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: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1gpma1 | GMP synthetase, central domain | 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 <-- 0.999 --> IntermediateDALI alignment (Z-score: 17.0 Raw score:1273.10) query 1 DADEEVYSALVVGLRAYVAkngFRSVLIGLSGGIDSALVAAIACDALGaQNVYGVSMPSK 60 ::::::::::::::::::: :::::::::::::::::::::::::: ::::::::::: d1gpma1 1 WTPAKIIDDAVARIREQVG---DDKVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVDNG 56 query 61 YSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMAsLGLTGLAEENLQSRLRGTTLMAI 119 ::::::::::: :::::::::::::::::::::::: ::::::::::::::::::::::: d1gpma1 57 LLRLNEAEQVLdMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFDEE 115 query 120 SNQE--GHIVLAPGNKSELAVGystlygdsvgAYGPIKDVYKTSIFRLAEWRNraaaerg 177 :::: :::::::::::::::: ::::::::::::::::::::: d1gpma1 116 ALKLedVKWLAQGTIYPDVIES-----aakmgLVEPLKELFKDEVRKIGLELG------- 163 query 178 qtppIPEASITKpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrr 237 :::::::: d1gpma1 164 ----LPYDMLYR------------------------------------------------ 171 query 238 qyppgtkisakgfgkdrrlpitnrwregh 266 d1gpma1 172 -------------------------hpfp 175 FAST alignment (Normalized score: 13.11 Raw score:2830.00) query 1 DADEEVYSALVVGLRAYVAKNGF---RSVLIGLSGGIDSALVAAIACDALGAQNVYGVSM 57 ::::::::::::::::: ::::::::::::::::::::::: :::::::::: d1gpma1 1 WTPAKIIDDAVARIREQ------VGDDKVILGLSGGVDSSVTAMLLHRA-IGKNLTCVFV 53 query 58 PSKYSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTL 116 :::::::::::::: :::::::::::::::::::::::::: :::::::::::::::::: d1gpma1 54 DNGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGE-NDPEAKRKIIGRVFVEVF 112 query 117 MAISNQEG----HIVLAPGNKSELAVGYSTLYGDSVG-------AYGPIKDVYKTSIFRL 165 :::::: ::::::::::::: :::::::::::::::: d1gpma1 113 DEEALK--LEDVKWLAQGTIYPDVI------------ESAAKMGLVEPLKELFKDEVRKI 158 query 166 AEWRNRAAAERGQTP-PIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVK 224 ::: :::::::: d1gpma1 159 GLE------------LGLPYDMLY------------------------------------ 170 query 225 TLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----- 266 d1gpma1 171 ------------------------------------------RHPFP 175 TMalign alignment (TM-score: 0.53 Raw score:140.98) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 ::::::::::::::::::: :: :::::::::::::::::::::::: ::::::::::: d1gpma1 1 WTPAKIIDDAVARIREQVG--DD-KVILGLSGGVDSSVTAMLLHRAIG-KNLTCVFVDNG 56 query 61 YSSDHSKGDAA-ELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAI 119 ::::::::::: :::::::::::::::::::::::: ::::::::::::::::::::::: d1gpma1 57 LLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALA-GENDPEAKRKIIGRVFVEVFDEE 115 query 120 SNQEG-H-IVLAPGNKSELAVG---YSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAA 174 ::::: : :::::::::::::: ::::::::::::::::::::::: d1gpma1 116 ALKLEDVKWLAQGTIYPDVIESAAK--------MGLVEPLKELFKDEVRKIGLELG---- 163 query 175 ERGQTPPIPEASITKPDY--PVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTA 232 :::::::: :: d1gpma1 164 -------LPYDMLYR-HPFP---------------------------------------- 175 query 233 EYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1gpma1 176 ---------------------------------- 176 HHsearch alignment (Probability: 1.00 E-value:0.00) query 4 EEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSS 63 ::::::::::::::::: ::::::::::::::::::::::::::: :::::::::::: d1gpma1 4 AKIIDDAVARIREQVGD---DKVILGLSGGVDSSVTAMLLHRAIGKN-LTCVFVDNGLLR 59 query 64 DHSKGD-AAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSRLRGTTLMAISNQ 122 :::::: ::::::::::::::::::::::::::::::::: ::::::::::::::::::: d1gpma1 60 LNEAEQVLDMFGDHFGLNIVHVPAEDRFLSALAGENDPEA-KRKIIGRVFVEVFDEEALK 118 query 123 EGHI-VLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPP 181 :::: :::::::::::::::::::: :::::::::::::::::::: d1gpma1 119 LEDVKWLAQGTIYPDVIESAAKMGL----VEPLKELFKDEVRKIGLELG----------- 163 query 182 IPEASITKPDYP 193 :::::::::::: d1gpma1 164 LPYDMLYRHPFP 175
Intermediate <-- 0.990 --> HitDALI alignment (Z-score: 11.4 Raw score:981.00) d1gpma1 1 ------------WTPAKIIDDAVARIREQVGDD-KVILGLSGGVDSSVTAMLLHRAIgKN 47 ::::::::::::::::::::: ::::::::::::::::::::::: :: d1q15a1 1 pasnqllalprePLLALIDRYLNAPLEDLAPRFdTVGIPLSGGLDSSLVTALASRHF-KK 59 d1gpma1 48 LTCVFVDNGLLRlnEAEQVLDMFGdHFGLNIVHVPAED-RFLS---alagendpEAKRKI 103 :::::::::::: :::::::::: ::::::::::::: :::: :::::: d1q15a1 60 LNTYSIGTELSN--EFEFSQQVAD-ALGTHHQMKILSEtEVINgiiesiyyneiFDGLSA 116 d1gpma1 104 IGRVFVEVFDEEALKLedVKWLAQGT-IYPD------------------viESAA----- 139 :::::::::::::::: :::::::: :::: :::: d1q15a1 117 EIQSGLFNVYRQAQGQ--VSCMLTGYgSDLLfggilkpgaqydnpnqllaeQVYRtrwtg 174 d1gpma1 140 ----------KMGLVEPLKE-------------------lfKDEVRKIGLELG-LPYDML 169 :::::::::: :::::::::::: :::::: d1q15a1 175 efathgascyGIDIRHPFWShslislchalhpdykifdnevKNILREYADSLQlLPKDIV 234 d1gpma1 170 YR-----------------------------------------------hpfp 175 :: d1q15a1 235 WRsvnqafanvlgstvdnyqtksrftyrvyqaflrgrlsitdvtpsqlkdlik 287 FAST alignment (Normalized score: 7.61 Raw score:1705.00) d1gpma1 1 W---------TPAKIIDDAVARIREQVGD------DKVILGLSGGVDSSVTAMLLHRAIG 45 :::::::::::::::::: :::::::::::::::::::::::: d1q15a1 1 -PASNQLLALPREPLLALIDRYLNAPLE-DLAPRFDTVGIPLSGGLDSSLVTALASRHF- 57 d1gpma1 46 KNLTCVFVDNGLLRL---NEAEQVLDMFGDHFGLNIVHVP-AEDRFLSALAGENDPE--- 98 :::::::::: ::::::: :::::::::::::: :::::::: d1q15a1 58 KKLNTYSIGT-----ELSNEFEFSQ-QVADALGTHHQMKILSETEVING--------IIE 103 d1gpma1 99 --------AKRKIIGRVFVEVFDEEALKLE-DVKWLAQGTI------------------- 130 ::::::::::::::::::: :::::::: d1q15a1 104 SIYYNEIFDGLSAEIQSGLFNVYRQAQ---GQVSCMLTG--YGSDLLFGGILKPGAQYDN 158 d1gpma1 131 -----YPDVIESA------------AKMGLVEPLKELF---------------------- 151 :::::::: ::::::::: d1q15a1 159 PNQLLAEQVYRTRWTGEFATHGASCYGIDIRHPF----WSHSLISLCHALHPDYKIFDNE 214 d1gpma1 152 -KDEVRKIGLEL-GLPYDMLYRHPFP---------------------------------- 175 ::::::::::: :::::: d1q15a1 215 VKNILREYADSLQLLPKDI-------VWRSVNQAFANVLGSTVDNYQTKSRFTYRVYQAF 267 d1gpma1 176 -------------------- 176 d1q15a1 268 LRGRLSITDVTPSQLKDLIK 287 TMalign alignment (TM-score: 0.65 Raw score:113.68) d1gpma1 1 ------------WTPAKIIDDAVARIREQVGDD-KVILGLSGGVDSSVTAMLLHRAIGKN 47 ::::::::::::::::::::: ::::::::::::::::::::::::: d1q15a1 1 PASNQLLALPREPLLALIDRYLNAPLEDLAPRFDTVGIPLSGGLDSSLVTALASRHFKK- 59 d1gpma1 48 LTCVFVDN-GLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLSAL--------------- 91 :::::::: ::: :::::: ::::::::::::: :: :::::: d1q15a1 60 LNTYSIGTELSN---EFEFSQ-QVADALGTHHQMK-IL-SETEVINGIIESIYYNEIFDG 113 d1gpma1 92 AGENDPEAKRKIIGRVFVEVFDEEALKLEDVKWLAQG-TI-YPD---------------- 133 :::::::::::::::::::: : ::::: :: ::: d1q15a1 114 ---------LSAEIQSGLFNVYRQAQGQV-S-CMLTGYGSDLLFGGILKPGAQYDNPNQL 162 d1gpma1 134 VI-ESAA------------K---MGLVEPLK---E---L-------F------KDEVRKI 158 :: :::: : :::::::: : : : ::::::: d1q15a1 163 LAEQVYRTRWTGEFATHGASCYGIDIRHPFWSHSLISLCHALHPDYKIFDNEVKNILREY 222 d1gpma1 159 GLEL-GLPYDMLYR---HPFP--------------------------------------- 175 :::: ::::::::: : d1q15a1 223 ADSLQLLPKDIVWRSVN---QAFANVLGSTVDNYQTKSRFTYRVYQAFLRGRLSITDVTP 279 d1gpma1 176 -------- 176 d1q15a1 280 SQLKDLIK 287 HHsearch alignment (Probability: 0.99 E-value:0.00) d1gpma1 6 IIDDAVAR-IREQVGD-DKVILGLSGGVDSSVTAMLLHRAIGKNLTCVFVDNGLLRLNEA 63 :::::::: ::::::: ::::::::::::::::::::::: ::::::::::::: ::: d1q15a1 17 LIDRYLNAPLEDLAPRFDTVGIPLSGGLDSSLVTALASRH-FKKLNTYSIGTEL---SNE 72 d1gpma1 64 EQVLDMFGDHFGLNIVHVPAEDRFL-SALAGENDPEAK-RKIIGRVFVEVFDEEALKLED 121 ::::::::::::::::::::::::: :::::::::::: ::::::::::::::::::::: d1q15a1 73 FEFSQQVADALGTHHQMKILSETEVINGIIESIYYNEIFDGLSAEIQSGLFNVYRQAQGQ 132 d1gpma1 122 VKWLAQGTIYPDVIESAAKM 141 :::::::::::::::::::: d1q15a1 133 VSCMLTGYGSDLLFGGILKP 152