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: T0542_Ad1.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1j93a_ | Uroporphyrinogen decarboxylase, UROD | UROD/MetE-like | TIM beta/alpha-barrel | α/β |
| Hit | d1k6wa2 | Cytosine deaminase catalytic domain | Metallo-dependent hydrolases | TIM beta/alpha-barrel | α/β |
Query <-- 0.875 --> IntermediateDALI alignment (Z-score: 2.8 Raw score:517.50) query 1 ------------------------------------------------------------ 1 d1j93a_ 1 tqpllldavrgkeverppvwlmrqagrymksyqllcekyplfrdrsenvdlvveislqpw 60 query 1 ------------------------------------------------------------ 1 d1j93a_ 61 kvfrpdgvilfsdiltplsgmnipfdiikgkgpvifdplrtaadvekvrefipeksvpyv 120 query 1 ------------sLQLRLALN-qidSTVG---------------------------DIAG 20 :::::::: :::: :::: d1j93a_ 121 gealtilrkevnnQAAVLGFVgapfTLASyvveggssknftkikrlafaepkvlhaLLQK 180 query 21 NAEAILRWTRHSAEQGAHLVAFPEMaltgypvedLALRSSFVEASRTALRELAARLAEEg 80 ::::::::::::::::::::::::: ::::::::::::::::::::::::: d1j93a_ 181 FATSMAKYIRYQADSGAQAVQIFDS------watELSPVDFEEFSLPYLKQIVDSVKLT- 233 query 81 FGELPVLVGY---lDRSEsaqpkygqpagaprnaaavlhrgRVALTFAKHhlpnygvfde 137 :::::::::: :::: ::::::::: d1j93a_ 234 HPNLPLILYAsgsgGLLE------------------rlpltGVDVVSLDW---------- 265 query 138 fryfvPGDTMpivrlhgvdialaiceDLWQD----ggrvPAARSAGaglllsvnaspyer 193 ::::: ::::: ::::::: d1j93a_ 266 -----TVDMAdgrrrlgpnvaiqgnvDPGVLfgskefitNRINDTV---kkagkgkhiln 317 query 194 dkddtRLELvRKRAQEAGcttaylamiggqdelvfdgdsivvdrdgevvarapqfsegcv 253 :::: :::::::: d1j93a_ 318 lghgiKVGTpEENFAHFF------------------------------------------ 335 query 254 vldldlpaaEAEPptgvvddglridrlviseeplpayeaelaggyadrl 302 :::: d1j93a_ 336 -----eiakGLRY------------------------------------ 343 FAST alignment (Normalized score: 2.91 Raw score:937.50) query 1 S----------------------------------------------------------- 1 d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 2 ------------------------------------------------------------ 2 d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 2 --------------LQLRLALNQIDSTV-------------------------------- 15 :::::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFV------GAPFTLASYVVEGGSSKNFTKIKRLAFAEPKV 173 query 16 --GDIAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLAL--------RSSFV-EA 64 ::::::::::::::::::::::::::: ::::: :: d1j93a_ 174 LHALLQKFATSMAKYIRYQADSGAQAVQI---------------FDSWATELSPVDFEEF 218 query 65 SRTALRELAARLAEEGFGELPVLVGYLDRSESAQPKYGQPAGAPRNAAAVLHRG------ 118 :::::::::::::: :::::::::: d1j93a_ 219 SLPYLKQIVDSVKL-THPNLPLILY-----------------------------ASGSGG 248 query 119 --------RVALTFAKHHLPNYGVFDEFRYFVPGDTMPIVRLHGVD-------------- 156 ::::::: d1j93a_ 249 LLERLPLTGVDVVSL-------------------------------DWTVDMADGRRRLG 277 query 157 ---IALAICEDLWQDG------------------GRVPAARSAGA---GLLLSV---NAS 189 ::::: ::::: ::::: ::: d1j93a_ 278 PNVAIQGN--------VDPGVLFGSKEFITNRINDTVKK------AGKGKHIL-NLGHGI 322 query 190 PYERDKD-----DTRLELVRKRAQEAGCTTAYLAMIGGQDELVFDGDSIVVDRDGEVVAR 244 : ::::::::::: d1j93a_ 323 K------VGTPEENFAHFFEIAK------------------------------------- 339 query 245 APQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLPAYEAELAGGYADRL-- 302 d1j93a_ 340 ----------------------------------------------------------GL 341 query 303 -- 303 d1j93a_ 342 RY 343 TMalign alignment (TM-score: 0.44 Raw score:131.70) query 1 SLQLRL------------------------------------------------------ 6 ::::: d1j93a_ 1 -TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQP 59 query 7 ------ALNQIDSTVGDIAGN--------------------------------A---E-A 24 ::::::::::::::: : : : d1j93a_ 60 WKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPY 119 query 25 ILRWTRHSAE--QGAHLVAFPEMAL-TG-YP-----VE--D-LAL---------RSSFVE 63 :::::::::: ::::::::::::: :: :: :: : ::: :::::: d1j93a_ 120 VGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQ 179 query 64 ASRTALRELAARLAEEGFGELPVLVGYLDRS--ESAQPKYGQPAGAPR-NAA-AV--LHR 117 :::::::::::::::: : ::::::::::: : :::::::::: ::: :: ::: d1j93a_ 180 KFATSMAKYIRYQADS-G--AQAVQIFDSWATE---L-SPVDFEEFSLPYLKQIVDSVKL 232 query 118 GRV-ALTFA-KHHLPNYGVFDEFRYFVPGDTMPIVRLHGVDIALAICEDLWQDGGRVPAA 175 ::: ::::: :::::: : :::::::::: ::::::::::::::::: d1j93a_ 233 THPNLPLILYASGSGG------L--LERLPLTGVD--------VVSLDWTVDMADGRRRL 276 query 176 RSAGAGLLLSVNASPYERDKDD--TRLELVRKRAQEAGCT-TAYLA-MIGGQDELVFD-G 230 ::: : ::::::: ::::::: :::::::::::::::: ::::: ::: :::: : d1j93a_ 277 GPN-V--AIQGNVD-PGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGI----KVGTPE 328 query 231 --DSIVVDRDGEVVARAPQFSEGCVVLDLDLPAAEAEPPTGVVDDGLRIDRLVISEEPLP 288 ::::: ::::: ::: d1j93a_ 329 ENFAHFF---EIAKG-------------LRY----------------------------- 343 query 289 AYEAELAGGYADRL 302 d1j93a_ 344 -------------- 344 HHsearch alignment (Probability: 0.14 E-value:0.02) query 18 IAGNAEAILRWTRHSAEQGAHLVAFPEMALTGYPVEDLALRSSFVEASRTALRELAARLA 77 ::::::::::::::::::::::::::::::::::::: ::::::::::::::::: d1j93a_ 178 LQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVD------FEEFSLPYLKQIVDSVK 231 query 78 EEGFGELPVLV 88 :::: :::::: d1j93a_ 232 LTHP-NLPLIL 241
Intermediate <-- 1.163 --> HitDALI alignment (Z-score: 8.8 Raw score:1067.20) d1j93a_ 1 tqpllldavrgkeverppVWLMR--QAGRymksyQLLCE-------------kyPLFRDr 45 ::::: :::: ::::: ::::: d1k6wa2 1 ---------------pfvEPHIHldTTQT-----AGQPNwnqsgtlfegierwaERKAL- 39 d1j93a_ 46 sENVDLVVEISLQPWKVF-----RPDGVILfsdILTPlsgmnipfdiikgkgpvifdplr 100 ::::::::::::::::: ::::::: :::: d1k6wa2 40 -LTHDDVKQRAWQTLKWQiangiQHVRTHV--dVSDA----------------------- 73 d1j93a_ 101 taadvekvrefipeksVPYVGEALTILRKEVN--NQAAVLGFVG-APFTLasyvveggss 157 :::::::::::::::: :::::::::: ::::: d1k6wa2 74 ----------------TLTALKAMLEVKQEVApwIDLQIVAFPQeGILSY---------- 107 d1j93a_ 158 knftkikrlafaepkvlhallqkfatSMAKYIRYQADSGAQAVQIFDSWAtelspvdFEE 217 :::::::::::::::::::::::: ::: d1k6wa2 108 -------------------------pNGEALLEEALRLGADVVGAIPHFE------fTRE 136 d1j93a_ 218 FSLPYLKQIVDsVKLTHPnLPLILYASGS--GGLL--ERLPLTG-------vDVVSLDWT 266 ::::::::::: :::::: :::::::::: :::: ::::::: :::::::: d1k6wa2 137 YGVESLHKTFA-LAQKYD-RLIDVHCDEIddEQSRfvETVAALAhhegmgarVTASHTTA 194 d1j93a_ 267 VD------madgRRRLGP-NVAIQGNV--DPGVlfgskefitnrindTVKKAG--KGKHI 315 :: :::::: :::::::: :::: :::::: ::::: d1k6wa2 195 MHsyngaytsrlFRLLKMsGINFVANPlvNIHLqgrfdtypkrrgitRVKEMLesGINVC 254 d1j93a_ 316 LN---lghgIKVGTpeenFAHF-------------feiakGLRY---------------- 343 :: ::::: :::: :::: d1k6wa2 255 FGhddvfdpWYPLG--taNMLQvlhmglhvcqlmgygqinDGLNlithhsartlnlqdyg 312 d1j93a_ 344 -------- 344 d1k6wa2 313 iaagnsan 320 FAST alignment (Normalized score: 3.74 Raw score:1240.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYP-------------------- 40 d1k6wa2 1 ----------------------------------------PFVEPHIHLDTTQTAGQPNW 20 d1j93a_ 41 ---------------LFRDRSENVDLVVEISLQPWK---VFRP--DGVILFSDILTPLSG 80 :::: ::::::::::::::: :::: :::: :::: d1k6wa2 21 NQSGTLFEGIERWAERKAL--LTHDDVKQRAWQTLKWQIANGIQHVRTH--VDVS----- 71 d1j93a_ 81 MNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSV---PYVGEALTILRKEVNN---- 133 ::::::::::::: d1k6wa2 72 -------------------------------------DATLTALKAMLEVKQE---VAPW 91 d1j93a_ 134 -QAAVLGFVGAPF---TLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFAT--SMAK 187 ::::::: :::: :::: d1k6wa2 92 IDLQIVAF-----PQEGILS----------------------------------YPNGEA 112 d1j93a_ 188 YIRYQADSGAQAVQIFDSWATE--LSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASG 245 :::::::::::::::::: ::::::: :::::::::::: :::::::: d1k6wa2 113 LLEEALRLGADVVGAIPH----FEFTREYGV-ESLHKTFALAQK-----YDRLIDVH--- 159 d1j93a_ 246 SG---------GLLERLPLTGVDVVSLDWTV-------------------------DMAD 271 :::::::: :::: d1k6wa2 160 --CDEIDDEQSRFVETVAA------------LAHHEGMGARVTASHTTAMHSYNGAYTSR 205 d1j93a_ 272 GRRRLG---PNVAIQGNVDPGVLFGSKEFITN------------------------RIND 304 :::: ::::: :::: d1k6wa2 206 LFRL--LKMSGINF------------------VANPLVNIHLQGRFDTYPKRRGITRVKE 245 d1j93a_ 305 TVKKAGKG---KHILNLGHGI---------KVGTPEENFAHFFEIAKGLRY--------- 343 ::: :::: :::::: d1k6wa2 246 MLE-----SGINVCF------GHDDVFDPWYPLGTA---------------NMLQVLHMG 279 d1j93a_ 344 ----------------------------------------- 344 d1k6wa2 280 LHVCQLMGYGQINDGLNLITHHSARTLNLQDYGIAAGNSAN 320 TMalign alignment (TM-score: 0.43 Raw score:146.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 d1k6wa2 1 ------------------------------------------------------------ 1 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYV 120 d1k6wa2 1 ------------------------------------------------------------ 1 d1j93a_ 121 GEALTILRKEVNNQAAVLGFVGAPFTLASYVVEG-G-------SSKNFTKIKRLAFAEPK 172 : : :::::::: ::::::::: : :::::::::::: d1k6wa2 1 P--F------------VEPHIHLD-TTQTAGQPNWNQSGTLFEGIERWAERKALL----- 40 d1j93a_ 173 VLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKL 232 ::::::::::::::::::: :: : :::::: :: :::: :: :::::::::::::: d1k6wa2 41 -THDDVKQRAWQTLKWQIAN-GI-Q-HVRTHV--DV-SDAT--LT-ALKAMLEVKQEVAP 90 d1j93a_ 233 THPNLPLILYA-SGSG-----G--LLERLPLTGVDVVSLDW--------T-VDMADGRRR 275 :: ::::::: :::: : ::::::::::::::::: : ::::::::: d1k6wa2 91 WI--DLQIVAFPQEGILSYPNGEALLEEALRLGADVVGAIPHFEFTREYGVESLHKTFAL 148 d1j93a_ 276 L-GPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEE-NFAH 333 : :::::::::::::::::: :::::::::::::::::::::: :::::::::: :::: d1k6wa2 149 AQKYDRLIDVHCDEIDDEQS--RFVETVAALAHHEGMGARVTAS-HTTAMHSYNGAYTSR 205 d1j93a_ 334 FFEIAKGLRY-------------------------------------------------- 343 :::::::::: d1k6wa2 206 LFRLLKMSGINFVANPLVNIHLQGRFDTYPKRRGITRVKEMLESGINVCFGHDDVFDPWY 265 d1j93a_ 344 ------------------------------------------------------- 344 d1k6wa2 266 PLGTANMLQVLHMGLHVCQLMGYGQINDGLNLITHHSARTLNLQDYGIAAGNSAN 320 HHsearch alignment (Probability: 0.10 E-value:0.09) d1j93a_ 62 VFRP 65 :::: d1k6wa2 58 ANGI 61