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 | d1vyra_ | Pentaerythritol tetranirate reductase | FMN-linked oxidoreductases | TIM beta/alpha-barrel | α/β |
Query <-- 1.000 --> 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 <-- 0.922 --> HitDALI alignment (Z-score: 6.8 Raw score:863.70) d1knwa2 1 daqiirrqiaalKQFD------------VVRFA-QKAC-----------sNIHILRLMRe 36 :::: ::::: :::: ::::::::: d1vyra_ 1 -----------aEKLFtplkvgavtapnRVFMApLTRLrsiepgdiptplMGEYYRQRA- 48 d1knwa2 37 QGVKVDSVSL---------------------geiERALAaGYNPqthpdDIVFTAD---- 71 :::::::::: ::::: :::: ::::::: d1vyra_ 49 SAGLIISEATqisaqakgyagapglhspeqiaawKKITA-GVHA--edgRIAVQLWhtgr 105 d1knwa2 72 -------------------------------------------------------vIDQA 76 :::: d1vyra_ 106 ishssiqpggqapvsasalnantrtslrdengnairvdtttpraleldeipgivndFRQA 165 d1knwa2 77 tLERVSEL-qIPVNAG--------------------------------SVDMLDQLGQVS 103 ::::::: :::::: :::::::::::: d1vyra_ 166 -VANAREAgfDLVELHsahgyllhqflspssnqrtdqyggsvenrarlVLEVVDAVCNEW 224 d1knwa2 104 PGHRVWLRVNPGFGHGHSqktntgGENS-khgiWYTDLPAALDviqrhhlQLVGIHMHIG 162 :::::::::::::::::: :::: :::::::::: :::::::::: d1vyra_ 225 SADRIGIRVSPIGTFQNV------DNGPneeadALYLIEELAK------rGIAYLHMSET 272 d1knwa2 163 SGVdyaHLEQvcGAMVRQVIefGQDLqAISAGGGLsvpyqqgeeavDTEHYYGLWNAARe 222 ::: :::: :::::::: :::: :::::::: ::::::::::::: d1vyra_ 273 DLA-ggKPYS-eAFRQKVRE--RFHG-VIIGAGAY-----------TAEKAEDLIGKGL- 315 d1knwa2 223 qiarhlghpvkLEIEPGRFLV---------------AQSG------------------ 247 :::::::::: :::: d1vyra_ 316 ----------iDAVAFGRDYIanpdlvarlqkkaelNPQRpesfygggaegytdypsl 363 FAST alignment (Normalized score: 3.39 Raw score:1015.00) d1knwa2 1 -----------------------------------DAQIIRRQIAALKQFDVVRFAQKAC 25 ::::::::::::::::::: d1vyra_ 1 AEKLFTPLKVGAVTAPNRVFMAPLTRLRSIEPGDIPTPLMGEYYRQRASAGLII------ 54 d1knwa2 26 S-----------------------NIHILRLMRE------QGVKVDSV------------ 44 :::::::::: ::::::: d1vyra_ 55 -SEATQISAQAKGYAGAPGLHSPEQIAAWKKITAGVHAEDGRIAVQL-WHTGRISHSSIQ 112 d1knwa2 45 -------------------------------------------------SLGEIERALAA 55 ::::::::::: d1vyra_ 113 PGGQAPVSASALNANTRTSLRDENGNAIRVDTTTPRALELDEIPGIVNDFRQAVANAREA 172 d1knwa2 56 GYNPQTHPD-DIVFTADVIDQATLERVSELQIPVNAG----------------------- 91 :: :::: d1vyra_ 173 GF-------DLVEL-----------------------HSAHGYLLHQFLSPSSNQRTDQY 202 d1knwa2 92 ----------SVDMLDQLGQVSPGH------RVWLRV-NPGFGHGHSQKTNTGGENSKHG 134 ::::::::: :::::: ::::: d1vyra_ 203 GGSVENRARLVLEVVDAVC------NEWSADRIGIRVSPIGTF----------------- 239 d1knwa2 135 IWYT--------DLPAALDVIQRH--HLQLVGIHMHIGSGVDYAHLEQVCGA-------- 176 ::::::::::: :::::::::: d1vyra_ 240 ----QNVDNGPNEEADALYLIEE-LAKRGIAYLHMS----------------ETDLAGGK 278 d1knwa2 177 --MVRQVIEFGQD-----LQAISAGGGLSVPYQQGEEAVDTEH--YYGLWNAAREQIARH 227 ::::::: :::::::: :::::::::: d1vyra_ 279 PYSEAFRQK----VRERFHGVIIGAG-----------------AYTAEKAEDLIG----- 312 d1knwa2 228 LGHPVK----LEIEPGRFLVAQSG------------------------------------ 247 ::::::::: d1vyra_ 313 ------KGLIDAVAFGRDY-----IANPDLVARLQKKAELNPQRPESFYGGGAEGYTDYP 361 d1knwa2 248 -- 248 d1vyra_ 362 SL 363 TMalign alignment (TM-score: 0.58 Raw score:143.39) d1knwa2 1 -----------------DAQIIRRQIAALKQFDVVRFAQKACSN------IHILRLMREQ 37 ::::::::::::: :::::::::: d1vyra_ 1 AEKLFTPLKVGAVTAPN--------------RVFMAPLTRLRSIEPGDIPTPLMGEYYRQ 46 d1knwa2 38 GV----K-VDSVSLG---------EIE----RALAA-GYNP-QT---HPDDIVFTADV-- 72 :: : ::::::: ::: ::::: :::: :: ::::::::::: d1vyra_ 47 RASAGLIISEATQISAQAKGYAGAPGLHSPEQIAAWKKITAGVHAEDGRIAVQLWHTGRI 106 d1knwa2 73 ---------------------------------------------------IDQATLERV 81 ::::::::: d1vyra_ 107 SHSSIQPGGQAPVSASALNANTRTSLRDENGNAIRVDTTTPRALELDEIPGIVNDFRQAV 166 d1knwa2 82 SE-L-----QIPVNAG-----S---------------------VDMLDQLGQVSP----G 105 :: : ::::::: : :::::::::::: : d1vyra_ 167 ANAREAGFDLVELHSAHGYLLHQFLSPSSNQRTDQYGGSVENRARLVLEVVDAVCNEWSA 226 d1knwa2 106 -HRVWLRVNPGFGHGHSQKTNTGGEN-SKHGIWYTDLPAALDVIQRHHLQLVGIHMHIGS 163 :::::::::::: :::::: ::::::::::::::::::::::::::::: d1vyra_ 227 DRIGIRVSPIGTF-------QNVDNGP----NEEADALYLIEELAKRGIAYLHMSETDLA 275 d1knwa2 164 GVDYAHLEQVCGAMVRQVIEFG--QD-LQAISAGGGLSVPYQQGEEAVDTEHYYGLWNAA 220 : :: ::::::::::: :: :::::: : ::::: d1vyra_ 276 -----G--GK-PYSEAFRQKVRERFHGVIIGAG-------------------A--YTAEK 306 d1knwa2 221 REQIARHLGHPVKLEIEP--G------------------RF-LVA-Q--SG------- 247 ::::::::: :::::::: : :: ::: : :: d1vyra_ 307 AEDLIGKGL-IDAVAFGRDYIANPDLVARLQKKAELNPQRPESFYGGGAEGYTDYPSL 363 HHsearch alignment (Probability: 0.92 E-value:0.00) d1knwa2 50 ERALAAGYNPQTHPDDIVFTADVIDQATLERV-----------SELQIPVNAGSVDMLDQ 98 ::::::::::: ::::::::::::::::: :::::::: :::::: d1vyra_ 167 ANAREAGFDLV----ELHSAHGYLLHQFLSPSSNQRTDQYGGSVENRARLV---LEVVDA 219 d1knwa2 99 LGQVSPGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGIH 158 ::::::::::::::::::::: :::::::::::::::::::::::::: :: d1vyra_ 220 VCNEWSADRIGIRVSPIGTFQ---------NVDNGPNEEADALYLIEELAKRGIAY--LH 268 d1knwa2 159 MHIGSGVDYAHLEQVCGAMV 178 :::::::::::::::::::: d1vyra_ 269 MSETDLAGGKPYSEAFRQKV 288