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 | d1qama_ | rRNA adenine dimethylase | 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 <-- 0.916 --> HitDALI alignment (Z-score: 3.9 Raw score:393.40) d1gpma1 1 ---wtPAKIIDDAVARIreQVGD-DKVILGLsggvdsSVTAMLLHRAIgKNLTCVFVdng 56 :::::::::::: :::: ::::::: ::::::::::: :::::::: d1qama_ 1 qnfitSKHNIDKIMTNI--RLNEhDNIFEIG---sgkGHFTLELVQRC-NFVTAIEI--- 51 d1gpma1 57 llrlneAEQVLDMFGDHFG----lNIVHVpaedrflsalagendpeakrkiigrvfveVF 112 ::::::::::::: ::::: :: d1qama_ 52 ------DHKLCKTTENKLVdhdnfQVLNK-----------------------------DI 76 d1gpma1 113 DEEalKLED--vKWLAQGT-------iypdviesaaKMGLVE------------------ 145 ::: :::: ::::::: :::::: d1qama_ 77 LQF--KFPKnqsYKIFGNIpynistdiirkivfdsiADEIYLiveygfakrllntkrsla 134 d1gpma1 146 ----------plkELFKDEVR--------------------------------------- 156 :::::::: d1qama_ 135 lflmaevdisilsMVPREYFHpkpkvnsslirlnrkksrishkdkqkynyfvmkwvnkey 194 d1gpma1 157 ----------------------kiglelglpydmlyrhpfp 175 d1qama_ 195 kkiftknqfnnslkhagiddlnnisfeqflslfnsyklfnk 235 FAST alignment (Normalized score: 2.92 Raw score:592.10) d1gpma1 1 WT-----PAKIIDDAVARIREQ---VGDDKVILGLSGGVDS-----SVTAMLLHRAIGK- 46 ::::::::::: :::::::: :::::::::: d1qama_ 1 --QNFITSKHNIDKIMTN----IRLNEHDNIFE--------IGSGKGHFTLELVQR---C 43 d1gpma1 47 -NLTCVFVDNGLLRLNE-AEQVLDMFGDHF------GLNIVHVPAEDRFLSALAGENDPE 98 :::::: :::::::::: ::::: d1qama_ 44 NFVTAIE----------IDHKLCKTTEN--KLVDHDNFQVL------------------- 72 d1gpma1 99 AKRKIIGRVFVE--VFDEEALKLEDV--------KWLA---------------------- 126 :::: :::: d1qama_ 73 ------------NKDILQ--------FKFPKNQSYKIFGNIPYNISTDIIRKIVFDSIAD 112 d1gpma1 127 ---QGTIYPDVIESAAKMGLVEPL--------------------KELFKDEVRKIGLELG 163 ::::::::::: ::::::: d1qama_ 113 EIYLIVEYGFAKRL----------LNTKRSLALFLMAEVDISILSMVPREY--------- 153 d1gpma1 164 LPYDMLYRHPFP------------------------------------------------ 175 d1qama_ 154 ------------FHPKPKVNSSLIRLNRKKSRISHKDKQKYNYFVMKWVNKEYKKIFTKN 201 d1gpma1 176 ---------------------------------- 176 d1qama_ 202 QFNNSLKHAGIDDLNNISFEQFLSLFNSYKLFNK 235 TMalign alignment (TM-score: 0.45 Raw score:78.31) d1gpma1 1 -----WTPAKIIDDAVARIREQVG-DDKVILGLSGGVDSSVTAMLLHRAIG--KNLTCVF 52 :::::::::::: ::: :::::::: ::: ::::::::: ::::::: d1qama_ 1 QNFIT--SKHNIDKIMTNI--RLNEHDNIFEIG-----SGK-GHFTLELVQRCNFVTAIE 50 d1gpma1 53 VDNGLLRLNEAEQVLDMFGDHFG-----LNIVHVPAEDRFLSALAGENDPEAKRKIIGRV 107 : ::::::::: ::: :::::: : d1qama_ 51 I---------DHKLCKTTE-NKLVDHDNFQVLNK-D------------------------ 75 d1gpma1 108 FVEVFDEEALKLEDVKWLAQG------------------------TIYP-DVIESAA--- 139 :: :: : ::: ::::::::: :::: ::::::: d1qama_ 76 IL-QF-K-FPK-NQSYKIFGNIPYNISTDIIRKIVFDSIADEIYLIVEYGFAKRLLNTKR 131 d1gpma1 140 --------KMGLVEPLKELFKDEVRKIGLELGLPYDMLYRHP------------------ 173 :::::::::::::: : ::::: d1qama_ 132 SLALFLMA-EVDISILSMVPREY-F------------HPKPKVNSSLIRLNRKKSRISHK 177 d1gpma1 174 ----------------------------------------------------------FP 175 d1qama_ 178 DKQKYNYFVMKWVNKEYKKIFTKNQFNNSLKHAGIDDLNNISFEQFLSLFNSYKLFNK-- 235 HHsearch alignment (Probability: 0.00 E-value:0.54) d1gpma1 18 VGDDKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLL 58 ::::::::::::::: ::::::::: :::::::::::::: d1qama_ 19 LNEHDNIFEIGSGKG-HFTLELVQR--CNFVTAIEIDHKLC 56