV 111 :: :::::::::: :: ::::::: :: :: : d1qyra_ 52 -------DR-DLAARLQTHPFLGPKLTIYQQD--------------------AM--TF-N 80 d1gpma1 112 FDEEALKLEDVKWLAQG-------------------------TIYP-DVIES-A-----A 139 ::::::::::::::::: :::: ::::: : : d1qyra_ 81 FGELAEKMGQPLRVFGNLPYNISTPLMFHLFSYTDAIADMHFMLQKEVVNRLVAGPNSKA 140 d1gpma1 140 -----------KMGL-VEPLKELFKDEVRKIGLELGLPYDMLYRHP-------------- 173 :: :::::::::: : ::::: d1qyra_ 141 YGRLSVMAQYY--CNV-IPVLEVPPSA-F------------TPPPKVDSAVVRLVPHATM 184 d1gpma1 174 ------------------------------------------------------------ 174 d1qyra_ 185 PHPVKDVRVLSRITTEAFNQRRKTIRNSLGNLFSVEVLTGMGIDPAMRAENISVAQYCQM 244 d1gpma1 174 --------FP 175 d1qyra_ 245 ANYLAENA-- 252 HHsearch alignment (Probability: 0.00 E-value:1.40) d1gpma1 11 VARIREQV--GDDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLL 58 :::::::: ::::::::::::::: :::::::: :::::::::::::: d1qyra_ 10 IDSIVSAINPQKGQAMVEIGPGLAA-LTEPVGER--LDQLTVIELDRDLA 56