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_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 0.853 --> Intermediate <-- 1.153 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1ngvb_) through the intermediate protein (d1nyta1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1nyta1 Shikimate 5-​dehydrogenase AroENAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β
Hit d1ngvb_ UBA3Activating enzymes of the ubiquitin-​like proteinsActivating enzymes of the ubiquitin-​like proteinsα/β

Supporting Alignments

Query <-- 0.853 --> Intermediate
DALI alignment (Z-score: 3.8 Raw score:453.70) query 1 dadeevYSALVVGL--rAYVAkngfRSVLIGLSgGIDSALVAAIACDALGaqNVYGVSMp 58 :::::::: :::: :::::::: :::::::::::::::: ::::::: d1nyta1 1 -----dGVGLLSDLerlSFIR--pgLRILLIGA-GGASRGVLLPLLSLDC--AVTITNR- 49 query 59 skyssdhSKGDAAELARRTG----LNFRTVSiepmfdaymaslgltglaeenlqsrlrgt 114 ::::::::::::: ::::::: d1nyta1 50 -------TVSRAEELAKLFAhtgsIQALSMD----------------------------- 73 query 115 tlmaisNQEGH-IVLAPgnkselavGYSTLY-------gdsvgAYGPikdvyktsifrla 166 ::::: ::::: :::::: :::: d1nyta1 74 ----elEGHEFdLIINA----tssgISGDIPaipsslihpgiyCYDM------------- 112 query 167 ewrnraaaergqtppipeasitkpdypvldailelyvdrdtgadaivaagydrelvvktl 226 d1nyta1 113 ------------------------------------------------------------ 113 query 227 rmvdtaeyKRRQY-------------PPGTK-------------------iSAKGFG-KD 253 ::::: ::::: :::::: :: d1nyta1 113 ------fyQKGKTpflawceqrgskrNADGLgmlvaqaahafllwhgvlpdVEPVIKqLQ 166 query 254 RRlpitnrwregh 266 :: d1nyta1 167 EE---------ls 170 FAST alignment (Normalized score: 2.78 Raw score:591.60) query 1 DADEEV-YSALVVGLRAYVAKNGF-------RSVLIGLSGGIDSALVAAIACDALGAQ-N 51 :::::::::: ::::: :::::::::::::::: : d1nyta1 1 ------DGVGLLSDLER-------LSFIRPGLRILL-IGAGGASRGVLLPLLS-----LD 41 query 52 VYGVSMPSKYSSDH--SKGDAAELARRTG----LNFRTVSIEPMFDAYMASLGLTGLAEE 105 :::::: ::::::::::: :::::: d1nyta1 42 CAVTIT--------NRTVSRAEELAKL--FAHTGSIQAL--------------------- 70 query 106 NLQSRLRGTTLMAISNQEG---HIVLAPGNK-SELAVGYSTLYGDSVGAYGPIKDVYKTS 161 ::::::: :::::: :::::::::: d1nyta1 71 ------SMDELEG------HEFDLIINA---TSSGISGDIPA------------------ 97 query 162 IFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDREL 221 d1nyta1 98 ------------------------------------------------------------ 98 query 222 VVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH--------------- 266 d1nyta1 98 ---------------------------------------------IPSSLIHPGIYCYDM 112 query 267 ---------------------------------------------------------- 267 d1nyta1 113 FYQKGKTPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS 170 TMalign alignment (TM-score: 0.35 Raw score:94.08) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSK 60 :: :::::::::::::: :::::::::::::::::::::::: : :::::::: d1nyta1 1 --DG-VGLLSDLERLSFIR---PGLRILLIGAGGASRGVLLPLLSL-D--CAVTITNR-- 49 query 61 YSSDHSKGDAAELARRTGLNFRTVSIE-PM-------------FDAYMASLGLTGL-AEE 105 ::: :::::::::::::::::::::: : : :: d1nyta1 50 -TVS-RAEELAKLFAHTGSIQALSMDEL-EGHEFDLIINATSS------------GI-SG 93 query 106 NLQSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDS--V----G-AYGPIKDVY 158 : :: :::::::: : : :::::: :::::::: : : : : ::::::::: d1nyta1 94 D-IP-AIPSSLIH--P--G-IYCYDM---FYQKGKTP--F-LAWCEQRGSKRNADGLGML 140 query 159 KTSI-FRL--AEW------RNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGA 209 :::: :: : d1nyta1 141 VAQAA-HAFL--LWHGVLP----------------------------------------- 156 query 210 DAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 :::::::::::::: d1nyta1 157 -----------------------------------DVEPVIKQLQEELS-------- 170 HHsearch alignment (Probability: 0.04 E-value:0.17) query 7 YSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHS 66 ::::::::::::::::::::::::::::::::::::: ::::::::: ::: d1nyta1 2 GVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLL--SLDCAVTIT---------NRT 50 query 67 KGDAAELARRTGLNFRTVSIE 87 ::::::::::::::::::::: d1nyta1 51 VSRAEELAKLFAHTGSIQALS 71
Intermediate <-- 1.153 --> Hit
DALI alignment (Z-score: 5.4 Raw score:572.40) d1nyta1 1 -------------------dgvgllsdlerlsfiRPGLRILLIGAGGASRGVLLPLLSLD 41 :::::::::::::::::::::::::: d1ngvb_ 1 dwegrwnhvkkflersgpfthpdfepsteslqflLDTCKVLVIGAGGLGCELLKNLALSG 60 d1nyta1 42 C-AVTITNRT-------------------vSRAEELAKLFAH---TGSIQALSM---DEL 75 : :::::::: :::::::::::: ::::::::: ::: d1ngvb_ 61 FrQIHVIDMDtidvsnlnrqflfrpkdigrPKAEVAAEFLNDrvpNCNVVPHFNkiqDFN 120 d1nyta1 76 EGH--EFDLIINATSSGisgDIPA-ipSSLI------------hPGIYCYDMF------- 113 ::: :::::::::::: :::: :::: ::::::::: d1ngvb_ 121 DTFyrQFHIIVCGLDSI---IARRwinGMLIsllnyedgvldpsSIVPLIDGGtegfkgn 177 d1nyta1 114 -------------yQKGKT----------------------------------------- 119 ::::: d1ngvb_ 178 arvilpgmtaciecTLELYppqvnfpmctiasmprlpehcieyvrmlqwpkeqpfgegvp 237 d1nyta1 120 ------------------------------------------------------pflawc 125 d1ngvb_ 238 ldgddpehiqwifqkslerasqynirgvtyrltqgvvkriipavastnaviaavcatevf 297 d1nyta1 126 eqrgskrnadglGMLVaqaAHAFllwhgvLPDVEpvikqLQEE----------------- 168 :::: :::: ::::: :::: d1ngvb_ 298 kiatsayiplnnYLVF---NDVD------GLYTY----tFEAErkencpacsqlpqniql 344 d1nyta1 169 ----------------------------------------------------ls 170 d1ngvb_ 345 qevldyltnsaslqmkspaitatrtlylqseertrpnladvttpqtvlfklhft 398 FAST alignment (Normalized score: 3.53 Raw score:919.10) d1nyta1 1 DGVGLLSDLERLSFI----------------------------------RPGLRILLIGA 26 ::::::::::: d1ngvb_ 1 ---------------DWEGRWNHVKKFLERSGPFTHPDFEPSTESLQFLLDTCKVLVIGA 45 d1nyta1 27 GGASRGVLLPLLSLD-CAVTITNRTV----------------------SRAEELAKLFAH 63 ::::::::::::::: ::::::: ::::::::::: d1ngvb_ 46 GGLGCELLKNLALSGFRQIHVID---MDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLN- 101 d1nyta1 64 T-----GSIQAL--SMDELEG-----HEFDLIINATSSGISGDIPAI-------PSSLIH 104 :::::: ::::: ::::::::::: :::: d1ngvb_ 102 -DRVPNCNVVPHFNKIQDF--NDTFYRQFHIIVCGLD----------SIIARRWINGM-- 146 d1nyta1 105 ---------------PGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGMLVAQAAHAFL 149 ::::::: d1ngvb_ 147 LISLLNYEDGVLDPSSIVPLID-------------------------------------- 168 d1nyta1 150 LWHGVLPDVEPVIKQLQEELS--------------------------------------- 170 d1ngvb_ 169 ---------------------GGTEGFKGNARVILPGMTACIECTLELYPPQVNFPMCTI 207 d1nyta1 171 ------------------------------------------------------------ 171 d1ngvb_ 208 ASMPRLPEHCIEYVRMLQWPKEQPFGEGVPLDGDDPEHIQWIFQKSLERASQYNIRGVTY 267 d1nyta1 171 ------------------------------------------------------------ 171 d1ngvb_ 268 RLTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYTYTFEAE 327 d1nyta1 171 ------------------------------------------------------------ 171 d1ngvb_ 328 RKENCPACSQLPQNIQLQEVLDYLTNSASLQMKSPAITATRTLYLQSEERTRPNLADVTT 387 d1nyta1 171 ----------- 171 d1ngvb_ 388 PQTVLFKLHFT 398 TMalign alignment (TM-score: 0.54 Raw score:92.34) d1nyta1 1 ------------------DGVGLLSDLERLS--------FIRP--G---LRILLIGAGGA 29 ::: :: : ::::::::::: d1ngvb_ 1 DWEGRWNHVKKFLERSGP----------FTHPDFEPSTE--SLQFLLDTCKVLVIGAGGL 48 d1nyta1 30 SRGVLLPLLSLDC-AVTITNRTV-------------------SRAEELAKLFAH-T--GS 66 ::::::::::::: ::::::::: :::::::::::: : :: d1ngvb_ 49 GCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAEVAAEFLNDRVPNCN 108 d1nyta1 67 IQAL-S-M-DEL-EGH-EFDLIINATSSGISGDIP-AI-PSS-LIH----------PGIY 108 :::: : : ::: ::: :::::::::::: ::: :: ::: ::: :::: d1ngvb_ 109 VVPHFNKIQDFNDTFYRQFHIIVCGLDSI---IARRWINGMLISLLNYEDGVLDPSSIVP 165 d1nyta1 109 CYDMF------YQ--------KGKTPFLA------------------------------- 123 ::::: :: ::::::: d1ngvb_ 166 LIDGGTEGFKGNARVILPGMT-ACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRML 224 d1nyta1 124 ------------------------------------------------------------ 124 d1ngvb_ 225 QWPKEQPFGEGVPLDGDDPEHIQWIFQKSLERASQYNIRGVTYRLTQGVVKRIIPAVAST 284 d1nyta1 124 --------------WCEQRGSKR------NADGLGMLVAQA--AHAFLLWHGVLPDVEPV 161 : :::::: :: :: :: : : : d1ngvb_ 285 NAVIAAVCATEVFK--------IATSAYIPLNNYL-VF-NDVD--GL-------Y-T--Y 322 d1nyta1 162 IKQLQEELS--------------------------------------------------- 170 : :: :: d1ngvb_ 323 T---FE-AERKENCPACSQLPQNIQLQEVLDYLTNSASLQMKSPAITATRTLYLQSEERT 378 d1nyta1 171 -------------------- 171 d1ngvb_ 379 RPNLADVTTPQTVLFKLHFT 398 HHsearch alignment (Probability: 0.96 E-value:0.00) d1nyta1 16 RPGLRILLIGAGGASRGVLLPLLSLDCA-VTITNR----------T---------VSRAE 55 :::::::::::::::::::::::::::: :::::: : ::::: d1ngvb_ 35 LDTCKVLVIGAGGLGCELLKNLALSGFRQIHVIDMDTIDVSNLNRQFLFRPKDIGRPKAE 94 d1nyta1 56 ELAKLFAHTGSIQALSM--------DELEGHEFDLIINATS 88 ::::::::::::::::: :::::::::::::::: d1ngvb_ 95 VAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVCGLD 135