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 | d1o94a1 | Trimethylamine dehydrogenase, N-terminal domain | 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 <-- 2.544 --> HitDALI alignment (Z-score: 18.1 Raw score:2066.80) d1d3ga_ 1 matgderfyaehlmptlqglldpesahrlavrftslgllpfqdSDMLEVRVL-GHKFRNP 59 ::::::::: ::::::: d1o94a1 1 -------------------------------------ardpkhDILFEPIQIgPKTLRNR 23 d1d3ga_ 60 VGIAAGFD-KHGE-------AVDGLYKMGFGFVEIGSVTPKP--QEGNprprvfrlpedq 109 :::::::: :::: :::::::::::::::::::::: :::: d1o94a1 24 FYQVPHCIgAGSDkpgfqsaHRSVKAEGGWAALNTEYCSINPesDDTH------------ 71 d1d3ga_ 110 avinrygfNSHGLS--VVEHRLRARQQKQAKLTedgLPLGVNLGKNKT------------ 155 :::::: ::::::::::::::::: :::::::::::: d1o94a1 72 -------rLSARIWdeGDVRNLKAMTDEVHKYG---ALAGVELWYGGAhapnmesratpr 121 d1d3ga_ 156 ----------------------sVDAAEDYAEGVRVLGP-LADYLVVNVSSPnTAGL--- 189 :::::::::::::::: :::::::::::: :::: d1o94a1 122 gpsqyasefetlsyckemdlsdiAQVQQFYVDAAKRSRDaGFDIVYVYGAHS-YLPLqfl 180 d1d3ga_ 190 -----------------GKAELRRLLTKVLQERDGlrrvhRPAVLVKIAPD--------L 224 :::::::::::::::::: ::::::::::: : d1o94a1 181 npyynkrtdkyggslenRARFWLETLEKVKHAVGS-----DCAIATRFGVDtvygpgqiE 235 d1d3ga_ 225 TSQDKEDIASVVKeLGIDGLIVtNTTVsrpaglqgalrseTGGL--SGKP---lRDLSTQ 279 ::::::::::::: :::::::: :::: :::: :::: :::::: d1o94a1 236 AEVDGQKFVEMAD-SLVDMWDI-TIGD------------iAEWGedAGPSrfyqQGHTIP 281 d1d3ga_ 280 TIREMYALTqgRVPIIGVGGVSSGQDALEKI-RAGASLVQLYTALTFwGPPVVGKVKREl 338 ::::::::: :::::::::::::::::::: ::::::::::::::: ::::::::::: d1o94a1 282 WVKLVKQVS--KKPVLGVGRYTDPEKMIEIVtKGYADIIGCARPSIA-DPFLPQKVEQG- 337 d1d3ga_ 339 eallkeqgfggvtdaigadhrr 360 d1o94a1 338 -------------------ryd 340 FAST alignment (Normalized score: 9.91 Raw score:3467.00) d1d3ga_ 1 MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDM----------LEVR 50 :::: d1o94a1 1 ----------------------------------------------ARDPKHDILFEPIQ 14 d1d3ga_ 51 VLGHKFRNPVGIAAGFDK-------------HGEAVDGLYKMGFGFVEIGSVTPKPQEGN 97 ::::::::::::: :::::::::::::::::::::::: d1o94a1 15 IGPKTLRNRFYQV-----PHCIGAGSDKPGFQSAHRSVKAEGGWAALNTEYCSIN----- 64 d1d3ga_ 98 PRPRVFRLPEDQAVINRYGF--------NSHG--LSVVEHRLRARQQKQAKLTEDGLPLG 147 :::: ::::::::::::::::: :::::: d1o94a1 65 --------------------PESDDTHRLSARIWDEGDVRNLKAMTDEVHK---YGALAG 101 d1d3ga_ 148 VNLGKNKTSV----------------------------------------DAAEDYAEGV 167 :::: :::::::::: d1o94a1 102 VELW------YGGAHAPNMESRATPRGPSQYASEFETLSYCKEMDLSDIAQVQQFYVDAA 155 d1d3ga_ 168 RVLGP-LADYLVVNVSSPNTAGL-----------------------GKAELRRLLTKVLQ 203 ::::: ::::::::: :::: :::::::::::::: d1o94a1 156 KRSRDAGFDIVYVYG-AHSY---LPLQFLNPYYNKRTDKYGGSLENRARFWLETLEKVKH 211 d1d3ga_ 204 ERDGLRRVH---RPAVLVKIAPD----LTSQD----KEDIASVVKEL---GIDGLIVTNT 249 : ::::::::: :::: :::::::::: :::::: d1o94a1 212 A--------VGSDCAIATRFG--VDTVYGPG-QIEAEVDGQKFVEM-ADSLVDMWD---- 255 d1d3ga_ 250 TVSRPAGLQGALRSETGGLSGKP-------------------LRDLSTQTIREMYALTQG 290 ::::::::::::::: : d1o94a1 256 -----------------------ITIGDIAEWGEDAGPSRFYQQGHTIPWVKLVKQV--S 290 d1d3ga_ 291 RVPIIGVGGVSSGQDALEKIRA-GASLVQLYTALTFWGPPVVGKVKRELEALLKEQGFGG 349 :::::::::::::::::::::: ::::::::::::: ::::::::: d1o94a1 291 KKPVLGVGRYTDPEKMIEIVTKGYADIIGCARPSIA-DPFLPQKVE-------------- 335 d1d3ga_ 350 VTDAIGADHRR----- 360 d1o94a1 336 -----------QGRYD 340 TMalign alignment (TM-score: 0.60 Raw score:215.47) d1d3ga_ 1 -----MATGDERFYAEHLMPTLQGLLDPESAHRLAVRFTSLGLLPFQDSDMLEVRVL-GH 54 :::::::::: :: d1o94a1 1 ARDPK------------------------------------------HDILFEPIQIGPK 18 d1d3ga_ 55 KFRNPVGIAAGFD-KHG-----EA--VDGLYKMGFGFVEIGSVTPKP-QEGNPRPRVFRL 105 ::::::::::::: ::: :: ::::::::::::::::::::: ::::: d1o94a1 19 TLRNRFYQVPHCIGAGSDKPGFQSAHRSVKAEGGWAALNTEYCSINPESDDTH------- 71 d1d3ga_ 106 PEDQAVINRYGFNSHGL-S-VVEHRLRARQQKQAKLTEDGLPLGVNLGKN---K------ 154 : ::::: : :::::::::::::::: : :::::::::: : d1o94a1 72 ---------R--LSARIWDEGDVRNLKAMTDEVHKY--G-ALAGVELWYGGAHAPNMESR 117 d1d3ga_ 155 -TSV----------------------D--AAEDYAEGVRVLGP-LADYLVVNVSSPNT-A 187 ::: : :::::::::::::: :::::::::::::: : d1o94a1 118 ATPRGPSQYASEFETLSYCKEMDLSDIAQVQQFYVDAAKRSRDAGFDIVYVYGAHSYLPL 177 d1d3ga_ 188 GLG--------------K-AELRRLLTKVLQERDGLRRVHRPAVLVKIA-PD------LT 225 ::: : ::::::::::::::::::: ::::::::: :: :: d1o94a1 178 QFLNPYYNKRTDKYGGSLENRARFWLETLEKVKHAVGS--DCAIATRFGVDTVYGPGQIE 235 d1d3ga_ 226 -SQDKEDIASVVKELGIDGLIVTNTTVSRPAGLQGALRSETGGL--SG-K--PLRDLSTQ 279 :::::::::::: ::::::::: :::: :::: :: : :::::::: d1o94a1 236 AEVDGQKFVEMAD-SLVDMWDIT-IGDI------------AEWGEDAGPSRFYQQGHTIP 281 d1d3ga_ 280 TIREMYALTQGRVPIIGVGGVSSGQDALEKI-RAGASLVQLYTALTFWGPPVVGKVKREL 338 ::::::::: :::::::::::::::::::: :::::::::::::: :::::::::::: d1o94a1 282 WVKLVKQVS--KKPVLGVGRYTDPEKMIEIVTKGYADIIGCARPSI-ADPFLPQKVEQG- 337 d1d3ga_ 339 EA-LLKEQGFGGVTDAIGADHRR 360 :: d1o94a1 338 RYD-------------------- 340 HHsearch alignment (Probability: 1.00 E-value:0.00) d1d3ga_ 47 LEVRVLGHKFRNPVGIAA-----GFDKH---GEAVDGLYKMGFGFVEIGSVTPKPQEGN- 97 :::::::::::::::::: ::::: :::::::::::::::::::::::::::: d1o94a1 11 EPIQIGPKTLRNRFYQVPHCIGAGSDKPGFQSAHRSVKAEGGWAALNTEYCSINPESDDT 70 d1d3ga_ 98 P--RPRVFRLPEDQAVINRYGFNSHGLSVVEHRLRARQQKQAKL-----------TEDGL 144 : :::::: :: :: :::::::::::::::::::: ::::: d1o94a1 71 HRLSARIWD---EG-DV-------RNLKAMTDEVHKYGALAGVELWYGGAHAPNMESRAT 119 d1d3ga_ 145 PLGVNLGKNK---------TS----VDAAEDYAEGVRVL-GPLADYLVVNVS-------- 182 :::::::::: :: :::::::::::::: :::::::::::: d1o94a1 120 PRGPSQYASEFETLSYCKEMDLSDIAQVQQFYVDAAKRSRDAGFDIVYVYGAHSYLPLQF 179 d1d3ga_ 183 -SPNTAGLGKAEL----RRLLTKVLQERDGLRRVH--RPAVLVKIAPDLT-------SQD 228 ::::: :::::: :::::::::::::::::: ::::::::::::: ::: d1o94a1 180 LNPYYN-KRTDKYGGSLENRARFWLETLEKVKHAVGSDCAIATRFGVDTVYGPGQIEAEV 238 d1d3ga_ 229 KEDIASVVKELGIDGLIVTNTTVSRPAG-LQGALRSETGGLSGKPLRDLSTQTIREMYAL 287 :::::::::::::::::::::::::::: ::::::: ::::::::::::::: d1o94a1 239 DGQKFVEMADSLVDMWDITIGDIAEWGEDAGPSRFY---------QQGHTIPWVKLVKQV 289 d1d3ga_ 288 TQGRVPIIGVGGVSSGQDALEKIRAG-ASLVQLYTALTFWGPPVVGKVKRE 337 :: :::::::::::::::::::::: ::::::::::: :::::::::::: d1o94a1 290 SK--KPVLGVGRYTDPEKMIEIVTKGYADIIGCARPSI-ADPFLPQKVEQG 337