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 | d1jgta1 | beta-Lactam synthetase | 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 <-- 0.988 --> HitDALI alignment (Z-score: 8.7 Raw score:983.70) d1kqpa_ 1 smQEKIMrelhvKPSI-DPKQEIEDRVNFLKQYVKktgaKGFVLGISGGQDSTLAGRLAQ 59 ::::: :::: :::::::::::::::::: ::::::::::::::::::::: d1jgta1 1 -pGLSRR----iLPEGeAVAAVRAALEKAVAQRVT--pgDTPLVVLSGGIDSSGVAACAH 53 d1kqpa_ 60 LAVEsireeggdaQFIAVRLPHGTQQDEDDAQLALKFIKPdKSWKFDIKS-TVSAFSdqy 118 :::: ::::::::::::::::::::::::::: ::::::::: :::::: d1jgta1 54 RAAG---------ELDTVSMGTDTSNEFREARAVVDHLRT-RHREITIPTtELLAQL--- 100 d1kqpa_ 119 qqetgdqltdFNKGNVKARTRMIAQYAIgGQEGLLVLGT-DHAAEAV------------- 164 :::::::::::::::::: :::::::::: ::::::: d1jgta1 101 pyavwasesvDPDIIEYLLPLTALYRAL-DGPERRILTGyGADIPLGgmhredrlpaldt 159 d1kqpa_ 165 ---------tgfFTKY-----gdggADLLPLT-------------------gltKRQGRT 191 :::: ::::::: :::::: d1jgta1 160 vlahdmatfdglNEMSpvlstlaghWTTHPYWdrevldllvsleaglkrrhgrdKWVLRA 219 d1kqpa_ 192 LLKELgAPERLYLKEPTadlldekpqqsdetelgisydeiddylegkevsakvsealekr 251 ::::: ::::::::::: d1jgta1 220 AMADA-LPAETVNRPKL--------ssfsrllldhgvaedrvheakrqvvrelfdltvgg 270 d1kqpa_ 252 ysmtehkrqvpasmfddwwk 271 d1jgta1 271 grhpsevdtddvvrsvadrt 290 FAST alignment (Normalized score: 6.57 Raw score:1841.00) d1kqpa_ 1 SMQEKIMRELHVKPSI------------DPKQEIEDRVNFLKQYVKKTGA----KGFVLG 44 :::::::::::::::: :::::: d1jgta1 1 ----------------PGLSRRILPEGEAVAAVRAALEKAVAQR------VTPGDTPLVV 38 d1kqpa_ 45 ISGGQDSTLAGRLAQLAVESIREEGGD-AQFIAVRLPHGTQ--QDEDDAQLALKFIKPDK 101 ::::::::::::::::: ::::::::::: :::::::::::::: :: d1jgta1 39 LSGGIDSSGVAACAHRA----------AGELDTVSMGTD--TSNEFREARAVVDHLR-TR 85 d1kqpa_ 102 SWKFD-IKSTVSAFSDQYQQETGDQLTDF-----------NKGNVKARTRMIAQYAIGG- 148 ::::: :::::::: :::::::::::::::: d1jgta1 86 HREITIPTTELLAQ---------------LPYAVWASESVDPDIIEYLLPLTALYR---A 127 d1kqpa_ 149 --QEGLLVLGTDHAAEAVTGFFTKYGDGGA------------------------------ 176 ::::::::: d1jgta1 128 LDGPERRILTG-------------------YGADIPLGGMHREDRLPALDTVLAHDMATF 168 d1kqpa_ 177 -----------------DLLPLTGLT------------------------KRQGRTLLKE 195 :::: :::::::::: d1jgta1 169 DGLNEMSPVLSTLAGHWTTHP-----YWDREVLDLLVSLEAGLKRRHGRDKWVLRAAMAD 223 d1kqpa_ 196 LGAPERLYLKEPTADLLDEKPQQSDETELGISYDEIDDYLEGKEVSAKVSEALEKRYSMT 255 ::::::::::: d1jgta1 224 -ALPAETVNRPK------------------------------------------------ 234 d1kqpa_ 256 EHKRQVPASMFDDWWK-------------------------------------------- 271 d1jgta1 235 ----------------LSSFSRLLLDHGVAEDRVHEAKRQVVRELFDLTVGGGRHPSEVD 278 d1kqpa_ 272 ------------ 272 d1jgta1 279 TDDVVRSVADRT 290 TMalign alignment (TM-score: 0.51 Raw score:138.05) d1kqpa_ 1 SMQEKIMRELHVKPS--IDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLA 58 ::::: :::: ::::::::::::::::::: :::::::::::::::::::::: d1jgta1 1 ---PGLSR---RILPEGEAVAAVRAALEKAVAQRVT--PGDTPLVVLSGGIDSSGVAACA 52 d1kqpa_ 59 QLAVESIREEGGDAQFIAVRLPHGTQQDEDDAQLALKFIKPDKSWKFDIK-STVSAFSDQ 117 ::::: ::::::::::::::::::::::::::: :::::::: ::::::: : d1jgta1 53 HRAAG---------ELDTVSMGTDTSNEFREARAVVDHLRT-RHREITIPTTELLAQL-P 101 d1kqpa_ 118 Y--------QQETGDQLTDFNKGNVKARTRMIAQYAIGGQEGLLVLGTDH--AAEA---- 163 : ::::::::::::::::::::::::::::::: :::: d1jgta1 102 YAVWASESV----------DPDIIEYLLPLTALYRALDGPERRILTGYGADIPLGGMHRE 151 d1kqpa_ 164 ---------V-TGF--F-TKYGDGG---------ADLLP----LT-GL-------T---- 185 : ::: : ::::::: ::::: :: :: : d1jgta1 152 DRLPALDTVLAHDMATFDGLNEMSPVLSTLAGHWTTHPYWDREVLDLLVSLEAGLKRRHG 211 d1kqpa_ 186 --KRQGRTLLKELGAPERLYLKEPTADLLD-EK--------------------------- 215 :::::::::::::: :::::::: :: :: d1jgta1 212 RDKWVLRAAMADALPA-ETVNRPKL---SSFSRLLLDHGVAEDRVHEAKRQVVRELFDLT 267 d1kqpa_ 216 -----------------------PQQSDETELGISYDEIDDYLEGKEVSAKVSEALEKRY 252 d1jgta1 268 VGGGRHPSEVDTDDVVRSVADRT------------------------------------- 290 d1kqpa_ 253 SMTEHKRQVPASMFDDWWK 271 d1jgta1 291 ------------------- 291 HHsearch alignment (Probability: 0.99 E-value:0.00) d1kqpa_ 15 SIDPKQEIEDRVNFLKQYVKKT--GAKGFVLGISGGQDSTLAGRLAQLAVESIREEGGDA 72 :::::::::::::::::::::: ::::::::::::::::::::::::::: d1jgta1 7 ILPEGEAVAAVRAALEKAVAQRVTPGDTPLVVLSGGIDSSGVAACAHRAAG--------- 57 d1kqpa_ 73 QFIAVRLPHGTQQDEDDAQLALKFIKPDKSWKFDIKS-TVSAFSDQYQQETGDQLTDFNK 131 ::::::::::::::::::::::::::::::::::::: ::::::::::: ::: :::: d1jgta1 58 ELDTVSMGTDTSNEFREARAVVDHLRTRHREITIPTTELLAQLPYAVWA-SES-VDPD-- 113 d1kqpa_ 132 GNVKARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTK 170 :::::::::::::::::::::::::::::::::::::: d1jgta1 114 -IIEYLLPLTALYRALDGPERRILTGYGADIPLGGMHRE 151