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 | d1sura_ | Phosphoadenylyl sulphate (PAPS) reductase | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1e8ca2 | UDP-N-acetylmuramyl tripeptide synthetase MurE | MurD-like peptide ligases, peptide-binding domain | MurD-like peptide ligases, peptide-binding domain | α/β |
Query <-- 2.210 --> IntermediateDALI alignment (Z-score: 11.1 Raw score:953.30) query 1 ----------------------dadeevysALVVGLRAYVAKNGFrSVLIGLSGGIDSAL 38 ::::::::::::::: :::::::::::::: d1sura_ 1 skldlnalnelpkvdrilalaetnaeleklDAEGRVAWALDNLPG-EYVLSSSFGIQAAV 59 query 39 VAAIACDALGAqnVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIePMFDAYMASLG 98 ::::::::::: ::::::::::::::::::::::::::::::::::: ::::::::::: d1sura_ 60 SLHLVNQIRPD--IPVILTDTGYLFPETYRFIDELTDKLKLNLKVYRAtESAAWQEARYG 117 query 99 L---TGLAEENLQSR-LRGTTLMAISNQEGH-IVLAPGNKSElAVGY----stlygdsvg 149 : ::::::::::: ::::::::::::::: :::::::::: :::: d1sura_ 118 KlweQGVEGIEKYNDiNKVEPMNRALKELNAqTWFAGLRREQ-SGSRanlpvlaiqrgvf 176 query 150 AYGPIKDVYKTSIFRLAEWRNraaaergqtppipEASITKpdypvldailelyvdrdtga 209 ::::::::::::::::::::: :::::: d1sura_ 177 KVLPIIDWDNRTIYQYLQKHG------------lKYHPLW-------------------- 204 query 210 daivaagydrelvvktlrmvdtaeykrrqyppgtkisakgfgkdrrlpitnrwregh 266 d1sura_ 205 ----------------------------------------------degylsvgdth 215 FAST alignment (Normalized score: 7.94 Raw score:1898.00) query 1 DADEEVYS------------------------------ALVVGLRAYVAKNGFRSVLIGL 30 :::::::::::::: ::::::: d1sura_ 1 --------SKLDLNALNELPKVDRILALAETNAELEKLDAEGRVAWALDNLP-GEYVLSS 51 query 31 SGGIDSALVAAIACDALGAQ-NVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEP- 88 ::::::::::::::::: ::::::::::::::::::::::::::::::::::: d1sura_ 52 SFGIQAAVSLHLVNQIR---PDIPVILTDTGYLFPETYRFIDELTDKLKLNLKVYR---A 105 query 89 --MFDAYMASLGL-----TGLAEENLQSR-LRGTTLMAISNQEG-HIVLAPGNKSELAVG 139 ::::::::: ::::::::::: :::::::::::::: ::::::::: d1sura_ 106 TESAAWQEARY--GKLWEQGVEGIEKYNDINKVEPMNRALKELNAQTWFAGLRR------ 157 query 140 YSTLYGDSVG-------------------AYGPIKDVYKTSIFRLAEWRNRAAAERGQTP 180 ::::::::::::::::::: d1sura_ 158 ----------EQSGSRANLPVLAIQRGVFKVLPIIDWDNRTIYQYLQK------------ 195 query 181 ---PIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRR 237 :::: d1sura_ 196 HGLKYHP----------------------------------------------------- 202 query 238 QYPPGTKISAKGFGKDRRLPITNRWREGH------------- 266 d1sura_ 203 -----------------------------LWDEGYLSVGDTH 215 TMalign alignment (TM-score: 0.49 Raw score:131.05) query 1 -----------------------------DADEEVYSALVVGLRAYVAKNGFRSVLIGLS 31 :::::::::::::::::::::: : d1sura_ 1 SKLDLNALNELPKVDRILALAETNAELEK-------LDAEGRVAWALDNLPGEYVLSS-S 52 query 32 GGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMF- 90 ::::::::::::::::: : ::::::::::::::::::::::::::::::::::::::: d1sura_ 53 FGIQAAVSLHLVNQIRP-D-IPVILTDTGYLFPETYRFIDELTDKLKLNLKVYRATESAA 110 query 91 -DAYMASLGL-TGLAEENLQSR-LRGTTLMAISNQEGH-IVLAPGNKSELAVGY------ 140 ::::::::: ::::::::::: ::::::::::::::: ::::::::::: ::: d1sura_ 111 WQEARYGKLWEQGVEGIEKYNDINKVEPMNRALKELNAQTWFAGLRREQS-GSRANLPVL 169 query 141 --STLYGDSV--GAYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPEASITK--PDYP- 193 :: :::::::::::::::::::::: : :::::: ::: d1sura_ 170 AI------QRGVFKVLPIIDWDNRTIYQYLQKHG-----------L-KYHPLWDE-GYLS 210 query 194 -----VLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAK 248 d1sura_ 211 VGDTH------------------------------------------------------- 215 query 249 GFGKDRRLPITNRWREGH 266 d1sura_ 216 ------------------ 216 HHsearch alignment (Probability: 0.96 E-value:0.00) query 3 DEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYS 62 :::::::::::::::::::::::::::::::::::::::::::: :::::::::::::: d1sura_ 24 NAELEKLDAEGRVAWALDNLPGEYVLSSSFGIQAAVSLHLVNQI--RPDIPVILTDTGYL 81 query 63 SDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLG-----LTGLAEENLQSRLRGTTLM 117 :::::::::::::::::::::::::::::::::::: ::::::::::::::::::: d1sura_ 82 FPETYRFIDELTDKLKLNLKVYRATESAAWQEARYGKLWEQGVEGIEKYNDINKVEPMNR 141 query 118 AISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYG---PIKDVYKTSIFRLAEWRNRA 172 ::::::::::::::::::::::::::::::::::: :::::::::::::::::::: d1sura_ 142 ALKELNAQTWFAGLRREQSGSRANLPVLAIQRGVFKVLPIIDWDNRTIYQYLQKHGLK 199
Intermediate <-- 0.981 --> HitDALI alignment (Z-score: 3.0 Raw score:340.30) d1sura_ 1 ----skldLNALnelpkvdrilalaetnaeleklDAEGRVAWALDNLPGEYVLSSSFG-- 54 :::: :::::::::::::::::::::::: d1e8ca2 1 vcgrmevfTAPG---------kptvvvdyahtpdALEKALQAARLHCAGKLWCVFGCGgd 51 d1sura_ 55 ---iQAAVSLHLVNQIRpdIPVILTdtgyLFPETYRFIDELTD-KLKL-NLKVYRatesa 109 ::::::::::::: :::::: :::::::::::::: :::: :::::: d1e8ca2 52 rdkgKRPLMGAIAEEFA--DVAVVTddnpRTEEPRAIINDILAgMLDAgHAKVME----- 104 d1sura_ 110 awqearygklweqgvegiekyndiNKVEPMNRALKELN-aQTWF-AGLRrEQSGsranlp 167 :::::::::::::: :::: :::: :::: d1e8ca2 105 ------------------------GRAEAVTCAVMQAKenDVVLvAGKG-HEDY------ 133 d1sura_ 168 vlaiqrgvfkvlpiidwdnrtiyqylqkhglkyhplwdegylsvGDTH------------ 215 :::: d1e8ca2 134 -------------------------------------------qIVGNqrldysdrvtva 150 d1sura_ 216 ---------- 216 d1e8ca2 151 rllgviarsh 160 FAST alignment (Normalized score: 3.37 Raw score:625.10) d1sura_ 1 SKLDLNALNELPKVDRILALAETNAELEKL-------------------------DAEGR 35 ::::: d1e8ca2 1 ------------------------------VCGRMEVFTAPGKPTVVVDYAHTPDALEKA 30 d1sura_ 36 VAWALDNLPGEYVLSSSF------GIQAAVSLHLVNQIRPDIPVILTDTGYLF------P 83 ::::::::::::::::: ::::::::::::::: :::::: : d1e8ca2 31 LQAARLHCAGKLWCVFG-CGGDRDKGKRPLMGAIAEEFA--DVAVVT------DDNPRTE 81 d1sura_ 84 ETYRFIDELTDKLK-----LNLKVYRATESAAWQEARYGKLWEQGVEGIEKYNDI-NKVE 137 ::::::::::: :::::: :::: d1e8ca2 82 EPRAIINDILA---GMLDAGHAKVM------------------------------EGRAE 108 d1sura_ 138 PMNRALKELNA----QTWF-AGLRREQSGSRANLPVLAIQRGVFKVLPIIDWDNRTIYQY 192 :::::::: :::: :::: d1e8ca2 109 AVTCAVMQ---AKENDVVLVAGKG------------------------------------ 129 d1sura_ 193 LQKHGLKYHPLWDEGYLSVGDTH------------------------------- 215 d1e8ca2 130 -----------------------HEDYQIVGNQRLDYSDRVTVARLLGVIARSH 160 TMalign alignment (TM-score: 0.35 Raw score:74.65) d1sura_ 1 ----SKLDLNALNELPKVDRILALAETNAELEKLDAEGRVAWALDNLPGEYVLSS-SFG- 54 : :: :: :::::::::: ::: d1e8ca2 1 VCGR-------------------------------M--EV-FT--APGKPTVVVDYAHTP 24 d1sura_ 55 IQAAVSLHLVNQIR-PDIPVILTDTGYLFPETYRFIDELTDKLKLNLKVYRA---TESAA 110 :::::::::::::: ::::::::::::::::::::::::::::::::::::: ::: d1e8ca2 25 DALEKALQAARLHCAGKLWCVFGCGGDRDKGKRPLMGAIAEEFADVAVVTDDNPR--TEE 82 d1sura_ 111 WQ-------------------EARYGKLWEQGVEGIEKYNDINKVEPMNRALKEL-NAQ- 149 :: :::::::::: ::: d1e8ca2 83 PRAIINDILAGMLDAGHAKVM------------------------EGRAEAVTCAVMQAK 118 d1sura_ 150 ---TWFAGL-RREQSGS-------------RANLPVLAIQR--GV--FKVLPIIDWDNRT 188 :::::: : : :: ::: :: ::::: : d1e8ca2 119 ENDVVLVAGK-G-H-EDYQIVGNQRLDYSD--------RVTVARLLGVIARS-H------ 160 d1sura_ 189 IYQYLQKHGLKYHPLWDEGYLSVGDTH 215 d1e8ca2 161 --------------------------- 161 HHsearch alignment (Probability: 0.25 E-value:0.02) d1sura_ 42 NLPGEY--VLSSSFGIQAAVSLHLVNQIRPDIPVILTDTGYLF-PETYRFIDELTD 94 :::::: ::::::::::::::::::::::::::::::::::: :::::::::::: d1e8ca2 37 HCAGKLWCVFGCGGDRDKGKRPLMGAIAEEFADVAVVTDDNPRTEEPRAIINDILA 92