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 | d1k92a1 | Argininosuccinate synthetase, N-terminal 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 <-- 0.994 --> HitDALI alignment (Z-score: 9.9 Raw score:949.30) d1kqpa_ 1 smqekimrelhvkpsidpkqeiedrvnFLKQYVkktgakGFVLGISGGQDSTLAGRLAQL 60 :::::: ::::::::::::::::::::: d1k92a1 1 ----------------------ttilkHLPVGQ------RIGIAFSGGLDTSAALLWMRQ 32 d1kqpa_ 61 AVesireeggdaQFIAVRLPHGT--QQDEDDAQLALKFIKPDKSWKFDIKSTVSAFSDQY 118 :: ::::::::::: ::::::::::::::::::::::::::::::::::: d1k92a1 33 KG---------aVPYAYTANLGQpdEEDYDAIPRRAMEYGAENARLIDCRKQLVAEGIAA 83 d1kqpa_ 119 QQetgDQLT--------DFNKGNVKARTRMIAQYAIGGQEGL-LVLGTDhaaeavTGFFT 169 :: :::: ::::::::::::::::::::::::: :::::: ::::: d1k92a1 84 IQ---CGAFhnttggltYFNTTPLGRAVTGTMLVAAMKEDGVnIWGDGS-----tYKGND 135 d1kqpa_ 170 KYGDGG---------aDLLPLT-------gLTKRQGRTLLKELGAPErlYLKEptadlld 213 :::::: :::::: ::::::::::::::::: :::: d1k92a1 136 IERFYRyglltnaelqIYKPWLdtdfidelGGRHEMSEFMIACGFDY--KMSV------- 186 d1kqpa_ 214 ekpqqsdetelgisydeiddylegkevsakvsealekrysmtehkrqvpasmfddwwk 271 d1k92a1 187 --------------------------------------------------------ek 188 FAST alignment (Normalized score: 7.32 Raw score:1652.00) d1kqpa_ 1 SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQYVKKTGAK-----------GFVLGISGGQ 49 :::::::::: d1k92a1 1 ---------------------------------------TTILKHLPVGQRIGIAFSGGL 21 d1kqpa_ 50 DSTLAGRLAQLAVESIREEGG-DAQFIAVRLPHGTQQDEDDAQLALKF---IKPDKSWKF 105 ::::::::::: ::::::::::: :::::::::::::: ::::::::: d1k92a1 22 DTSAALLWMRQ----------KGAVPYAYTANL-GQPDEEDYDAIPRRAMEYGAENARLI 70 d1kqpa_ 106 DIKSTVSAFSDQYQQETGDQLTD-------------FNKGNVKARTRMIAQYAIGGQEG- 151 ::::::::::::::: ::::::::::::::::::::::: d1k92a1 71 DCRKQLVAEGIAAIQ--------CGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKEDGV 122 d1kqpa_ 152 LLVLGTDHAAEAVTGFFTKYGDGGA------------------DLLPLTG---------- 183 ::::::: :::: :::: d1k92a1 123 NIWGDGS---TYKG-----------NDIERFYRYGLLTNAELQIYKP---WLDTDFIDEL 165 d1kqpa_ 184 LTKRQGRTLLKELGAPERLYLKEPTADLLDEKPQQSDETELGISYDEIDDYLEGKEVSAK 243 ::::::::::::: d1k92a1 166 GGRHEMSEFMIAC----------------------------------------------- 178 d1kqpa_ 244 VSEALEKRYSMTEHKRQVPASMFDDWWK---------- 271 d1k92a1 179 ----------------------------GFDYKMSVEK 188 TMalign alignment (TM-score: 0.49 Raw score:131.52) d1kqpa_ 1 ----SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGR 56 : :::: : :::::::::::::::::: d1k92a1 1 TTIL------------------------K-HLPV--G-----QRIGIAFSGGLDTSAALL 28 d1kqpa_ 57 LAQLAVESIREEGGDAQFIAVRLPHGT--QQDEDDAQLALKFIKPDKSWKFDIKSTVSAF 114 ::::: :: ::::::::::: ::::::::::::::::::::::::::::::: d1k92a1 29 WMRQK--GA-------VPYAYTANLGQPDEEDYDAIPRRAMEYGAENARLIDCRKQLVAE 79 d1kqpa_ 115 SDQYQQETGDQL------TDFNKGNVKARTRMIAQYAIGGQEGL-LVLGTDHAAEAVTGF 167 :::::: ::::: :::::::::::::::::::::::::: :::::: :: :: d1k92a1 80 GIAAIQ-CGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKEDGVNIWGDGS---TY--KG 133 d1kqpa_ 168 FTKYGDG--G-------ADLLPLT----G---LTKRQGRTLLKELGAPERLYLKEPTADL 211 ::::::: : ::::::: : :::::::::::::::::: ::: d1k92a1 134 NDIERFYRYGLLTNAELQIYKPWLDTDFIDELGGRHEMSEFMIACGFDYK--MSV----- 186 d1kqpa_ 212 LDEKPQQSDETELGISYDEIDDYLEGKEVSAKVSEALEKRYSMTEHKRQVPASMFDDWWK 271 : : d1k92a1 187 -------E-K-------------------------------------------------- 188 HHsearch alignment (Probability: 0.99 E-value:0.00) d1kqpa_ 37 GAKGFVLGISGGQDSTLAGRLAQLAVESIREEGGDAQFIAVRLPHGTQQDEDDAQLALKF 96 :::::::::::::::::::::::::: ::::::::::::::::::::::::::: d1k92a1 9 VGQRIGIAFSGGLDTSAALLWMRQKG-------AVPYAYTANLGQPDEEDYDAIPRRAME 61 d1kqpa_ 97 IKPDKSWKFDIKSTVS-AFSDQ----YQQETGDQLTDFNKGNVKARTRMIAQYAIGGQEG 151 :::::::::::::::: ::::: :::::::::::::::::::::::::::::::::: d1k92a1 62 YGAENARLIDCRKQLVAEGIAAIQCGAFHNTTGGLTYFNTTPLGRAVTGTMLVAAMKEDG 121 d1kqpa_ 152 LLVLGTDHAA------EAVTGFFTKYGDGGADLLPLTGL-------TKRQGRTLLKELGA 198 :::::::::: ::::::::::::: ::::::::: :::::::::::::: d1k92a1 122 VNIWGDGSTYKGNDIERFYRYGLLTNAEL-QIYKPWLDTDFIDELGGRHEMSEFMIACGF 180 d1kqpa_ 199 PER 201 ::: d1k92a1 181 DYK 183