HorA Server Transitive Detail

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


Query <-- 0.875 --> Intermediate <-- 1.058 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1ec7a1) through the intermediate protein (d1j93a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1j93a_ Uroporphyrinogen decarboxylase,​ URODUROD/​MetE-​likeTIM beta/​alpha-​barrelα/β
Hit d1ec7a1 D-​glucarate dehydrataseEnolase C-​terminal domain-​likeTIM beta/​alpha-​barrelα/β

Supporting Alignments

Query <-- 0.875 --> Intermediate
DALI 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 <-- 1.058 --> Hit
DALI alignment (Z-score: 11.1 Raw score:1260.70) d1j93a_ 1 tqpllldavrgkevERPPVWLMR------------------qagRYMKSYQLlcekyplf 42 ::::::::: :::::::: d1ec7a1 1 ---------dgqqrSEVEMLGYLffvgnrkatplpyqsqpddscDWYRLRHE-------- 43 d1j93a_ 43 rDRSEnVDLVVEISLQPWKVFRPDGVILFSdILTPlsgmnipfdiikgkgpvifdplrta 102 :::: :::::::::::::::::::::::: :::: d1ec7a1 44 -EAMT-PDAVVRLAEAAYEKYGFNDFKLKG-GVLA------------------------- 75 d1j93a_ 103 advekvrefipeksVPYVGEALTILRKEVNNqAAVLGFVGApftlasyvveggssknftk 162 ::::::::::::::::: ::::::::: d1ec7a1 76 --------------GEEEAESIVALAQRFPQ-ARITLDPNG------------------- 101 d1j93a_ 163 ikrlafaepkvlhallqkFATSMAKYIRYQADsGAQAVQIfdswatelspvdfeEFSLPY 222 :::::::::::::: ::::::: :::::: d1ec7a1 102 ----------------awSLNEAIKIGKYLKG-SLAYAED-------pcgaeqgFSGREV 137 d1j93a_ 223 LKQIVDSVKlthpnLPLILYA-sGSGGLLERLP-LTGVDVVSLD-WTVD---MADGRRRL 276 ::::::::: ::::::: :::::::::: :::::::::: :::: :::::::: d1ec7a1 138 MAEFRRATG-----LPTATNMiaTDWRQMGHTLsLQSVDIPLADpHFWTmqgSVRVAQMC 192 d1j93a_ 277 -GPNVAIQGNVdPGVLfgskEFITNRINDTVKKAGKGKHILNLghgikvgTPEE----nf 331 :::::::::: :::: ::::::::::::::::::::::: :::: d1ec7a1 193 hEFGLTWGSHS-NNHF----DISLAMFTHVAAAAPGKITAIDT---hwiwQEGNqrltke 244 d1j93a_ 332 aHFFE-iAKGLR------------------------------------------------ 342 :::: ::::: d1ec7a1 245 pFEIKggLVQVPekpglgveidmdqvmkahelyqkhglgarddamgmqylipgwtfdnkr 304 d1j93a_ 343 ----y 343 d1ec7a1 305 pcmvr 309 FAST alignment (Normalized score: 5.93 Raw score:1932.00) d1j93a_ 1 TQPLLLDAVRGK---EVERPPVWLMRQAGRYM----------------------KSYQLL 35 ::::::::: :::::: d1ec7a1 1 ------------DGQQRSEVEMLG--------YLFFVGNRKATPLPYQSQPDDSCDWYRL 40 d1j93a_ 36 CEKYPLFRDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVI 95 ::: ::::::::::::::::::::::::::: d1ec7a1 41 RHE------EAMTPDAVVRLAEAAYEKYGFNDFKLK------------------------ 70 d1j93a_ 96 FDPLRTAADVEKVREFIPEKS-----VPYVGEALTILRKEVNNQAAVLGFVGAPFTLASY 150 ::::::::::::::: :::::::::: d1ec7a1 71 ---------------------GGVLAGEEEAESIVALAQRF-PQARITLDPN-------- 100 d1j93a_ 151 VVEGGSSKNFTKIKRLAFAEPKVLHALLQK---FATSMAKYIRYQADSGAQAVQIFDSWA 207 :::::::::::: ::::::: d1ec7a1 101 ------------------------------GAWSLNEAIKIGKYL-KGSLAYA------- 122 d1j93a_ 208 TELSPVDFE---------EFSLPYLKQIVDSVKLTHPNLPLILYASG-----SGGLLERL 253 ::::::::::::: ::::::: :::::::: d1ec7a1 123 ---------EDPCGAEQGFSGREVMAEFRRA-----TGLPTAT----NMIATDWRQMGHT 164 d1j93a_ 254 PLT-GVDVVSLDWTV-------DMADGRRRLG---PNVAIQGNVDPGVLFGS-------K 295 ::: :::::::: :::::::: ::::: : d1ec7a1 165 LSLQSVDIPLAD---PHFWTMQGSVRVAQM--CHEFGLTW------------GSHSNNHF 207 d1j93a_ 296 EFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGLRY------------ 343 :::::::::::::::: d1ec7a1 208 DISLAMFTHVAAAAPG--------------------------------KITAIDTHWIWQ 235 d1j93a_ 344 ------------------------------------------------------------ 344 d1ec7a1 236 EGNQRLTKEPFEIKGGLVQVPEKPGLGVEIDMDQVMKAHELYQKHGLGARDDAMGMQYLI 295 d1j93a_ 344 -------------- 344 d1ec7a1 296 PGWTFDNKRPCMVR 309 TMalign alignment (TM-score: 0.52 Raw score:176.90) d1j93a_ 1 ----TQPLLLDAVRGKEVERPPVWLMRQAGR------------------YMKSYQLLCEK 38 :::::::::::::: ::::::: : d1ec7a1 1 DGQQ-------------RSEVEMLGYLFFVGNRKATPLPYQSQPDDSCDWYRLRHE-E-- 44 d1j93a_ 39 YPLFRDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDP 98 :: :::::::::::::::::::::::::::::: d1ec7a1 45 -----AM--TPDAVVRLAEAAYEKYGFNDFKLKGGVLAG--------------------- 76 d1j93a_ 99 LRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSK 158 : : ::: ::::::::::: ::::::::: :: d1ec7a1 77 --------------E---E-EAE-SIVALAQRFPQ-ARITLDPNG--AW----------- 103 d1j93a_ 159 NFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEF 218 :::::::::::::: ::::::::: :: ::::: d1ec7a1 104 ----------------------SLNEAIKIGKYLKG-SLAYAEDPC-GA------EQGFS 133 d1j93a_ 219 SLPYLKQIVDSVKLTHPNLPLILYASGSGG-LLERLP-LTGVDVVSLD-WTV---DMADG 272 ::::::::::::: :::::::::::: :::::: :::::::::: ::: ::::: d1ec7a1 134 GREVMAEFRRATG-----LPTATNMIATDWRQMGHTLSLQSVDIPLADPHFWTMQGSVRV 188 d1j93a_ 273 RRRL-GPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEEN- 330 :::: ::::::::::::: ::: ::: :::::::::::::::::: :::::::::: d1ec7a1 189 AQMCHEFGLTWGSHSNNH-FDI---SLA-MFTHVAAAAPGKITAIDT--HWIWQEGNQRL 241 d1j93a_ 331 --FAHFFE-IAKGLR--------------------------------------------- 342 :::::: :::::: d1ec7a1 242 TKEPFEIKGGLVQVPEKPGLGVEIDMDQVMKAHELYQKHGLGARDDAMGMQYLIPGWTFD 301 d1j93a_ 343 --------Y 343 d1ec7a1 302 NKRPCMVR- 309 HHsearch alignment (Probability: 0.08 E-value:0.03) d1j93a_ 43 RDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTA 102 ::::::::::::::::::::::::: :::::::: d1ec7a1 42 HEEAMTPDAVVRLAEAAYEKYGFND-----------------FKLKGGVL---------- 74 d1j93a_ 103 ADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTK 162 ::::: ::::::::::::::::::: ::::::::::::::: :::: d1ec7a1 75 ---------AGEEE----AESIVALAQRFPQARITLD-PNGAWSLNEAIKIGK---YLKG 117 d1j93a_ 163 IKRLAFAEPKVLH------ALLQKFATS------------MAKYIRYQADSGA-QAVQIF 203 :: :::::::::: ::::::::: ::::::::::::: :::::: d1ec7a1 118 SL-AYAEDPCGAEQGFSGREVMAEFRRATGLPTATNMIATDWRQMGHTLSLQSVDIPLAD 176 d1j93a_ 204 DSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGL-----LERLPLTGV 258 ::::::: :::::::::::: :::::::::::::: ::::::::: d1ec7a1 177 PHFWTMQ-----------GSVRVAQMCHEF--GLTWGSHSNNHFDISLAMFTHVAAAAPG 223 d1j93a_ 259 DVVSLDWTVDMADG-RRRLGPNVAIQ-GNVDPGV-----LFGSKEFITNRINDTVKKAGK 311 :::::::::::::: ::::::::::: ::::::: :::::::::::::::::: d1ec7a1 224 KITAIDTHWIWQEGNQRLTKEPFEIKGGLVQVPEKPGLGVEIDMDQVMKAHELYQKH--- 280 d1j93a_ 312 GKHILNLGHGIK 323 :::::::::::: d1ec7a1 281 GLGARDDAMGMQ 292