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: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1knwa2 | Diaminopimelate decarboxylase LysA | PLP-binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1vlpa2 | Nicotinate phosphoribosyltransferase, C-terminal domain | Nicotinate/Quinolinate PRTase C-terminal domain-like | alpha/beta-Hammerhead | α+β |
Query <-- 1.858 --> IntermediateDALI alignment (Z-score: 19.8 Raw score:1758.40) query 1 mietpyylidkaKLTRNMERIAHVRekSGAKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 ::::::::::::: ::::::::::::::::::::::::::::::::: d1knwa2 1 ------------DAQIIRRQIAALK--QFDVVRFAQKACSNIHILRLMREQGVKVDSVSL 46 query 61 FEVRLGRERFGK------ETHAYSVAYGDNEIDEVVSHaDKIIFNSISQLERFADKAAGI 114 :::::::::::: :::::::::::::::::::: ::::::::::::::::::::: d1knwa2 47 GEIERALAAGYNpqthpdDIVFTADVIDQATLERVSELqIPVNAGSVDMLDQLGQVSPGH 106 query 115 ARGLRLNPQ----------------RLGEW--DVPKVERVMD----RINGFMIHNNCeNK 152 ::::::::: ::::: :::::::::: ::::::::::: :: d1knwa2 107 RVWLRVNPGfghghsqktntggensKHGIWytDLPAALDVIQrhhlQLVGIHMHIGS-GV 165 query 153 DFGLFDRMLGEIEERFGALIARVDWVSLGGGIHF----tgDDYPVDAFSARLRAFSDRYG 208 :::::::::::::::::::::::::::::::::: :::::::::::::::::::: d1knwa2 166 DYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVpyqqgeEAVDTEHYYGLWNAAREQIA 225 query 209 ------VQIYLEPGEASITKsttlevtvldtlynknlaivdssieahmldlliyretakv 262 :::::::::::::: d1knwa2 226 rhlghpVKLEIEPGRFLVAQ---------------------------------------- 245 query 263 lpnegshsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpa 322 d1knwa2 246 ------------------------------------------------------------ 246 query 323 iaireldgsvrtvreftyadyeqsls 348 d1knwa2 246 ------------------------sg 247 FAST alignment (Normalized score: 11.38 Raw score:3336.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSG--AKALLALKCFATWSVFDLMRDYM--DGTT 56 ::::::::::::: ::::::::::::::::::::: :::: d1knwa2 1 ---------DAQIIRRQIAALK-------QFDVVRFAQKACSNIHILRLMRE--QGVKVD 42 query 57 SSSLFEVRLGRERFGK-----------ETHAYSVAYGDNEIDEVVSHA--DKIIFNSISQ 103 ::::::::::: ::::::::::::::::::: :::::::::: d1knwa2 43 SVSLGEIERAL-----AAGYNPQTHPDDIVFTADVIDQATLERVSE--LQIPVNAGSVDM 95 query 104 LERFADKAAGIARGLRLNP-----------------QRLGEW---DVPKVERVMD----- 138 :::::::::::::::::: ::::: :::::::: d1knwa2 96 LDQLGQVSPGHRVWLRVN-PGFGHGHSQKTNTGGENSKHGI-WYTDLPAALDV--IQRHH 151 query 139 -RINGFMIHNNCE---NKDFGLFDRMLGEIEERFGALIA----RVDWVSLGGGIHFTGD- 189 :::::::: ::::::::::::::::::: :::::::::: d1knwa2 152 LQLVGIHMH----IGSGVDYAHLEQVCGAMVRQVI----EFGQDLQAISAGGG------L 197 query 190 ---------DYPVDAFSARLRAFSDRY-------GVQIYLEPGEASITKSTTLEVTVLDT 233 ::::::::::::::::: ::::::::::::::: d1knwa2 198 SVPYQQGEEAVDTEHYYGLWNAAREQ-IARHLGHPVKLEIEPGRFLVAQ----------- 245 query 234 LYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEEL 293 d1knwa2 246 ------------------------------------------------------------ 246 query 294 KVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS-- 348 d1knwa2 246 -------------------------------------------------------SG 247 TMalign alignment (TM-score: 0.53 Raw score:185.85) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 :::::::::::: ::: : :::::::::::::::::::::::::::::: d1knwa2 1 ---------DAQIIRRQIAAL-KQF---D-VVRFAQKACSNIHILRLMREQGVKVDSVSL 46 query 61 FEVRLGRERFG----K--ETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAGI 114 ::::::::::: : :::::::::::::::::::::::::::::::::::::::::: d1knwa2 47 GEIERALAAGYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLGQVSPGH 106 query 115 ARGLRLNPQ----------------RLGE-WD-VPKVERVMD---RIN-GFMIHNNCENK 152 ::::::::: :::: :: ::::::::: ::: :::::::: :: d1knwa2 107 RVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGS-GV 165 query 153 DFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFT----GDDYPVDAFSARLRAFSDRYG 208 ::::::::::::::::::::::::::::::::::: ::::::::::::::::::::: d1knwa2 166 DYAHLEQVCGAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAAREQIA 225 query 209 ------VQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKV 262 :::::::::::::::: d1knwa2 226 RHLGHPVKLEIEPGRFLVAQSG-------------------------------------- 247 query 263 LPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPA 322 d1knwa2 248 ------------------------------------------------------------ 248 query 323 IAIRELDGSVRTVREFTYADYEQSLS 348 d1knwa2 248 -------------------------- 248 HHsearch alignment (Probability: 1.00 E-value:0.00) query 10 DKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFEVRLGRER 69 :::::::::::::::: ::::::::::::::::::::::::::::::::::::::: d1knwa2 1 DAQIIRRQIAALKQFD-----VVRFAQKACSNIHILRLMREQGVKVDSVSLGEIERALAA 55 query 70 FGKET------HAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAGIARGLRLNPQ 123 ::::: ::::::::::::::::::::::::::::::::::::::::::::::::: d1knwa2 56 GYNPQTHPDDIVFTADVIDQATLERVSELQIPVNAGSVDMLDQLGQVSPGHRVWLRVNPG 115 query 124 ----------------RLGEWDVPKV------ERVMDRINGFMIHNNCENKDFGLFDRML 161 :::::::::: :::::::::::::::::: ::::::::: d1knwa2 116 FGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGSGV-DYAHLEQVC 174 query 162 GEIEERFGALIARVDWVSLGGGIHFTGDD----YPVDAFSARLRAFSDRY------GVQI 211 ::::::::::::::::::::::::::::: ::::::::::::::::: :::: d1knwa2 175 GAMVRQVIEFGQDLQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAAREQIARHLGHPVKL 234 query 212 YLEPGEASITKST 224 ::::::::::::: d1knwa2 235 EIEPGRFLVAQSG 247
Intermediate <-- 1.346 --> HitDALI alignment (Z-score: 8.5 Raw score:919.40) d1knwa2 1 ------DAQIIRRQIAALK-QFDVVRFAQKAC-----sNIHILRLMREQG---------- 38 ::::::::::::: :::::::::::: :::::::::::: d1vlpa2 1 dwdyenQLEQAEKKAETLFdNGIRFSEFGTRRrrslkaQDLIMQGIMKAVngnpdrnksl 60 d1knwa2 39 VKVDSvslgEIERALAAGYnpqthpdDIVFT-ADVIdqatlervselqipvnagSVDMLD 97 ::::: :::::::::: ::::: :::: :::::: d1vlpa2 61 LLGTS----NILFAKKYGV-------KPIGTvAHEW----vmgvasisedylhaNKNAMD 105 d1knwa2 98 QLGQVSP-GHRVWLRVNpgfghghsqktntggenskhGIWYTD-LPAALDVIqrhhlQLV 155 ::::::: ::::::::: :::::: :::::::: ::: d1vlpa2 106 CWINTFGaKNAGLALTD--------------------TFGTDDfLKSFRPPY---sdAYV 142 d1knwa2 156 GIHMHIgsgvdyahleQVCGAMVRQVIEFG------qdLQAISAGGGLsvpyqqgeeavd 209 :::::: :::::::::::::: :::::::::: d1vlpa2 143 GVRQDS---------gDPVEYTKKISHHYHdvlklpkfSKIICYSDSL-----------n 182 d1knwa2 210 TEHYYgLWNAAREQIArhlghpVKLEIEPGRFLVAQS----------------------- 246 ::::: :::::::::: ::::::::::::::: d1vlpa2 183 VEKAI-TYSHAAKENG------MLATFGIGTNFTNDFrkksepqvkseplnivikllevn 235 d1knwa2 247 ------------------------------g 247 d1vlpa2 236 gnhaikisdnlgknmgdpatvkrvkeelgyt 266 FAST alignment (Normalized score: 3.00 Raw score:769.50) d1knwa2 1 DAQIIRRQIAALKQFDVVRFAQKACS----------NIHILRLMREQGVKVDSV------ 44 ::::::::::::::::: d1vlpa2 1 --------------------------DWDYENQLEQAEKKAETLFDNGIRFSE-FGTRRR 33 d1knwa2 45 -----SLGEIERALAAGYNPQTHPDDIVFTADVIDQA-----------------TLERVS 82 :::::::::: :::::: d1vlpa2 34 RSLKAQDLIMQGIMK----------------------AVNGNPDRNKSLLLGTSNILFAK 71 d1knwa2 83 ELQI--PVNAG------------------SVDMLDQLGQVSPGHR-----VWLRVNPGFG 117 :::: :::: :::::::::::: :::: d1vlpa2 72 KYGVKPIGTV-AHEWVMGVASISEDYLHANKNAMDCWINTF----GAKNAGLAL------ 120 d1knwa2 118 HGHSQKTNTGGENSKHGI--------WYTD-LPAALDVIQRHHLQLVGIHMHIGSGVDYA 168 :::: :::::: :::::::: d1vlpa2 121 ------------------TDTFGTDDFLKSFRPPYSD-------AYVGVRQD-------- 147 d1knwa2 169 HLE--QVCGAMVRQVIEFGQDL-----------QAISAGGGLSVPYQQGEEAVDT---EH 212 :::::::::::: ::::::: :: d1vlpa2 148 ---SGDPVEYTKKISHH-----YHDVLKLPKFSKIICYSD---------------SLNVE 184 d1knwa2 213 YYGLWNAAREQIARHLGH-PVKLEIEPGRFLVAQSG------------------------ 247 ::::::::::: ::::::::::::: d1vlpa2 185 KAITYSHAAKE-------NGMLATFGIGTNFT----NDFRKKSEPQVKSEPLNIVIKLLE 233 d1knwa2 248 --------------------------------- 248 d1vlpa2 234 VNGNHAIKISDNLGKNMGDPATVKRVKEELGYT 266 TMalign alignment (TM-score: 0.54 Raw score:134.18) d1knwa2 1 ------DAQIIRRQIAALK-QFDVVRFAQK-AC-SN--IHILRL-MRE-Q-------G-- 38 ::::::::::::: :::::::::: :: :: :::::: ::: : : d1vlpa2 1 DWDYENQLEQAEKKAETLFDNGIRFSEFGTRRRRSLKAQDLIMQGIMKAVNGNPDRNKSL 60 d1knwa2 39 VKVDSVSLGEIERALAAGYNPQTHPDDIVFTADVID------------QATLERVSELQI 86 ::::: ::::::::::: :::::::::: d1vlpa2 61 LLGTS----NILFAKKYGVK------PIGTVAHEWVMGVASISEDYLH------------ 98 d1knwa2 87 PVNAGSVDMLDQLGQVSPGHR-VWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALD 145 ::::::::::::::::: :::::: ::::::::::::: d1vlpa2 99 ----ANKNAMDCWINTFGAKNAGLALTD-------------------TFGTDDFLKSFRP 135 d1knwa2 146 VIQRHHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFG-QD--LQAISAGGGLSVPYQ 202 ::: ::::::::::: ::::::::::::::::: :: ::::::::::: d1vlpa2 136 PYS---DAYVGVRQDSG------DPVEYTKKISHHYHDVLKLPKFSKIICYSDSLN---- 182 d1knwa2 203 QGEEAVDTEHYYGLWNAAREQIARHLGHPVKLEIEPGRFLVAQSG--------------- 247 : : ::::::::::::: :::::::::::::::: d1vlpa2 183 -----V-E-KAITYSHAAKENG-------MLATFGIGTNFTNDFRKKSEPQVKSEPLNIV 228 d1knwa2 248 -------------------------------------- 248 d1vlpa2 229 IKLLEVNGNHAIKISDNLGKNMGDPATVKRVKEELGYT 266 HHsearch alignment (Probability: 0.02 E-value:0.16) d1knwa2 38 GVKVDSVSLGEIERALAAGYNPQ 60 :::::::: ::::::::::::: d1vlpa2 58 KSLLLGTS--NILFAKKYGVKPI 78