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 <-- 1.308 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1gk8a1) 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 d1gk8a1 Ribulose 1,​5-​bisphosphate carboxylase-​oxygenaseRuBisCo,​ C-​terminal domainTIM 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 <-- 1.308 --> Hit
DALI alignment (Z-score: 12.3 Raw score:1457.00) d1j93a_ 1 tqpllldaVRGK---EVERPPVWLMrQAGRymksyqllcekyplfrdRSENVdLVVEISL 57 :::: :::::::::: :::: ::::: ::::::: d1gk8a1 1 -gxphgiqVERDklnKYGRGLLGCT-IKPK----------------lGLSAK-NYGRAVY 41 d1j93a_ 58 QPWKvFRPDGVIL-fsDILTplsgmnipfdiikgkgpvifdplrtaadvekvrefipekS 116 :::: :::::::: :::: : d1gk8a1 42 ECLR-GGLDFTXDdenVNSQ------------------------------------pfmR 64 d1j93a_ 117 VPYVGEALTILRKEVN----NQAAVLGFVGAPftlasyvveggssknftkikrlafaepk 172 :::::::::::::::: :::::::::::: d1gk8a1 65 WRDRFLFVAEAIYKAQaetgEVKGHYLNATAG---------------------------- 96 d1j93a_ 173 vlhallqkFATSMAKYIRYQADSGAQAVQIFDSWatelspvdfeefSLPYLKQIVDSVKL 232 :::::::::::::::::::::::::: :::::::::::::: d1gk8a1 97 --------TCEEMMKRAVXAKELGVPIIMHDYLT-----------gGFTANTSLAIYCRD 137 d1j93a_ 233 thPNLPLILYASGS-------------GGLLERLPLTGVDVVSLD-----WTVD---MAD 271 :::::::::::: :::::::::::::::::: :::: ::: d1gk8a1 138 --NGLLLHIHRAMHavidrqrnhgihfRVLAKALRMSGGDHLHSGtvvgkLEGErevTLG 195 d1j93a_ 272 GRRRLGP---------------------NVAIQGNVDPgvlfgskefITNRINDTVKKAG 310 ::::::: :::::::::: ::::::::::::: d1gk8a1 196 FVDLMRDdyvekdrsrgiyftqdwxsmpGVMPVASGGI---------HVWHMPALVEIFG 246 d1j93a_ 311 KGkHILNlghgikvgTPEE----nfAHFFEIAKGLR------------------------ 342 :: :::: :::: ::::::::::: d1gk8a1 247 DD-ACLQ--fgggtlGHPWgnapgaAANRVALEACTqarnegrdlareggdvirsackws 303 d1j93a_ 343 ----------------------y 343 d1gk8a1 304 pelaaacevwkeikfefdtidkl 326 FAST alignment (Normalized score: 6.76 Raw score:2261.00) d1j93a_ 1 TQPLLLDAVRGKE---------------VERPPVWLMRQAGRYMKSYQLLCEKYPLFRDR 45 :::::::: d1gk8a1 1 -------------GAPHGIQVERDKLNKYGRGLLGC------------------------ 23 d1j93a_ 46 S-------ENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDP 98 ::::::::::::::: ::::::: :::: d1gk8a1 24 -TIKPKLGLSAKNYGRAVYECLR-GGLDFTA--DDEN----------------------- 56 d1j93a_ 99 LRTAADVEKVREFIPEKS------------VPYVGEALTILRKEVNN--QAAVLGFVGAP 144 ::::::::::::::: ::::::: d1gk8a1 57 ------------------VNSQPFMRWRDRFLFVAEAIYKAQAET--GEVKGHYLN---- 92 d1j93a_ 145 FTLASYVVEGGSSKNFTKIKRLAFAEPKVLHAL----LQKFATSMAKYIRYQADSGAQAV 200 :::::::::::::: :::::: d1gk8a1 93 ---------------------------------ATAGTCEEMMKRAVAAKE---LGVPII 116 d1j93a_ 201 QIFDSWATELSPVDFEEF-SLPYLKQIVDSVKLTHPNLPLILYASGS------------- 246 :::::: :::::::::::::: :::::::::::: d1gk8a1 117 MHDYLT------------GGFTANTSLAIYCRD--NGLLLHIHRAMHAVIDRQRNHGIHF 162 d1j93a_ 247 GGLLERLPLTGVDVVSLDWTV-----------DMADGRRRLGP----------------- 278 :::::::::::::::::: :::::::: d1gk8a1 163 RVLAKALRMSGGDHLHSG---TVVGKLEGEREVTLGFVDL---MRDDYVEKDRSRGIYFT 216 d1j93a_ 279 -------NVAIQGNVDPGVLFGSKEF------ITNRINDTVKKAGKGKHILNLGHGIKVG 325 :::: :::::::::::: ::::::: d1gk8a1 217 QDWASMPGVMP---------------VASGGIHVWHMPALVEIF-GDDACLQ-------- 252 d1j93a_ 326 TP------------EENFAHFFEIAKGLRY------------------------------ 343 ::::::::::::: d1gk8a1 253 --FGGGTLGHPWGNAPGAAANRVALEA---CTQARNEGRDLAREGGDVIRSACKWSPELA 307 d1j93a_ 344 ------------------- 344 d1gk8a1 308 AACEVWKEIKFEFDTIDKL 326 TMalign alignment (TM-score: 0.48 Raw score:163.76) d1j93a_ 1 ----TQPLLLDAVRG---KEVERPPVWLMRQAGR-YMKSYQLLC---------------- 36 ::::::: :::::::::::::: ::::::::: d1gk8a1 1 GAPH----GIQVERDKLN--KYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTADD 54 d1j93a_ 37 ----EKYPLFRDRSENVDLVVEISLQPW-K--VFRPDGVILFSDILTPLSGMNIPFDIIK 89 :::::::: ::::::::::: : ::::::::::::: : : : d1gk8a1 55 ENVN----SQPFMRWR-DRFLFVAEAIYKAQAETGEVKGHYLNAT-A-G-T--------- 97 d1j93a_ 90 GKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLAS 149 ::: ::::::::::::: :::::::: :: d1gk8a1 98 ---------------------CEE--MMKRAVAAKELGV--------PIIMHDYL-TG-- 123 d1j93a_ 150 YVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATE 209 :::::::::::::::::: :::::::::: d1gk8a1 124 -------------------------------GFTANTSLAIYCRDNGLL-LHIHRAMHAV 151 d1j93a_ 210 L--SPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYA----SGSGGLLER-LPLTGVDV-- 260 : ::::::: :::::::::::: ::::::: ::::::::: :::::::: d1gk8a1 152 IDRQRNHGIH-FRVLAKALRMSG------GDHLHSGTVVGKLEGEREVTLGFVDLMRDDY 204 d1j93a_ 261 -----VSLDWTVDMADGRRRLG---P------NVAIQGNVDPGVLFGSKEFITNRINDTV 306 :::: : :::::::::: : : ::::::: d1gk8a1 205 VEKDR-------------SRGIYFTQDWASMPGVMPVASGGI-H-------V-WHMPALV 242 d1j93a_ 307 KKAGKGKHILNLGHGIKVGTP-E--ENFAHFFEIAKG-LR--Y----------------- 343 :::: ::::::: :::::::: : :::::::::::: :: : d1gk8a1 243 EIFG-DDACLQF-GGGTLGHPWGNAPGAAANRVALEACTQARNEGRDLAREGGDVIRSAC 300 d1j93a_ 344 -------------------------- 344 d1gk8a1 301 KWSPELAAACEVWKEIKFEFDTIDKL 326 HHsearch alignment (Probability: 0.71 E-value:0.00) d1j93a_ 113 PEKSVPYVGEALTILRKEVNNQAAVLGF-VGAPFTLASYVVEGGSSKNFTKIKRLAFAEP 171 ::::::::::::::::::::::: :::: ::: ::: d1gk8a1 65 WRDRFLFVAEAIYKAQAETGEVK-GHYLNATA-------------------------GTC 98 d1j93a_ 172 KVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVK 231 : ::: ::::::::::::::::::::::::: :::::::: d1gk8a1 99 E---EMM--------KRAVXAKELGVPIIMHDYLTGGFTA--------NTSLAIYC---- 135 d1j93a_ 232 LTHPNLPLILYASGSGGLLERLPLTGVDVVSLDWTVDMADGRRRLGPNVAIQGNVDPGVL 291 :::::::::::::::::: :::: ::::::: ::::::::::::::::::: ::: d1gk8a1 136 -RDNGLLLHIHRAMHAVID-RQRN-----HGIHFRV-LAKALRMSGGDHLHSGTVV-GKL 186 d1j93a_ 292 FGSKEFITNRINDTVK 307 :::::::::::::::: d1gk8a1 187 EGEREVTLGFVDLMRD 202