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 <-- 1.175 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1t8qa_) 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 d1t8qa_ Glycerophosphodiester phosphodiesterase GlpQPLC-​like phosphodiesterasesTIM 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 <-- 1.175 --> Hit
DALI alignment (Z-score: 10.1 Raw score:1205.90) d1j93a_ 1 tqpllldavrgkevERPPVWLMRQAGRYMKsyqllcekyplfrdrsenvdlVVEISLQPW 60 :::::::::::::::: ::::::::: d1t8qa_ 1 --------------NEKIVIAHRGASGYLP-------------------ehTLPAKAMAY 27 d1j93a_ 61 KvFRPDGVILfsdILTPLSGM---nipfDIIK---------------GKGP--------- 93 : :::::::: :::::::: :::: :::: d1t8qa_ 28 A-QGADYLEQ--dLVMTKDDNlvvlhdhYLDRvtdvadrfpdrarkdGRYYaidftldei 84 d1j93a_ 94 ---------vifdplrtaadvekvrefipeksvpYVGEALTILRKEVN---NQAAVLGFV 141 :::::::::::::: ::::::::: d1t8qa_ 85 kslkftegfdiengkkvqtypgrfpmgksdfrvhTFEEEIEFVQGLNHstgKNIGIYPEI 144 d1j93a_ 142 GAPFTLASYvveggssknftkikrlafaepkvlhallqkfaTSMAKYIRYQADSG----- 196 ::::::::: :::::::::::::: d1t8qa_ 145 KAPWFHHQE------------------------------gkDIAAKTLEVLKKYGytgkd 174 d1j93a_ 197 -aQAVQIFDswatelspvdfeefsLPYLKQIVD-SVKLTHPNLPLILYAS---------- 244 ::::::: ::::::::: :::::::::::::::: d1t8qa_ 175 dkVYLQCFD---------------ADELKRIKNeLEPKMGMELNLVQLIAytdwnetqqk 219 d1j93a_ 245 ------------GSGG--LLERLPLtGVDVVSLDWTVD-----------mADGRRRLGP- 278 :::: ::::::: :::::::::::: ::::::::: d1t8qa_ 220 qpdgswvnynydWMFKpgAMKQVAE-YADGIGPDYHMLieetsqpgniklTGMVQDAQQn 278 d1j93a_ 279 NVAIQGNVDP--GVLFgskEFITNRINDTVKKAGkgkHILNLghgikvgtpeenfAHFFE 336 :::::::::: :::: ::::::::::::::: ::::: ::::: d1t8qa_ 279 KLVVHPYTVRsdKLPE-ytPDVNQLYDALYNKAG--vNGLFT----------dfpDKAVK 325 d1j93a_ 337 IAKglry 343 ::: d1t8qa_ 326 FLN---- 328 FAST alignment (Normalized score: 4.73 Raw score:1587.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDL--------- 51 :::::::: d1t8qa_ 1 --------------NEKIVIAH-----------------------------RGASGYLPE 17 d1j93a_ 52 -VVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVRE 110 :::::::::: ::::::::: d1t8qa_ 18 HTLPAKAMAYA-QGADYLEQD--------------------------------------- 37 d1j93a_ 111 FIPEKSVP---------------------------------------------------- 118 d1t8qa_ 38 --------LVMTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKF 89 d1j93a_ 119 -----------------------------YVGEALTILRKEVNN------QAAVLGFVG- 142 :::::::::::: :::::::: d1t8qa_ 90 TEGFDIENGKKVQTYPGRFPMGKSDFRVHTFEEEIEFVQGL---NHSTGKNIGIYPEI-K 145 d1j93a_ 143 APFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQ---KFATSMAKYIRYQADSGA-- 197 ::::::: :::::::::::: d1t8qa_ 146 APWFHHQ------------------------------EGKDIAAKTLEVLKK------YG 169 d1j93a_ 198 -------QAVQIFDSWATELSPVDFEEF-SLPYLKQIVD-SVKLTH--PNLPLILYASGS 246 ::::: :::::::::: :::: ::::::::: d1t8qa_ 170 YTGKDDKVYLQC----------------FDADELKRIKNELEPK--MGMELNLVQLI--- 208 d1j93a_ 247 ---------------------------GGLLERLPLTGVDVVSLDWTV------------ 267 ::::::::: :::::::::: d1t8qa_ 209 AYTDWNETQQKQPDGSWVNYNYDWMFKPGAMKQVAE-YADGIGPDYH-MLIEETSQPGNI 266 d1j93a_ 268 ----DMADGRRRLGPNVAIQGNVDPGVLFGSKE---------------FITNRINDTVKK 308 ::::::: ::::: :::::::::::: d1t8qa_ 267 KLTGMVQDAQQ---NKLVV--------------HPYTVRSDKLPEYTPDVNQLYDALYNK 309 d1j93a_ 309 AGKGKHILNLGHGIKVGTPEE---------NFAHFFEIAKGLRY-- 343 :::::::: d1t8qa_ 310 ---------------------AGVNGLFTDFPDKAVKF------LN 328 TMalign alignment (TM-score: 0.49 Raw score:166.82) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPW 60 :: ::::::::::: :: : :::: ::::::::::: d1t8qa_ 1 --NE-------------KIVIAHRGASG--YL---P--------EHTL-PAKAMAYAQGA 31 d1j93a_ 61 KVFRPDGVILFSDILTPLSGMNIP----FDIIKGKGPV-IF--DPLR------TAADVEK 107 :::: :::: :::::::: :::::::::: :: :::: :: d1t8qa_ 32 ------DYLE-QDLV-MTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYA-----ID 78 d1j93a_ 108 VRE------------------------------------FIPEKSVPYVGEALTILRK-E 130 ::: ::::::::::::::: : d1t8qa_ 79 FTLDEIKSLKFTEGFDIENGKKVQTYPGRFPMGKSDFRV----HTFEEEIEFVQGLNHST 134 d1j93a_ 131 VNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIR 190 ::: :::::::::::: : :: :::::::::::::: d1t8qa_ 135 GKN-IGIYPEIKAPWF-H-------------------------HQ-EGKDIAAKTLEVLK 166 d1j93a_ 191 YQADS---GAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSG 247 ::::: ::::::::: ::::::::::::::::::::::::::::: d1t8qa_ 167 KYGYTGKDDKVYLQCFD--------------ADELKRIKNELEPKMGMELNLVQLIAYTD 212 d1j93a_ 248 -GLL-ERL---------PLTGVDVVSLDWTVDMADGRRRLGPNVAIQGN-VDPGVLF-GS 294 ::: :: ::::::::::::::::::::::: ::::::: :: d1t8qa_ 213 WNETQ-QKQPDGSWVNY---------NYDWMFKPGAMKQVAEYADGIGPDYHMLIEETSQ 262 d1j93a_ 295 KEFITNRINDTVKKAGKGKHILNLGHGIK-VGT-----PEENFAH-FFEIAKGL------ 341 :::: ::: ::::::::::::::: :::: ::: ::::::: :::::::: d1t8qa_ 263 PGNI-KLT-GMVQDAQQNKLVVHP-YTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDF 319 d1j93a_ 342 ---------RY 343 d1t8qa_ 320 PDKAVKFLN-- 328 HHsearch alignment (Probability: 0.02 E-value:0.09) d1j93a_ 253 LPLTGVDVVSLDW 265 ::::::::::::: d1t8qa_ 307 YNKAGVNGLFTDF 319