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 | d1ps9a1 | 2,4-dienoyl-CoA reductase, N-terminal domain | 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 <-- 0.914 --> HitDALI alignment (Z-score: 6.6 Raw score:825.00) d1knwa2 1 ----daqiirrqiaalkQFDVVRFAqKACS-----NIHILRLMREQGV------KVDSVS 45 :::::::: :::: ::::::::::::: :::::: d1ps9a1 1 sypslfapldlgfttlkNRVLMGSM-HTGLeeypdGAERLAAFYAERArhgvalIVSGGI 59 d1knwa2 46 L----------GEIE------raLAAGY--npqthpDDIVFTADV--------------- 72 : :::: ::::: ::::::::: d1ps9a1 60 ApdltgvgmegGAMLndasqiphHRTITeavhqeggKIALQILHTgrysyqphlvapsal 119 d1knwa2 73 -------------------iDQATLERVSELQ-----IPVNAG----------------- 91 :::::::::::: :::::: d1ps9a1 120 qapinrfvphelsheeilqlIDNFARCAQLAReagydGVEVMGsegylinefltlrtnqr 179 d1knwa2 92 ----------sVDMLDQLGQVSP------ghRVWLRVNPGFghghsqktntgGENSkhgi 135 :::::::::::: :::::::::: :::: d1ps9a1 180 sdqwggdyrnrMRFAVEVVRAVRervgndfiIIYRLSMLDL-----------VEDG---g 225 d1knwa2 136 WYTDLPAALDVIQRHhLQLVGIHMHI-------GSGVDYAhLEQVCGAMVrQVIEfGQDL 188 ::::::::::::::: :::::::::: ::::::: ::::::::: :::: :::: d1ps9a1 226 TFAETVELAQAIEAA-GATIINTGIGwhearipTIATPVP-RGAFSWVTR-KLKG-HVSL 281 d1knwa2 189 QAISAggglsvpyqqgeeavdtehYYGLWNAAREQIArhlghpVKLEIEP-GRFL----- 242 ::::: ::::::::::::: ::::::: :::: d1ps9a1 282 PLVTT---------------nrinDPQVADDILSRGD-----aDMVSMARpFLADaells 321 d1knwa2 243 ----vaqsg 247 d1ps9a1 322 kaqsgrade 330 FAST alignment (Normalized score: 4.10 Raw score:1170.00) d1knwa2 1 D-----------------------------------AQIIRRQIAAL---KQFDVVRFAQ 22 :::::::::: ::::::: d1ps9a1 1 -SYPSLFAPLDLGFTTLKNRVLMGSMHTGLEEYPDGAERLAAFYAE-RARHGVALIV--- 55 d1knwa2 23 KACS-----------------------NIHILRLMRE----QGVKVDSV----------- 44 :::::::::: ::::::: d1ps9a1 56 ----SGGIAPDLTGVGMEGGAMLNDASQIPHHRTITEAVHQEGGKIAL-QILHTGRYSYQ 110 d1knwa2 45 --------------------------------SLGEIERALAAGYNPQTHPDDIVFTADV 72 :::::::::::: d1ps9a1 111 PHLVAPSALQAPINRFVPHELSHEEILQLIDNFARCAQLAREAG---------------- 154 d1knwa2 73 IDQATLERVSELQ-IPVNAG---------------------------------SVDMLDQ 98 ::::: ::::::: d1ps9a1 155 -------------YDGVEV-MGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEVVRA 200 d1knwa2 99 LGQVSP-GHRVWLRVNPGFGHGHSQKTNTGGENSKHGI--------WYTDLPAALDVIQR 149 :::::: ::::::::: ::::: :::::::::: d1ps9a1 201 VRERVGNDFIIIYRLS-MLDLV----------------EDGGTFAETVELAQAIEA---- 239 d1knwa2 150 HHLQLVGIHMHIGSGVDYAHL------------------EQVCGAMVRQVIEFGQDL-QA 190 :::::::: :::::::::::::: :: d1ps9a1 240 --AGATIINT-----------GIGWHEARIPTIATPVPRGAFSWVTRKLKGHV----SLP 282 d1knwa2 191 ISAGGGLSVPYQQGEEAVDTEH----YYGLWNAAREQIARHLGHPVK----LEIEPGRFL 242 :::: :::::::::: ::::::::: d1ps9a1 283 LVTT------------------NRINDPQVADDILS-----------RGDADMVSMARPF 313 d1knwa2 243 VAQSG----------------- 247 d1ps9a1 314 -----LADAELLSKAQSGRADE 330 TMalign alignment (TM-score: 0.52 Raw score:128.15) d1knwa2 1 ----DAQIIRRQIAALKQFD--------------VVRFAQKACSNIHILRLMREQGVKVD 42 : ::::: d1ps9a1 1 SYPS---------------LFAPLDLGFTTLKNR---------------------VLMGS 24 d1knwa2 43 SVSLGE----I--ERALAAGYNPQT-HPDDIVFTADV-----------ID----Q-ATLE 79 :::::: : :::::::::::: ::::::::::: :: : :::: d1ps9a1 25 MHTGLEEYPDGAERLAAFYAERARHGVALIVSGGIAPDLTGVGMEGGAMLNDASQIPHHR 84 d1knwa2 80 RVSELQ------IPVNAG----------------------------------------SV 93 :::::: :::::: :: d1ps9a1 85 TITEAVHQEGGKIALQILHTGRYSYQPHLVAPSALQAPINRFVPHELSHEEILQLIDNFA 144 d1knwa2 94 DMLDQLGQVSPGHRVWLRV-----NP-GFGHGHSQK---TNTGGE--------NSKHGIW 136 :::::::::: :::::::: :: ::::::::: :: :: d1ps9a1 145 RCAQLAREAG-YDGVEVMGSEGYLINEFLTLRTNQRSDQ----WGGDYRNRMR-----FA 194 d1knwa2 137 YTDLPAALDVIQRHHLQLVGIHMHIGSGVDYAHLEQVCGAMVRQVIEFGQDLQAISAGGG 196 :::::::::::: :::::::::::::::::::::::::::::::::::: : ::::::: d1ps9a1 195 VEVVRAVRERVG--NDFIIIYRLSMLDLVEDGGTFAETVELAQAIEAAGA-T-IINTGIG 250 d1knwa2 197 L--SVPY----QQGEEAVDTEHYYGLWNAAREQIARHLGHPVKLEIEP------------ 238 : :::: ::::::::::::::::::: : ::::::: d1ps9a1 251 WHEARIPTIAT-----PVPRGAFSWVTRKLKGHVS--L---PLVTTNRINDPQVADDILS 300 d1knwa2 239 ---------GRFLV-------------------AQSG 247 :: d1ps9a1 301 RGDADMVSM---ARPFLADAELLSKAQSGRADE---- 330 HHsearch alignment (Probability: 0.91 E-value:0.00) d1knwa2 50 ERALAAGYNPQTHPDDIVFTADVIDQATLER-----------VSELQIPVNAGSVDMLDQ 98 ::::::::::: :::::::::::::::: :::::::::::: ::: d1ps9a1 148 QLAREAGYDGV----EVMGSEGYLINEFLTLRTNQRSDQWGGDYRNRMRFAVEV---VRA 200 d1knwa2 99 LGQVS-PGHRVWLRVNPGFGHGHSQKTNTGGENSKHGIWYTDLPAALDVIQRHHLQLVGI 157 ::::: ::::::::::::: :::::::::::::::::::::::::: d1ps9a1 201 VRERVGNDFIIIYRLSMLD-------------LVEDGGTFAETVELAQAIEAAGATII-- 245 d1knwa2 158 HMHIGSGVDYA-----HL-EQVCGAMVRQVIEFGQDLQAISAGGG 196 ::::::::::: :: :::::::::::::: ::::::::::: d1ps9a1 246 NTGIGWHEARIPTIATPVPRGAFSWVTRKLKGH-VSLPLVTTNRI 289