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: 542d3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1kqpa_ | NH3-dependent NAD+-synthetase | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1gpma1 | GMP synthetase, central domain | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
Query <-- 0.944 --> IntermediateDALI alignment (Z-score: 0.0 Raw score:55.40) query 1 ------------------------------------------------------------ 1 d1kqpa_ 1 smqekimrelhvkpsidpkqeiedrvnflkqyvkktgakgfvlgisggqdstlagrlaql 60 query 1 --------pdypvLDAI------------------------------------------- 9 :::: d1kqpa_ 61 avesireeggdaqFIAVrlphgtqqdeddaqlalkfikpdkswkfdikstvsafsdqyqq 120 query 10 ---------lelyvdrdtGADAIVAAGYdrelvvkTLRM--------------------- 39 :::::::::: :::: d1kqpa_ 121 etgdqltdfnkgnvkartRMIAQYAIGG-qegllvLGTDhaaeavtgfftkygdggadll 179 query 40 --vdtaEYKRRQY--PPGTKIsakgFGKDRRL---------------------------- 67 ::::::: :::::: ::::::: d1kqpa_ 180 pltgltKRQGRTLlkELGAPE---rLYLKEPTadlldekpqqsdetelgisydeiddyle 236 query 68 -------------------------pitnrwregh 77 d1kqpa_ 237 gkevsakvsealekrysmtehkrqvpasmfddwwk 271 FAST alignment (Normalized score: 1.55 Raw score:223.30) query 1 P---------------------DYPVLDAILELYVDRDTGADAIVAAGY----------- 28 :::::::::::::::::: d1kqpa_ 1 -SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQYVKKTGAK---------GFVLGISGGQD 50 query 29 ---DRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH-------- 77 :::::::::::::: d1kqpa_ 51 STLAGRLAQLAVESIRE-----------------------------------EGGDAQFI 75 query 78 ------------------------------------------------------------ 78 d1kqpa_ 76 AVRLPHGTQQDEDDAQLALKFIKPDKSWKFDIKSTVSAFSDQYQQETGDQLTDFNKGNVK 135 query 78 ------------------------------------------------------------ 78 d1kqpa_ 136 ARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTKYGDGGADLLPLTGLTKRQGRTLLKE 195 query 78 ------------------------------------------------------------ 78 d1kqpa_ 196 LGAPERLYLKEPTADLLDEKPQQSDETELGISYDEIDDYLEGKEVSAKVSEALEKRYSMT 255 query 78 ---------------- 78 d1kqpa_ 256 EHKRQVPASMFDDWWK 271 TMalign alignment (TM-score: 0.35 Raw score:26.86) query 1 ----------------------PDY-PVL-DAILELYVDRDTGADAIVA------AG-YD 29 ::: ::: :: ::: ::::: : : :: : :: d1kqpa_ 1 SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQY-VKK-TGAKG-F-V-LGISGGQD-STLA 54 query 30 RELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRR----------------------- 66 ::::::::::::::: : : d1kqpa_ 55 GRLAQLAVESIREEG----------------G----DAQFIAVRLPHGTQQDEDDAQLAL 94 query 67 ---LPITNRWREGH---------------------------------------------- 77 ::: d1kqpa_ 95 KFI--------KPDKSWKFDIKSTVSAFSDQYQQETGDQLTDFNKGNVKARTRMIAQYAI 146 query 78 ------------------------------------------------------------ 78 d1kqpa_ 147 GGQEGLLVLGTDHAAEAVTGFFTKYGDGGADLLPLTGLTKRQGRTLLKELGAPERLYLKE 206 query 78 ------------------------------------------------------------ 78 d1kqpa_ 207 PTADLLDEKPQQSDETELGISYDEIDDYLEGKEVSAKVSEALEKRYSMTEHKRQVPASMF 266 query 78 ----- 78 d1kqpa_ 267 DDWWK 271 HHsearch alignment (Probability: 0.94 E-value:0.00) query 2 DYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGT 54 :::::::::::: ::::::::::::::::::::: :::::: d1kqpa_ 227 SYDEIDDYLEGK-------------EVSAKVSEALEKRYSMTEHKR-QVPASM 265
Intermediate <-- 1.000 --> HitDALI alignment (Z-score: 14.5 Raw score:1288.10) d1kqpa_ 1 smqekimrelhvkpsIDPKQEIEDRVNFLKQYVKktgAKGFVLGISGGQDSTLAGRLAQL 60 ::::::::::::::::::: ::::::::::::::::::::::: d1gpma1 1 ---------------WTPAKIIDDAVARIREQVG---DDKVILGLSGGVDSSVTAMLLHR 42 d1kqpa_ 61 AVEsireeggdAQFIAVRLPHGTQQ--DEDDAQLALK-fIKPDkSWKFDIKSTVSAFSDQ 117 ::: :::::::::::::: :::::::::: :::: :::::::::::::::: d1gpma1 43 AIG--------KNLTCVFVDNGLLRlnEAEQVLDMFGdhFGLN-IVHVPAEDRFLSALAG 93 d1kqpa_ 118 YqqetgdqLTDFNKGNVKARTRMIAQYAIGGQE--GLLVLGTDHAAEAVTGfftkygdgg 175 : ::::::::::::::::::::::::: :::::::::::::::: d1gpma1 94 E-------NDPEAKRKIIGRVFVEVFDEEALKLedVKWLAQGTIYPDVIES-----aakm 141 d1kqpa_ 176 aDLLPLTGLTKRQGRTLLKELGAPERLYLKEPTAdlldekpqqsdetelgisydeiddyl 235 ::::::::::::::::::::::::::::::::: d1gpma1 142 gLVEPLKELFKDEVRKIGLELGLPYDMLYRHPFP-------------------------- 175 d1kqpa_ 236 egkevsakvsealekrysmtehkrqvpasmfddwwk 271 d1gpma1 176 ------------------------------------ 176 FAST alignment (Normalized score: 12.55 Raw score:2733.00) d1kqpa_ 1 SMQEKIMRELHVKPSI-DPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLAQ 59 ::::::::::::::::: ::: :::::::::::::::::::: d1gpma1 1 ----------------WTPAKIIDDAVARIREQV--GDD-KVILGLSGGVDSSVTAMLLH 41 d1kqpa_ 60 LAVESIREEGGDA---QFIAVRLPHGTQ---QDEDDA-QLALKFIKPDKSWKFDIKSTVS 112 :: ::::::::::: :::::: :::::::: ::::::::::::: d1gpma1 42 RA-----------IGKNLTCVFVDNGL-LRLNEAEQVLDMFGDHFG-LNIVHVPAEDRFL 88 d1kqpa_ 113 AFSDQYQQETGDQ-LTDFNKGNVKARTRMIAQYAIGGQEG----LLVLGTDHAAEAVTGF 167 ::::: :::::::::::::::::::::::: ::::::::::::: d1gpma1 89 SALAG--------ENDPEAKRKIIGRVFVEVFDEEALK--LEDVKWLAQGTIYPDVI--- 135 d1kqpa_ 168 FTKYGDGGA-------DLLPLTGLTKRQGRTLLKELGAPERLYLKEPTADLLDEKPQQSD 220 :::::::::::::::::::::::::::::::: d1gpma1 136 ---------ESAAKMGLVEPLKELFKDEVRKIGLELGLPYDMLYRHPF------------ 174 d1kqpa_ 221 ETELGISYDEIDDYLEGKEVSAKVSEALEKRYSMTEHKRQVPASMFDDWWK- 271 d1gpma1 175 ---------------------------------------------------P 175 TMalign alignment (TM-score: 0.52 Raw score:141.32) d1kqpa_ 1 SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLAQL 60 ::::::::::::::::::: :: ::::::::::::::::::::: d1gpma1 1 ---------------WTPAKIIDDAVARIREQVG--DD-KVILGLSGGVDSSVTAMLLHR 42 d1kqpa_ 61 AVESIREEGGDAQFIAVRLPHGTQQ--DEDDAQLAL-KFIKPDKSWKFDIKSTVSAFSDQ 117 ::: :::::::::::::: ::::::::: ::::: :::::::::::::::: d1gpma1 43 AIG--------KNLTCVFVDNGLLRLNEAEQVLDMFGDHFGL-NIVHVPAEDRFLSALA- 92 d1kqpa_ 118 YQQETGDQLTDFNKGNVKARTRMIAQYAIGGQE-GL-LVLGTDHAAEAVTG---FFTKYG 172 : :::::::::::::::::::::::::: :: :::::::::::::: d1gpma1 93 -G-----ENDPEAKRKIIGRVFVEVFDEEALKLEDVKWLAQGTIYPDVIESAAK------ 140 d1kqpa_ 173 DGGADLLPLTGLTKRQGRTLLKELGAPERLYLKEPTADLLDEKPQQSDETELGISYDEID 232 ::::::::::::::::::::::::::::::::::: d1gpma1 141 --MGLVEPLKELFKDEVRKIGLELGLPYDMLYRHPFP----------------------- 175 d1kqpa_ 233 DYLEGKEVSAKVSEALEKRYSMTEHKRQVPASMFDDWWK 271 d1gpma1 176 --------------------------------------- 176 HHsearch alignment (Probability: 1.00 E-value:0.00) d1kqpa_ 16 IDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVESIREEGGDAQFI 75 :::::::::::::::::: :::::::::::::::::::::::::::: ::::: d1gpma1 1 WTPAKIIDDAVARIREQV---GDDKVILGLSGGVDSSVTAMLLHRAIGK------NLTCV 51 d1kqpa_ 76 AVRLPH-GTQQDEDDAQLALKFIKPDKSWKFDIKSTVSAFSDQYQQETGDQLTDFNKGNV 134 :::::: ::::::::::::::::::::: :::::::::::::: :::::::::: d1gpma1 52 FVDNGLLRLNEAEQVLDMFGDHFGLNIV-HVPAEDRFLSALAG-------ENDPEAKRKI 103 d1kqpa_ 135 KARTRMIAQYAIGGQEG-LLVLGTDHAAEAVTGFFTKYGDGGADLLPLTGLTKRQGRTLL 193 ::::::::::::::::: :::::::::::::::::::::: :::::::::::::::: d1gpma1 104 IGRVFVEVFDEEALKLEDVKWLAQGTIYPDVIESAAKMGL----VEPLKELFKDEVRKIG 159 d1kqpa_ 194 KELGAPERLYLKEPTA 209 :::::::::::::::: d1gpma1 160 LELGLPYDMLYRHPFP 175