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 | d1q15a1 | 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 <-- 0.985 --> HitDALI alignment (Z-score: 10.4 Raw score:1072.00) d1kqpa_ 1 -sMQEKimrelhvKPSI-DPKQEIEDRVNFLKQYVKktGAKGFVLGISGGQDSTLAGRLA 58 :::: :::: :::::::::::::::::: :::::::::::::::::::::: d1q15a1 1 paSNQL-----laLPREpLLALIDRYLNAPLEDLAP--RFDTVGIPLSGGLDSSLVTALA 53 d1kqpa_ 59 QLAVesireeggdAQFIAVRLPHGTQQDEDDAQLALKFIKPdKSWKFDIKS-TVSAfsdq 117 :::: :::::::::::::::::::::::::::: ::::::::: :::: d1q15a1 54 SRHF---------KKLNTYSIGTELSNEFEFSQQVADALGT-HHQMKILSEtEVIN---- 99 d1kqpa_ 118 yqqetgdqltdFNKGNVKARTRMIAQYAIGGQEGLLVLGT-DHAAE-------------- 162 ::::::::::::::::::::::::::::: ::::: d1q15a1 100 giiesiyyneiFDGLSAEIQSGLFNVYRQAQGQVSCMLTGyGSDLLfggilkpgaqydnp 159 d1kqpa_ 163 ---AVTGF------FTKY-----gdggaDLLPLT-------------------gltKRQG 189 ::::: :::: :::::: :::: d1q15a1 160 nqlLAEQVyrtrwtGEFAthgascygidIRHPFWshslislchalhpdykifdnevKNIL 219 d1kqpa_ 190 RTLLKELG-APERLYLkeptadlldekpqqsdetelgisydeiddylegkevsakvseal 248 :::::::: ::::::: d1q15a1 220 REYADSLQlLPKDIVW---------------rsvnqafanvlgstvdnyqtksrftyrvy 264 d1kqpa_ 249 ekrysmtehkrqvpasmfddwwk 271 d1q15a1 265 qaflrgrlsitdvtpsqlkdlik 287 FAST alignment (Normalized score: 6.92 Raw score:1931.00) d1kqpa_ 1 SMQEKIMRELHVKPSI-------------DPKQEIEDRVNFLKQYVKKTGAKGFVLGISG 47 :::::::::::::::::: ::::::::::: d1q15a1 1 ----------------PASNQLLALPREPLLALIDRYLNAPLEDLAP--RFDTVGIPLSG 42 d1kqpa_ 48 GQDSTLAGRLAQLAVESIREEGGD-AQFIAVRLPHGTQ--QDEDDAQLALKFIKPDKSWK 104 :::::::::::::: ::::::::::: :::::::::::::: ::::: d1q15a1 43 GLDSSLVTALASRH----------FKKLNTYSIGTE--LSNEFEFSQQVADALG-THHQM 89 d1kqpa_ 105 FD-----IKSTVSAFSDQYQQETGDQLTDF-----NKGNVKARTRMIAQYAIGGQEG--L 152 :: :::::::::: :::::::::::::::::::: : d1q15a1 90 KILSETEVINGIIESIY-------------YNEIFDGLSAEIQSGLFNVYRQAQG--QVS 134 d1kqpa_ 153 LVLGTDH------AAEAVTGFFTKYGDGGA------------------------------ 176 ::::: :::: d1q15a1 135 CMLTG--YGSDLLFGGI-------------LKPGAQYDNPNQLLAEQVYRTRWTGEFATH 179 d1kqpa_ 177 --------DLLPLTGLT-----------------------KRQGRTLLKEL-GAPERLYL 204 ::::: ::::::::::: :::::: d1q15a1 180 GASCYGIDIRHPF----WSHSLISLCHALHPDYKIFDNEVKNILREYADSLQLLPKDI-- 233 d1kqpa_ 205 KEPTADLLDEKPQQSDETELGISYDEIDDYLEGKEVSAKVSEALEKRYSMTEHKRQVPAS 264 d1q15a1 234 ------------------------------------------------------------ 234 d1kqpa_ 265 MFDDWWK----------------------------------------------------- 271 d1q15a1 234 -------VWRSVNQAFANVLGSTVDNYQTKSRFTYRVYQAFLRGRLSITDVTPSQLKDLI 286 d1kqpa_ 272 - 272 d1q15a1 287 K 287 TMalign alignment (TM-score: 0.52 Raw score:140.78) d1kqpa_ 1 -SMQEKIMRELHVKPS-IDPKQEIEDRVNFLKQYVKKTGAKGFVLGISGGQDSTLAGRLA 58 :::: :: :::: ::::::::::::::::::: :::::::::::::::::::::: d1q15a1 1 PASNQ-LL----ALPREPLLALIDRYLNAPLEDLAP--RFDTVGIPLSGGLDSSLVTALA 53 d1kqpa_ 59 QLAVESIREEGGDAQFIAVRLPHGTQQDEDDAQLALKFIKPDKSWKFDIK-STVSAFSD- 116 ::::: ::::::::::::::::::::::::::: :::::::: :::::::: d1q15a1 54 SRHFK---------KLNTYSIGTELSNEFEFSQQVADALGT-HHQMKILSETEVINGIIE 103 d1kqpa_ 117 --------QYQQETGDQLTDFNKGNVKARTRMIAQYAIGGQEGLLVLGT-DH--AAE--- 162 :: :::::::::::::::::::::::::: :: ::: d1q15a1 104 SIYYNEIF------------DG-LSAEIQSGLFNVYRQAQGQVSCMLTGYGSDLLFGGIL 150 d1kqpa_ 163 ------------AVTGF-FT--KYGDGGA---------DLLPLT---G---L-------T 185 ::::: :: ::: ::: :::::: : : : d1q15a1 151 KPGAQYDNPNQLLAEQVYRTRWTGE-FATHGASCYGIDIRHPFWSHSLISLCHALHPDYK 209 d1kqpa_ 186 ------KRQGRTLLKELG-APERLYLKEPTADLLDE---------KPQQSDETE------ 223 :::::::::::: :::::::: ::::: : d1q15a1 210 IFDNEVKNILREYADSLQLLPKDIVWR----SVNQAFANVLGSTV--------DNYQTKS 257 d1kqpa_ 224 ------------------------------LGISYDEIDDYLEGKEVSAKVSEALEKRYS 253 d1q15a1 258 RFTYRVYQAFLRGRLSITDVTPSQLKDLIK------------------------------ 287 d1kqpa_ 254 MTEHKRQVPASMFDDWWK 271 d1q15a1 288 ------------------ 288 HHsearch alignment (Probability: 0.99 E-value:0.00) d1kqpa_ 12 VKPSIDPKQEIEDRVNFLKQYVKKTGAKG--FVLGISGGQDSTLAGRLAQLAVESIREEG 69 ::::::::::::::::::::::::::::: :::::::::::::::::::::::: d1q15a1 5 QLLALPREPLLALIDRYLNAPLEDLAPRFDTVGIPLSGGLDSSLVTALASRHFKK----- 59 d1kqpa_ 70 GDAQFIAVRLPHGTQQDEDDAQLALKFIKPDKSWKFDIKSTVSAFSDQYQQETGDQLTDF 129 : ::::::::::::::::::::::::::::::::::::::::::::::::::: :: d1q15a1 60 --L--NTYSIGTELSNEFEFSQQVADALGTHHQMKILSETEVINGIIESIYYNEIF-DG- 113 d1kqpa_ 130 NKGNVKARTRMIAQYAIGGQEGLLVLGTDHAAEAVTGFFTKYG 172 : :::::::::::::::::::::::::::::::::::::::: d1q15a1 114 L--SAEIQSGLFNVYRQAQGQVSCMLTGYGSDLLFGGILKPGA 154