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 <-- 0.889 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1p1ma2) 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 d1p1ma2 Hypothetical protein TM0936,​ probable catalytic domainMetallo-​dependent hydrolasesTIM 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 <-- 0.889 --> Hit
DALI alignment (Z-score: 7.9 Raw score:986.30) d1j93a_ 1 tqpllldavrgkeverpPVWLMR--QAGRYMK-----syqllcekypLFRDRsENVDLVV 53 :::::: ::::::: ::::: ::::::: d1p1ma2 1 ---------------alFNTHTHapMTLLRGVaedlsfeewlfskvlPIEDR-LTEKMAY 44 d1j93a_ 54 EISLQPWKVFR----pDGVILFSdiltplsgmnipfdiikgkgpvifdplrtaadvekvr 109 ::::::::::: ::::::: d1p1ma2 45 YGTILAQMEMArhgiaGFVDMYF------------------------------------- 67 d1j93a_ 110 efipeksvpyVGEALTILRKEVNnQAAVLGFVGAPftlasyvveggssknftkikrlafa 169 ::::::::::::: ::::::::::: d1p1ma2 68 ----------HEEWIAKAVRDFG-MRALLTRGLVD------------------------- 91 d1j93a_ 170 epkvlhaLLQKFatSMAKYIRYQADSG-------AQAVQIFDSWAtelspvdfeefSLPY 222 ::::: ::::::::::::: ::::::::::: :::: d1p1ma2 92 -------SNGDD-gGRLEENLKLYNEWngfegriFVGFGPHSPYL----------cSEEY 133 d1j93a_ 223 LKQIVDSVKLthPNLPLILYASG---SGGLLERLPLTGV---DVVS-LDWTVDmADGRRR 275 :::::::::: ::::::::::: ::::::::::::: :::: :::::: :::::: d1p1ma2 134 LKRVFDTAKS--LNAPVTIHLYEtskEEYDLEDILNIGLkevKTIAaHCVHLP-ERYFGV 190 d1j93a_ 276 LGPNVAIQGNVD-PGVLFGskefitnrindTVKKAG--KGKHILN-lghgIKVGtpeenf 331 :::::::::::: :::::: :::::: ::::::: :::: d1p1ma2 191 LKDIPFFVSHNPaSNLKLG-------ngiaPVQRMIehGMKVTLGtdgaaSNNS------ 237 d1j93a_ 332 ahFFEIAK------------------GLRY--------------- 343 :::::: :::: d1p1ma2 238 -lNLFFEMrlasllqkaqnprnldvnTCLKmvtydgaqamgfksg 281 FAST alignment (Normalized score: 3.03 Raw score:941.00) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRS-------------- 46 d1p1ma2 1 ----------------------------------------------ALFNTHTHAPMTLL 14 d1j93a_ 47 -----------------------ENVDLVVEISLQPWK---VFRPDGVILFSDILTPLSG 80 ::::::::::::::: :::::::: d1p1ma2 15 RGVAEDLSFEEWLFSKVLPIEDRLTEKMAYYGTILAQMEMARHGIAGFV----------- 63 d1j93a_ 81 MNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVP----YVGEALTILRKEVNN-QA 135 ::::::::::: :: d1p1ma2 64 --------------------------------------DMYFHEEWIAKAVRD----FGM 81 d1j93a_ 136 AVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFA--------TSMAK 187 ::::::: ::::: d1p1ma2 82 RALLTRG----------------------------------------LVDSNGDDGGRLE 101 d1j93a_ 188 YIRYQADSGA------QAVQIFDSWATELSPVDFEEF-------SLPYLKQIVDSVKLTH 234 ::::::::: :::::: :::::::::::::: d1p1ma2 102 ENLKLYNEW-NGFEGRIFVGFG---------------PHSPYLCSEEYLKRVFDTAKS-- 143 d1j93a_ 235 PNLPLILYASGSGG---------LLERLPLTGVDVVSLDWTVD--------------MAD 271 :::::::: ::::::::: ::: d1p1ma2 144 LNAPVTIH------LYETSKEEYDLEDILNIG-----------LKEVKTIAAHCVHLPER 186 d1j93a_ 272 GRRRLGP-NVAIQGNVDPGVLFGSKEFITN---------------RINDTVKKAGKG--- 312 ::::::: :::: ::::::: d1p1ma2 187 YFGVLKDIPFFV------------------SHNPASNLKLGNGIAPVQRMIE-----HGM 223 d1j93a_ 313 KHILNLGHGIKVGTPEENFAHFFEIAKGLRY----------------------------- 343 ::::: d1p1ma2 224 KVTLG--------------------------TDGAASNNSLNLFFEMRLASLLQKAQNPR 257 d1j93a_ 344 ------------------------ 344 d1p1ma2 258 NLDVNTCLKMVTYDGAQAMGFKSG 281 TMalign alignment (TM-score: 0.49 Raw score:166.54) d1j93a_ 1 TQPLLLDAVRGKEVERPPVWLMRQ-AG-RYMK----------------SYQLLCEKYPLF 42 :: ::::::: :: :::: :: d1p1ma2 1 --AL-------------FNTHTHAPMTLLRGVAEDLSFEEWLFSKVLP----------IE 35 d1j93a_ 43 RDRSEN-VDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRT 101 :::::: ::::::::::::::::::::::: :: :: d1p1ma2 36 DRLTEKMAYYGTILAQMEMARHGIAGFVDM-YF-HE------------------------ 69 d1j93a_ 102 AADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFT 161 : ::::::::: :: :::::::: : : d1p1ma2 70 ---------------E-WIAKAVRDF--GM----RALLTRGL--V--D------------ 91 d1j93a_ 162 KIKRLAFAEPKVLHALLQKFATSMAKYIRYQADS--GAQAVQIFDSWATELSPVDFEEFS 219 : : : ::::::::::::::::::: :::::::::: :::: :: ::: d1p1ma2 92 -S---N------G--DDGGRLEENLKLYNEWNGFEGRIFVGFGPHS-PYLC---SE-EYL 134 d1j93a_ 220 LPYLKQIVDSVKLTHPNLPLILYASG----SGGLLERLP-LT--GVDVVSLDWTVDMADG 272 : :::::::::: : ::::::: ::::::::: :: :::::::::::::::: d1p1ma2 135 K-RVFDTAKSLN-----A-PVTIHLYETSKEEYDLEDILNIGLKEVKTIAAHCVHLPERY 187 d1j93a_ 273 RRRLGPNVAIQGNVD-PGVLFG-SKEFITNRINDTVKKAG-KGKHILNLGHGIKVGTPEE 329 ::::::::::::::: :::::: : :: ::::::: :::::::: ::::: :::: d1p1ma2 188 FGVLKDIPFFVSHNPASNLKLGN----G--IA-PVQRMIEHGMKVTLGT-DGAAS-NNSL 238 d1j93a_ 330 NFAHFFEIAK-----------GLRY------------------ 343 :::::::::: :::: d1p1ma2 239 NLFFEMRLASLLQKAQNPRNLDVNTCLKMVTYDGAQAMGFKSG 281 HHsearch alignment (Probability: 0.13 E-value:0.10) d1j93a_ 44 DRSENVDLVVEISLQPWKV 62 ::::::::::::::::::: d1p1ma2 35 EDRLTEKMAYYGTILAQME 53