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 | d1d3ga_ | Dihydroorotate dehydrogenase | FMN-linked oxidoreductases | TIM beta/alpha-barrel | α/β |
| Hit | d1gk8a1 | Ribulose 1,5-bisphosphate carboxylase-oxygenase | RuBisCo, C-terminal domain | TIM beta/alpha-barrel | α/β |
Query <-- 1.647 --> IntermediateDALI alignment (Z-score: 7.2 Raw score:865.90) query 1 mietpyyLIDKAK-----------------------------------ltrnmeriahvr 25 :::::: d1d3ga_ 1 -------MATGDErfyaehlmptlqglldpesahrlavrftslgllpfqdsdmlevrvlg 53 query 26 eksgaKALLALKcfatwsvfDLMRD-YMDGTTSSSL------------------------ 60 ::::::: ::::: :::::::::: d1d3ga_ 54 hkfrnPVGIAAGfdkhgeavDGLYKmGFGFVEIGSVtpkpqegnprprvfrlpedqavin 113 query 61 ----------------fevrlgRERFG---KETHAYSVA---------YGDNEIDEVVSH 92 ::::: ::::::::: :::::::::::: d1d3ga_ 114 rygfnshglsvvehrlrarqqkQAKLTedgLPLGVNLGKnktsvdaaeDYAEGVRVLGPL 173 query 93 ADKIIFNS-------------ISQLERFADKAA------GIARGLRLNPQrlgewDVPKV 133 :::::::: :::::::::::: ::::::::::: ::::: d1d3ga_ 174 ADYLVVNVsspntaglgkaelRRLLTKVLQERDglrrvhRPAVLVKIAPD-ltsqDKEDI 232 query 134 ERVM--DRINGFMIHNN-------------------CENKdfglFDRMLGEIEErFGALI 172 :::: ::::::::::: :::: :::::::::: ::::: d1d3ga_ 233 ASVVkeLGIDGLIVTNTtvsrpaglqgalrsetgglSGKP---lRDLSTQTIREmYALTQ 289 query 173 ARVdWVSLGGGIHFtgddypvdAFSARLRAFSdrygvqIYLEPGEASITKSttlevtvld 232 ::: :::::::::: :::::::::: ::::::::::::: d1d3ga_ 290 GRV-PIIGVGGVSS-------gQDALEKIRAG-----aSLVQLYTALTFWG--------- 327 query 233 tlynknlaivdssieahmldlliyretakvlpnegshsymicgksclagdvfgefrfaee 292 d1d3ga_ 328 ------------------------------------------------------------ 328 query 293 lkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1d3ga_ 328 -----------------------ppvvgkvkreleallkeqgfggvtdaigadhrr 360 FAST alignment (Normalized score: 4.17 Raw score:1474.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGA------------------------------ 30 d1d3ga_ 1 ------------------------------MATGDERFYAEHLMPTLQGLLDPESAHRLA 30 query 31 ----------------------------KALLALKCFA--TWSVFDLMR-DYMDGTTSS- 58 :::::::: ::::::::: ::::::: d1d3ga_ 31 VRFTSLGLLPFQDSDMLEVRVLGHKFRNPVGIAAGF--DKHGEAVDGLYKMGFGFVE--I 86 query 59 -----------------------------------SLFEVRLGRERFG------------ 71 :::::::::: d1d3ga_ 87 GSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRA---RQQKQAKLTEDG 143 query 72 KETHAYSVAY------------GDNEIDEVVSHADKIIFN--------------SISQLE 105 ::::::: ::::::::::::::::: :::::: d1d3ga_ 144 LPLGVNL---GKNKTSVDAAEDYAEGVRVLGPLADYLVV-NVSSPNTAGLGKAELRRLLT 199 query 106 RFADKAA------GIARGLRLNPQRLGEW---------DVPKVERVMD-RINGFMIHNNC 149 ::::::: :::::::::: ::::::: :::::: d1d3ga_ 200 KVLQERDGLRRVHRPAVLVKIAP------DLTSQDKEDIASVVKE---LGIDGLI----- 245 query 150 ENK---------------------------DFGLFDRMLGEIEERFGALIARV----DWV 178 ::::::::::::::: ::: d1d3ga_ 246 ---VTNTTVSRPAGLQGALRSETGGLSGKPLRDLSTQTIREMYAL--------TQGRVPI 294 query 179 SLGGGIHFTGDDYPVDA-FSARLRAFSDRYGVQ--IYLEPGEASITKSTTLEVTVLDTLY 235 :::::: ::::::::::: ::::::::: d1d3ga_ 295 IGVGGV-----------SSGQDALEKIRA----GASLVQLYTAL---------------- 323 query 236 NKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKV 295 d1d3ga_ 324 ------------------------------------------------------------ 324 query 296 GDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS------- 348 d1d3ga_ 324 -----------------------------------------------------TFWGPPV 330 query 349 ------------------------------ 349 d1d3ga_ 331 VGKVKRELEALLKEQGFGGVTDAIGADHRR 360 TMalign alignment (TM-score: 0.36 Raw score:123.76) query 1 ---------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWS-------- 43 :: d1d3ga_ 1 MATGDERFY-----------------------------------------AEHLMPTLQG 19 query 44 -------VFDLMRDYMDGTTSSSLFE--VR----L-GRE---------------RFGKET 74 ::::: : : :: :::: d1d3ga_ 20 LLDPESA--------------HRLAVRF-TSLGLLP-FQDSDMLEVRVLGHKFR--NPVG 61 query 75 HAY--SVAYGDNEIDEVVSH-A-DKIIF-N------------------------------ 99 ::: ::::: :::::::: : ::::: : d1d3ga_ 62 IAAGFDKHGE--AVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYGFNS 119 query 100 --SISQLERFA-D--KAA-G----IARGLRLNPQR-L--G-EWDVPKVERVMDRINGFMI 145 ::::::::: : ::: : ::::::::::: : : ::::::::::::::::::: d1d3ga_ 120 HGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADYLVV 179 query 146 HNNCEN---KDFGLFDRMLGEIEERFGALIA------RVDWVSLGGGIHFTGDDYPVDAF 196 :::::: :::::::::::::::::: ::::::::: ::: ::: :: d1d3ga_ 180 NVSSPNTAG----LGKAELRRLLTKVLQERDGLRRVHRPAVLVKIA-PDL----TSQ-DK 229 query 197 SARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIY 256 :::::::::::::::::::::: ::::::: :::::: : d1d3ga_ 230 EDIASVVKELGIDGLIVTNTTV-SRPAGLQ---------------------GALRSE--T 265 query 257 RETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMV------ 310 : :::::: d1d3ga_ 266 -G----------------------------------------------GLSGKPLRDLST 278 query 311 ------------------------------------------------------------ 311 d1d3ga_ 279 QTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKREL 338 query 311 ----------------------KKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1d3ga_ 339 EALLKEQGFGGVTDAIGADHRR-------------------------------------- 360 HHsearch alignment (Probability: 0.13 E-value:0.02) query 98 FNSISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDR-INGFMI----------- 145 :::::::::::::::::::::::::::::::::::::::::: :::::: d1d3ga_ 198 LTKVLQERDGLRRVHRPAVLVKIAPDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGL 257 query 146 -----HNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGG 182 ::::::::::::::::::::::::::::::::::::: d1d3ga_ 258 QGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGG 299
Intermediate <-- 1.544 --> HitDALI alignment (Z-score: 12.2 Raw score:1453.00) d1d3ga_ 1 matgderfyaehlmptlqglldpesahrlavrftslgllpfqdsdmlevRVLGHKF--rn 58 ::::::: d1gk8a1 1 -----------------------------------------gxphgiqvERDKLNKygrg 19 d1d3ga_ 59 PVGIAaGFDK-------HGEAVDGLYKMGFGFVEIG-SVTPKPQegnprprvfrlpedqa 110 ::::: :::: ::::::::::::::::::: ::::::: d1gk8a1 20 LLGCT-IKPKlglsaknYGRAVYECLRGGLDFTXDDeNVNSQPF---------------- 62 d1d3ga_ 111 vinrygfnsHGLSVVEHRLRARQQKQAKltEDGLPLGVNLGKnktsvDAAEDYAEGVRVL 170 ::::::::::::::::::: :::::::::::: ::::::::::::: d1gk8a1 63 ---------MRWRDRFLFVAEAIYKAQAetGEVKGHYLNATA-----GTCEEMMKRAVXA 108 d1d3ga_ 171 G-PLADYLVVNVSSpntaglgkaeLRRLLTKVLQERDGLrrvhRPAVLVKIA-pDLTS-- 226 : :::::::::::: ::::::::::::::: ::::::::: :::: d1gk8a1 109 KeLGVPIIMHDYLT---------gGFTANTSLAIYCRDN----GLLLHIHRAmhAVIDrq 155 d1d3ga_ 227 ----QDKEDIASVVKELGIDGLIVTnttvsrpaglqgalrsetgglsgkpLRDL--stqt 280 ::::::::::::::::::::: :::: d1gk8a1 156 rnhgIHFRVLAKALRMSGGDHLHSG-----------------------tvVGKLegerev 192 d1d3ga_ 281 iREMYALTQG---------------------RVPIIGVGGVSSgQDALEKIRAG--ASLV 317 ::::::::: :::::::::::: :::::::::: :::: d1gk8a1 193 tLGFVDLMRDdyvekdrsrgiyftqdwxsmpGVMPVASGGIHV-WHMPALVEIFgdDACL 251 d1d3ga_ 318 QLYTA-LTFWGP--PVVGKVKRELEALLKEQGFG-------------------------- 348 ::::: :::::: :::::::::::::::::::: d1gk8a1 252 QFGGGtLGHPWGnaPGAAANRVALEACTQARNEGrdlareggdvirsackwspelaaace 311 d1d3ga_ 349 ---gvtdaigadhrr 360 d1gk8a1 312 vwkeikfefdtidkl 326 FAST alignment (Normalized score: 6.32 Raw score:2164.00) d1d3ga_ 1 MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDMLEVRVLGHKFRN-- 58 d1gk8a1 1 ----------------------------------------------------------GA 2 d1d3ga_ 59 -----------------PVGIAAGFDK-----------HGEAVDGLYKMGFGFVEIG-SV 89 ::::: ::::::::::::::::::: :: d1gk8a1 3 PHGIQVERDKLNKYGRGLLGCT-----IKPKLGLSAKNYGRAVYECLRGGLDFTADDENV 57 d1d3ga_ 90 TPKPQEGNPRPRVFRLPEDQAVINRYGFNS---HGLSVVEHRLRARQQKQAKLTE---DG 143 :: :::::::::::: ::::::: :: d1gk8a1 58 NS----------------------------QPFMRWRDRFLFVAE---AIYKAQAETGEV 86 d1d3ga_ 144 LPLGVNLGKNKTSVD--AAEDYAEGVRVLGP-LADYLVVNVSSPNTAG--LGKAELRRLL 198 :::::::: :::::::::::::: ::::::::: :::::::::: d1gk8a1 87 KGHYLNAT-------AGTCEEMMKRAVAAKELGVPIIMHDY-------LTGGFTANTSLA 132 d1d3ga_ 199 TKVLQERDGLRRVH-RPAVLVKIAPDLTSQ---------------DKEDIASVVKELGID 242 ::::: ::::::: ::::::::::::::: d1gk8a1 133 IYCRD---------NGLLLHIH--------RAMHAVIDRQRNHGIHFRVLAKALRMSGGD 175 d1d3ga_ 243 GLIVTNTTVSRPAGLQGALRSETGGLSGKP----------LRDLSTQTIREMYALTQG-- 290 ::: ::::::::::::: d1gk8a1 176 HLH---------------------------SGTVVGKLEGEREVTLGFVDLMR-----DD 203 d1d3ga_ 291 --------------------RVPIIGVGGVSSGQDALEKIRAGA-----SLVQLYTALTF 325 :::::::::: :::::::::: :::::::::: d1gk8a1 204 YVEKDRSRGIYFTQDWASMPGVMPVASGGI-HVWHMPALVE---IFGDDACLQFGGGTL- 258 d1d3ga_ 326 WG----------PPVVGKVKRELEALLKEQGFGGVTDAIGADHRR--------------- 360 :::::::::::::::: d1gk8a1 259 --GHPWGNAPGAAANRVALEACTQARNE-----------------GRDLAREGGDVIRSA 299 d1d3ga_ 361 --------------------------- 361 d1gk8a1 300 CKWSPELAAACEVWKEIKFEFDTIDKL 326 TMalign alignment (TM-score: 0.53 Raw score:189.91) d1d3ga_ 1 -------MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDMLEVRVLG 53 ::::: d1gk8a1 1 GAPHGIQ------------------------------------------------VERDK 12 d1d3ga_ 54 HKFR-N-PVGIAAGFD--K-H--GEA-VDGLYKMGFGFVEIGS-VTPKPQEGNPRPRVFR 104 :::: : ::::::::: : : ::: :::::::::::::::: :: ::: d1gk8a1 13 LNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTADDENVN--SQP--------- 61 d1d3ga_ 105 LPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYA 164 :::::::::::::::::::::::::::::::::: : : ::::: d1gk8a1 62 --------------FMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATA---G-T-CEEMM 102 d1d3ga_ 165 EGVRVLGPL-ADYLVVNVSSPNTAGLGKAELRRLLTKVLQERDGLRRVHRPAVLVKIA-P 222 ::::::::: ::::::::: : :::::::::::::::: ::::::::: : d1gk8a1 103 KRAVAAKELGVPIIMHDYL------T---GGFTANTSLAIYCRDN----GLLLHIHRAMH 149 d1d3ga_ 223 D-LT-----SQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDL 276 : :: ::::::::::::::::::::::: ::::::: d1gk8a1 150 AVIDRQRNHGIHFRVLAKALRMSGGDHLHSGT---------------------VVGKLEG 188 d1d3ga_ 277 STQTIREMYALTQG---------------------RVPIIGVGGVSSGQDALEKIRAG-- 313 :::::::::::::: :::::::::::: :::::::::: d1gk8a1 189 EREVTLGFVDLMRDDYVEKDRSRGIYFTQDWASMPGVMPVASGGIHV-WHMPALVEIFGD 247 d1d3ga_ 314 ASLVQLYTALTFWG-P--PVVGKVKRELEALLKEQGFGG--------------------- 349 :::::::::::::: : ::::::::::::::::::::: d1gk8a1 248 DACLQFGGGTLGHPWGNAPGAAANRVALEACTQARNEGRDLAREGGDVIRSACKWSPELA 307 d1d3ga_ 350 -------------------VTDAIGADHRR 360 d1gk8a1 308 AACEVWKEIKFEFDTIDKL----------- 326 HHsearch alignment (Probability: 0.89 E-value:0.00) d1d3ga_ 51 VLGHKFRNPVGIAAGFDKHGEAVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVFRLPEDQA 110 :::::::::::::: :::::::::::::::::::: ::: d1gk8a1 20 LLGCTIKPKLGLSA--KNYGRAVYECLRGGLDFTXD---------------------DEN 56 d1d3ga_ 111 VINRYGFN--SHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVR 168 ::: :::: ::::::::::::::::: ::::::::::: :::::::::::::::: d1gk8a1 57 VNS-QPFMRWRDRFLFVAEAIYKAQAE----TGEVKGHYLNA--TAGTCEEMMKRAVXAK 109 d1d3ga_ 169 VLGPLADYLVVNVSSPNTAGLGKAELRRLLTKVLQERDGLRRVHRPAVLVK--------I 220 ::: :::::::: :::::::::: : :::::::::::::: : d1gk8a1 110 ELG--VPIIMHDY---LTGGFTANTS------L----AIYCRDNGLLLHIHRAMHAVIDR 154 d1d3ga_ 221 APDLTSQDKEDIASVVKELGIDGLIVTNTTVSRPA------------------------- 255 :::::: ::::::::::::::::::: :::::::: d1gk8a1 155 QRNHGI-HFRVLAKALRMSGGDHLHS-GTVVGKLEGEREVTLGFVDLMRDDYVEKDRSRG 212 d1d3ga_ 256 --------GLQGALRSETGGLSGKPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQD 305 :::::::::::::: :::::::::::::::::::::::::::: d1gk8a1 213 IYFTQDWXSMPGVMPVASGGIH--------VWHMPALVEIFGDDACLQFGGGTLGHPW 262