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 | d1p3da2 | UDP-N-acetylmuramate-alanine ligase MurC | MurD-like peptide ligases, peptide-binding domain | MurD-like peptide ligases, peptide-binding domain | α/β |
Query <-- 2.152 --> 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 <-- 0.974 --> HitDALI alignment (Z-score: 2.8 Raw score:303.80) d1gpma1 1 -------------------------wtpakiidDAVARIREQVGDDKVILGLSGG----- 30 :::::::::::::::::::::: d1p3da2 1 gagrrfdqlgefirpngkvrlvddyghhptevgVTIKAAREGWGDKRIVMIFQPHrysrt 60 d1gpma1 31 ----vdssVTAMLLhraigknLTCVFVDNGL----LRLN-EAEQVLDMFGDHFGLNIVHV 81 :::::: :::::::::: :::: :::::::::::::::::::: d1p3da2 61 rdlfddfvQVLSQV-------DALIMLDVYAageaPIVGaDSKSLCRSIRNLGKVDPILV 113 d1gpma1 82 PaedrflsalagendpeakrkiigrvFVEVFDEEALKLED-vKWLAQgtiypdviesaak 140 : :::::::::::::: ::::: d1p3da2 114 S-------------------------DTSQLGDVLDQIIQdgDLILA------------- 135 d1gpma1 141 mglveplkelfkdevrkiglelglpydmlyrhpfp 175 d1p3da2 136 ------------------qgagsvskisrglaesw 152 FAST alignment (Normalized score: 2.52 Raw score:410.50) d1gpma1 1 WTPAKIIDDAVARIREQVG----------------DDKVILGLSG----GVDSSVTAMLL 40 :::::::: ::::::::::: d1p3da2 1 -------------------GAGRRFDQLGEFIRPNGKVRLVDD--YGHHPTEVGVTIKAA 39 d1gpma1 41 HRAIGK-NLTCVFVDNGLL-------RLNEAEQVLDMFGDHFG-LNIVHVPAEDRFLSAL 91 :::::: ::::::::: ::::::::::: :::::: d1p3da2 40 REGWGDKRIVMIFQPH---RYSRTRDLFDDFVQVLSQ------VDALIML---------- 80 d1gpma1 92 AGENDPEAKRKIIG---------------------------------------------- 105 d1p3da2 81 --------------DVYAAGEAPIVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQI 126 d1gpma1 106 ------------RVFVEVFDEEALKLEDVKWLAQGTIYPDVIESAAKMGLVEPLKELFKD 153 :::::::::::: d1p3da2 127 IQDGDLILAQGAGSVSKISRGLAE------------------------------------ 150 d1gpma1 154 EVRKIGLELGLPYDMLYRHPFP-- 175 d1p3da2 151 ----------------------SW 152 TMalign alignment (TM-score: 0.34 Raw score:59.08) d1gpma1 1 -----WTPAKIIDDAVARI---REQVG-------DDKVILGLSGGVDSSVTAMLLHRAI- 44 : :: ::::::::::::::::::::::::: d1p3da2 1 GAGRR-------------FDQL---GEFIRPNGKVRLVDDYGHHPTEVGVTIKAAREGWG 44 d1gpma1 45 -GKNLTCVFVDNGLLRLNEAEQVLDMFGDHFGLNIVHVPAEDRFLS-------------- 89 :::::::::::::::::::::: ::::::::::::::::: :::: d1p3da2 45 DKRIVMIFQPHRYSRTRDLFDDF-VQVLSQVDALIMLDVYA-AGEAPIVGADSKSLCRSI 102 d1gpma1 90 -----------------------------------ALAGENDPEAKRKIIGRVFVEVFDE 114 :: :::: d1p3da2 103 RNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQG------------------AG-SVSK 143 d1gpma1 115 EALKLEDVKWLAQGTIYPDVIESAAKMGLVEPLKELFKDEVRKIGLELGLPYDMLYRHPF 174 ::::::::: d1p3da2 144 ISRGLAESW--------------------------------------------------- 152 d1gpma1 175 P 175 d1p3da2 153 - 153 HHsearch alignment (Probability: 0.60 E-value:0.00) d1gpma1 5 KIIDDAVARIREQVGDDKVILGLSGGVDSSVTAML 39 ::::::::::::::::::::::::::::::::::: d1p3da2 30 TEVGVTIKAAREGWGDKRIVMIFQPHRYSRTRDLF 64