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 | d1viza_ | PcrB protein homolog YerE | FMN-linked oxidoreductases | 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 <-- 2.005 --> HitDALI alignment (Z-score: 10.7 Raw score:1183.10) d1d3ga_ 1 matgderfyaehlmptlqglldpesahrlavrftslgllpfqdsdmleVRVLghkfrNPV 60 :::: ::: d1viza_ 1 -----------------------------------------------sLYDV---teWKH 10 d1d3ga_ 61 GIAagFDKH----geAVDGLYKMGFGFVEIGSvtpkpqegnprprvfrlpedqavinryg 116 ::: :::: ::::::::::::::::: d1viza_ 11 VFK--LDPNkdlpdeQLEILCESGTDAVIIGG---------------------------- 40 d1d3ga_ 117 fnshGLSVVEHRLRArqqkQAKLtedgLPLGVNLGknktsvdaaedYAEGvrvLGPLA-D 175 ::::::::::: :::: :::::::: :::: ::::: : d1viza_ 41 ----TEDNVLRMMSK---vRRFL----VPCVLEVS-----------AIEA---IVPGFdL 75 d1d3ga_ 176 YLVVNVsspntaglgkaeLRRL-LTKVLQERDG----LRRVHRPAVLVKIAPD------- 223 :::::: :::: :::::::::: :::::::::::::::: d1viza_ 76 YFIPSV---------lnsKNADwIVGMHQKAMKeygeLMSMEEIVAEGYCIANpdckaaa 126 d1d3ga_ 224 -------LTSQDKEDIASVVKELGIDGLIVTNTtvsrpaglqgalrsetgglsgkpLRDL 276 :::::::::::::::::::::::::: :::: d1viza_ 127 lteadadLNMDDIVAYARVSELLQLPIFYLEYS----------------------gVLGD 164 d1d3ga_ 277 sTQTIREMYALTqGRVPIIGVGGVSSGQDALEKIRAgASLVQLYTALTFWGPPVVgKVKR 336 ::::::::::: ::::::::::::::::::::::: :::::::::::::::::: :::: d1viza_ 165 -IEAVKKTKAVL-ETSTLFYGGGIKDAETAKQYAEH-ADVIVVGNAVYEDFDRAL-KTVA 220 d1d3ga_ 337 ELEALlkeqgfggvtdaigadhrr 360 ::::: d1viza_ 221 AVKGE------------------- 225 FAST alignment (Normalized score: 7.98 Raw score:2272.00) d1d3ga_ 1 MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDMLEVRVLGHKFR--- 57 d1viza_ 1 ---------------------------------------------------------SLY 3 d1d3ga_ 58 ----NPVGIAAGFDKHGE----------AVDGLYKMGFGFVEIGSVTPKPQEGNPRPRVF 103 :::::: :::::::::::::::: d1viza_ 4 DVTEWKHVFK--------LDPNKDLPDEQLEILCESGTDAVIIG---------------- 39 d1d3ga_ 104 RLPEDQAVINRYGFNSH-GLSVVEHRLRARQQKQAKLTED-GLPLGVNLGKNKTSVDAAE 161 ::::::::: ::::: :::::::: d1viza_ 40 -----------------GTEDNVLRMM----SKVRR----FLVPCVLEV----------- 63 d1d3ga_ 162 D-YAEGVRVL-GPLADY--LVVNVSSPNTAGLGKAELR---RLLTKVLQERDGL------ 208 :::: :::::: ::::::: ::::::::::: d1viza_ 64 -SAIEA----IVPGFDLYFIPSVLNS------------KNADWIVGMHQKAM--KEYGEL 104 d1d3ga_ 209 RRVHRPAVLVKIA---------------PDLTSQDKEDIASVVKELGIDGLIVTNTTVSR 253 :::::::::::: :::::::::::::::::::::::: d1viza_ 105 MSMEEIVAEGYC-IANPDCKAAALTEADADLNMDDIVAYARVSELLQLPIFY-------- 155 d1d3ga_ 254 PAGLQGALRSETGGLSGKPLRDL--------STQTIREMYALTQGRVPIIGVGGVSSGQD 305 :::::::::::: :::::::::::::::: d1viza_ 156 -----------------------LEYSGVLGDIEAVKKTKAVL-ETSTLFYGGGIKDAET 191 d1d3ga_ 306 ALEKIRAGASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGGVTDAIGADHRR--- 360 :::::: ::::::::::::: :::::::::::: d1viza_ 192 AKQYAE-HADVIVVGNAVYE-DFDRALKTVAAV----------------------KGE 225 TMalign alignment (TM-score: 0.44 Raw score:159.84) d1d3ga_ 1 MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDMLEVRVLGHKFRNPV 60 :::::: :: :: d1viza_ 1 -----------------------------------------------SLYDVT-EW--KH 10 d1d3ga_ 61 GIAAGFDKHGEAVD-GLYKM--GFG-FVEIGSVTPKPQEGNPRPRVFRLPEDQAVINRYG 116 ::: ::::::::: ::::: ::: :::::: d1viza_ 11 VFK--LDPNKDLPDEQLEILCESGTDAVIIGG---------------------------- 40 d1d3ga_ 117 FNSHGLSVVEHRLRARQQKQAKLTEDGLPLGVNLGKNKTSVDAAEDYAEGVRVLGPLADY 176 : :::::::: :: :: :: : ::::::::: ::: :::::::: d1viza_ 41 ---T--EDNVLRMM-SK-VR-RF--L-VPCVLEVSA------------IEA-IVPGFDLY 76 d1d3ga_ 177 LVVNVSSPNTAGLGKAELRRLLTKVL-QER-DG--LRRVHRPAVLVKIAP---------- 222 :::::: ::: ::: ::::::: ::: :: ::: ::::::::::: d1viza_ 77 FIPSVL-----NSK-NAD-WIVGMHQKAMKEYGELMSM-EEIVAEGYCIANPDCKAAALT 128 d1d3ga_ 223 ----DLTSQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGLSGKPLRDLST 278 ::::::::::::::::::::::::::: : :::: : d1viza_ 129 EADADLNMDDIVAYARVSELLQLPIFYLEYS-------------------G---VLGD-I 165 d1d3ga_ 279 QTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPVVGKVKREL 338 :::::::::: ::::::::::::::::::::::: :::::::::::: :::::::::::: d1viza_ 166 EAVKKTKAVL-ETSTLFYGGGIKDAETAKQYAEH-ADVIVVGNAVYE-DFDRALKTVAAV 222 d1d3ga_ 339 EALLKEQGFGGVTDAIGADHRR 360 : :: d1viza_ 223 K--GE----------------- 225 HHsearch alignment (Probability: 0.98 E-value:0.00) d1d3ga_ 213 RPAVLVKIAPDLTSQDKEDIASVVKELG--IDGLIVTNTTVSRPAGLQGALRSETGGLSG 270 :::::::::::::::::::::::::::: ::::::::: d1viza_ 123 KAAALTEADADLNMDDIVAYARVSELLQLPIFYLEYSGV--------------------- 161 d1d3ga_ 271 KPLRDLSTQTIREMYALTQGRVPIIGVGGVSSGQDALEKIRAGASLVQLYTALTFWGPPV 330 :::::::::::::: ::::::::::::::::::: ::::::::::::::: ::::: d1viza_ 162 ----LGDIEAVKKTKAVL-ETSTLFYGGGIKDAETAKQ-YAEHADVIVVGNAVY-EDFDR 214 d1d3ga_ 331 VGKVKRELE 339 ::::::::: d1viza_ 215 ALKTVAAVK 223