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 <-- 1.019 --> Hit

SVM
score
SVM
score

The query (T0542_Ad1.pdb) is transitively linked to the hit (d1qnra_) 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 d1qnra_ Beta-​mannanase(Trans)glycosidasesTIM 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 <-- 1.019 --> Hit
DALI alignment (Z-score: 14.1 Raw score:1644.70) d1j93a_ 1 -TQPLlldavRGKE-------VERPPVWLMRQAgrymksyqllcekyplfrdrSENVDLV 52 :::: :::: :::::::::::: ::::::: d1qnra_ 1 aSSFV-----TISGtqfnidgKVGYFAGTNCYW------------------csFLTNHAD 37 d1j93a_ 53 VEISLQPWKVFRPDGVILFSdilTPLS----------GMNIpfdiikgkgpvifdplrta 102 :::::::::::::::::::: :::: :::: d1qnra_ 38 VDSTFSHISSSGLKVVRVWG---FNDVntqpspgqiwFQKL------------------- 75 d1j93a_ 103 adVEKVReFIPE-KSVPYVGEALTILRKEVnnqAAVLGFVG---apftLASYVVEGgssk 158 ::::: :::: ::::::::::::::::: :::::::: :::::::: d1qnra_ 76 -sATGST-INTGaDGLQTLDYVVQSAEQHN---LKLIIPFVnnwsdygGINAYVNA---- 126 d1j93a_ 159 nfTKIKRlafaepkvLHALLQKFATSMAKYIRYQADS-GAQAVQIFDSWaTELSpVDFEE 217 ::::: :::::::::::::::::::::: ::::::::::: :::: ::::: d1qnra_ 127 fgGNATT-----wytNTAAQTQYRKYVQAVVSRYANStAIFAWELGNEP-RCNG-CSTDV 179 d1j93a_ 218 fSLPYLKQIVDSVKLTHPNLPLILYASGSGG---------------LLERLPLT-GVDVV 261 :::::::::::::::::::::::::::::: :::::::: ::::: d1qnra_ 180 -IVQWATSVSQYVKSLDSNHLVTLGDEGLGLstgdgaypytygegtDFAKNVQIkSLDFG 238 d1j93a_ 262 SLDWT------------vDMADGRRRLGPN-VAIQGNVDPGvlFGSKEFITNRINDTVKk 308 ::::: :::::::::::: :::::::::: :::::::::::::::: d1qnra_ 239 TFHLYpdswgtnytwgngWIQTHAAACLAAgKPCVFEEYGA--QQNPCTNEAPWQTTSL- 295 d1j93a_ 309 aGKGKHILNLgHGIK----------VGTP-----EENFAHFFEIAKGLRy 343 ::::::::: :::: :::: ::::::::::::::: d1qnra_ 296 tTRGMGGDMF-WQWGdtfangaqsnSDPYtvwynSSNWQCLVKNHVDAIn 344 FAST alignment (Normalized score: 6.50 Raw score:2231.00) d1j93a_ 1 TQPLLLDA----VRGKEV---------ERPPVWLMRQAGRYMKSYQLLCEKYPLFRDR-- 45 :::: ::::::: d1qnra_ 1 --------ASSFVTIS--GTQFNIDGKVGYFAGT------------------------NC 26 d1j93a_ 46 -----SENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLR 100 :::::::::::::::: :::::: d1qnra_ 27 YWCSFLTNHADVDSTFSHISS-SGLKVV-------------------------------- 53 d1j93a_ 101 TAADVEKVREFIP--------------------------------EKSVPYVGEALTILR 128 ::::::::::::::: d1qnra_ 54 -------------RVWGFNDVNTQPSPGQIWFQKLSATGSTINTGADGLQTLDYVVQSAE 100 d1j93a_ 129 KEVNN-QAAVLGFVGAPFT------------LASYVVEGGSSKNFT---KIKRLAFAEPK 172 : ::::::: ::::: :::: d1qnra_ 101 Q----HNLKLIIP------FVNNWSDYGGINAYVNA----------FGGNATT------- 133 d1j93a_ 173 V---LHALLQKFATSMAKYIRYQADS-GAQAVQIFDS-----WATELSPVDFEEFSLPYL 223 :::::::::::::::::::::: :::::: :::::::: :::::: d1qnra_ 134 -WYTNTAAQTQYRKYVQAVVSRYANSTAIFAWE----LGNEPRCNGCSTD----VIVQWA 184 d1j93a_ 224 KQIVDSVKLTHPNLPLILYASGSGG--------------------LLERLPLT-GVDVVS 262 :::::::::::::::::::: :::::::: :::::: d1qnra_ 185 TSVSQYVKSLDSNHLVTLGD-----EGLGLSTGDGAYPYTYGEGTDFAKNVQIKSLDFGT 239 d1j93a_ 263 LDWTV---------------DMADGRRRLG---PNVAIQGNVDPGVLFG----------S 294 :: :::::::: ::::: : d1qnra_ 240 FH---LYPDSWGTNYTWGNGWIQTHAAA--CLAAGKPC-----------VFEEYGAQQNP 283 d1j93a_ 295 KEFITNRINDTVKKAGKGK----HILNLGHGIKVGTPEE--------------------- 329 ::::::::::::: :::: :::: d1qnra_ 284 CTNEAPWQTTSLT------TRGMGGDM-FWQW-------GDTFANGAQSNSDPYTVWYNS 329 d1j93a_ 330 -----NFAHFFEIAKGLRY-- 343 :::::::: d1qnra_ 330 SNWQCLVKNHVDA------IN 344 TMalign alignment (TM-score: 0.65 Raw score:222.24) d1j93a_ 1 TQPLLLDAVRGKE---VERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISL 57 ::::::::::::: ::::::::::::: ::::::::::::: d1qnra_ 1 ASSFVTISGTQFNIDGKVGYFAGTNCYWC------------------SFLTNHADVDSTF 42 d1j93a_ 58 QPWKVFRPDGVILFSDILTPLSGMNIPFDII-KGKGPVIFDPLRTAADVEKVREFIPEK- 115 :::::::::::: ::::: :: :::::: :::::::: : :::: ::::: d1qnra_ 43 SHISSSGLKVVR-VWGFN--DV---NTQPSPG---QIWFQKLS----A-TGST-INTGAD 87 d1j93a_ 116 SVPYVGEALTILRKEVNNQAAVLGFVGAPFT---LASYVVEGG-SSKNFTKIKRLAFAEP 171 :::::::::::::::: ::::::::::: ::::::::: ::::: :: : d1qnra_ 88 GLQTLDYVVQSAEQHN----LKLIIPFVNNWSDYGGINAYVNAF-----GGNAT-TW--Y 135 d1j93a_ 172 KVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVK 231 : :::::::::::::::::::::::::::::::::::::::: ::: ::::::::::::: d1qnra_ 136 T-NTAAQTQYRKYVQAVVSRYANSTAIFAWELGNEPRCNGCS-TDV-IVQWATSVSQYVK 192 d1j93a_ 232 LTHPNLPLILYASGSG-----------G---L-LERLP-LTGVDVVSLDWT--------- 266 :::::::::::::::: : : ::::: :::::::::::: d1qnra_ 193 SLDSNHLVTLGDEGLGLSTGDGAYPYTYGEGTDFAKNVQIKSLDFGTFHLYPDSWGTNYT 252 d1j93a_ 267 -V--DMADGRRRL-GPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGI 322 : ::::::::: ::::::::::::::::::: :::::::::::::: :::::: ::: d1qnra_ 253 WGNGWIQTHAAACLAAGKPCVFEEYGAQQNPCT-NEAPWQTTSLTTRG--MGGDMF-WQW 308 d1j93a_ 323 -------------KVGTP--EENFAHFFEIAKGLRY 343 ::::: :::::::::::::::: d1qnra_ 309 GDTFANGAQSNSDPYTVWYNSSNWQCLVKNHVDAIN 344 HHsearch alignment (Probability: 0.61 E-value:0.03) d1j93a_ 166 LAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQ 225 ::::::::::::::::::::::::: ::::::::::::::::::::::::::::: d1qnra_ 133 TWYTNTAAQTQYRKYVQAVVSRYAN------STAIFAWELGNEPRCNGCSTDVIVQWATS 186 d1j93a_ 226 IVDSVKLTHPNLPLILYASG 245 :::::::::::::::::::: d1qnra_ 187 VSQYVKSLDSNHLVTLGDEG 206