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 | d1sura_ | Phosphoadenylyl sulphate (PAPS) reductase | 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 <-- 0.990 --> HitDALI alignment (Z-score: 9.6 Raw score:971.90) d1kqpa_ 1 -------smqekimrelhvkpsidpkqeiEDRVNFLKQYVKKTGAKGFVLgISGGQDSTL 53 ::::::::::::::::::::: ::::::::: d1sura_ 1 skldlnalnelpkvdrilalaetnaelekLDAEGRVAWALDNLPGEYVLS-SSFGIQAAV 59 d1kqpa_ 54 AGRLAQLAVEsireeggdaQFIAVRLPHGTQQ--DEDDAQLALKFIKPdKSWKFDIKSTV 111 :::::::::: ::::::::::::: :::::::::::::: ::::::::::: d1sura_ 60 SLHLVNQIRP---------DIPVILTDTGYLFpeTYRFIDELTDKLKL-NLKVYRATESA 109 d1kqpa_ 112 SAFSDQYQqetgdQLTDFNKGNVKARTRMIAQYAIGGQEGL-LVLGTDHAAEaVTGF--- 167 :::::::: :::::::::::::::::::::::::::: :::::::::: :::: d1sura_ 110 AWQEARYG--klwEQGVEGIEKYNDINKVEPMNRALKELNAqTWFAGLRREQ-SGSRanl 166 d1kqpa_ 168 -ftkygdggaDLLPLTGLTKRQGRTLLKELGAPerLYLKE----PTADLLDekpqqsdet 222 ::::::::::::::::::::::: ::::: ::::::: d1sura_ 167 pvlaiqrgvfKVLPIIDWDNRTIYQYLQKHGLK--YHPLWdegyLSVGDTH--------- 215 d1kqpa_ 223 elgisydeiddylegkevsakvsealekrysmtehkrqvpasmfddwwk 271 d1sura_ 216 ------------------------------------------------- 216 FAST alignment (Normalized score: 7.68 Raw score:1854.00) d1kqpa_ 1 SMQEKIMRELHVKPSIDPKQEIE------------------------------DRVNFLK 30 ::::::: d1sura_ 1 -----------------------SKLDLNALNELPKVDRILALAETNAELEKLDAEGRVA 37 d1kqpa_ 31 QYVKKTGAKGFVLGISGGQDSTLAGRLAQLAVESIREEGGD-AQFIAVRLPHGTQQ---- 85 ::::::::: ::::::::::::::::::::: :::::::::::: d1sura_ 38 WALDNLPGE-YVLSSSFGIQAAVSLHLVNQI----------RPDIPVILTDTGY--LFPE 84 d1kqpa_ 86 DEDDAQLALKFIKPDKSWKFDIKS---TVSAFSDQYQQETGDQLT-------DFNKGNVK 135 :::::::::::::: :::::: :::::::: :::::::: d1sura_ 85 TYRFIDELTDKLKL-NLKVYR---ATESAAWQEAR----------YGKLWEQGVEGIEKY 130 d1kqpa_ 136 AR-TRMIAQYAIGGQEG-LLVLGTDHAAEAVTGFFTKYGDGGA----------------- 176 :: :::::::::::::: ::::::::: d1sura_ 131 NDINKVEPMNRALKELNAQTWFAGLRR----------------EQSGSRANLPVLAIQRG 174 d1kqpa_ 177 --DLLPLTGLTKRQGRTLLKELGAPERLY-------LKEPTADLLDEKPQQSDETELGIS 227 ::::::::::::::::::::::: ::::: d1sura_ 175 VFKVLPIIDWDNRTIYQYLQKHGLK----YHPLWDEGYLSV------------------- 211 d1kqpa_ 228 YDEIDDYLEGKEVSAKVSEALEKRYSMTEHKRQVPASMFDDWWK---- 271 d1sura_ 212 --------------------------------------------GDTH 215 TMalign alignment (TM-score: 0.50 Raw score:134.84) d1kqpa_ 1 -----------------------------SMQEKIMRELHVKPSIDPKQEIEDRVNFLKQ 31 ::::::::: d1sura_ 1 SKLDLNALNELPKVDRILALAETNAELEK----------------------LDAEGRVAW 38 d1kqpa_ 32 YVKKTGAKGFVLGISGGQDSTLAGRLAQLAVESIREEGGDAQFIAVRLPHGTQ-QD-EDD 89 ::::::::::::::: :::::::::::::::: :::::::::::: :: ::: d1sura_ 39 ALDNLPGEYVLSSSF-GIQAAVSLHLVNQIRP---------DIPVILTDTGYLFPETYRF 88 d1kqpa_ 90 AQLALKFIKPDKSWKFDIKSTV-SAFSDQYQQETGDQLTDFN-KGNVKAR-TRMIAQYAI 146 :::::::::: ::::::::::: :::::: : ::::::: ::::::: ::::::::: d1sura_ 89 IDELTDKLKL-NLKVYRATESAAWQEARY-G----KLWEQGVEGIEKYNDINKVEPMNRA 142 d1kqpa_ 147 GGQEGL-LVLGTDHAAEAVTGFF--------TKYGDGGA---DLLPLTGLTKRQGRTLLK 194 :::::: :::::::::: :::: :: :::::::::::::::::: d1sura_ 143 LKELNAQTWFAGLRREQ--SGSRANLPVLAI------QRGVFKVLPIIDWDNRTIYQYLQ 194 d1kqpa_ 195 ELGAPERLYLK---EPTADLLDEKPQQSDETELGISYDEIDDYLEGKEVSAKVSEALEKR 251 :::: :::::: :::::::: d1sura_ 195 KHGL-KYHPLWDEGYLSVGDTH-------------------------------------- 215 d1kqpa_ 252 YSMTEHKRQVPASMFDDWWK 271 d1sura_ 216 -------------------- 216 HHsearch alignment (Probability: 0.99 E-value:0.00) d1kqpa_ 39 KGFVLGISGGQDSTLAGRLAQLAVESIREEGGDAQFIAVRLPHGTQQDEDDAQLALKFIK 98 :::::::::::::::::::::::: ::::::::::::::::::::::::::::: d1sura_ 45 GEYVLSSSFGIQAAVSLHLVNQIR-------PDIPVILTDTGYLFPETYRFIDELTDKLK 97 d1kqpa_ 99 PDKSWKFDIKSTVSAFSDQYQQETGDQLTDFNKGNVKARTRMIAQYAIGGQEGLLVLGTD 158 ::::: ::::::::::::::::::::::::::::::: ::::::::::::::::::::: d1sura_ 98 LNLKV-YRATESAAWQEARYGKLWEQGVEGIEKYNDI--NKVEPMNRALKELNAQTWFAG 154 d1kqpa_ 159 HAAEA-VTG--FFTKYGDGGA-DLLPLTGLTKRQGRTLLKELGAPERLYL 204 ::::: ::: :::::::::: :::::::::::::::::::::::::::: d1sura_ 155 LRREQSGSRANLPVLAIQRGVFKVLPIIDWDNRTIYQYLQKHGLKYHPLW 204