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 <-- 1.327 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1nv8a_) 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 d1nv8a_ N5-​glutamine methyltransferase,​ HemKS-​adenosyl-​L-​methionine-​dependent methyltransferasesS-​adenosyl-​L-​methionine-​dependent methyltransferasesα/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 <-- 1.327 --> Hit
DALI alignment (Z-score: 6.4 Raw score:589.20) d1nyta1 1 ------------------------------------------------------------ 1 d1nv8a_ 1 rkiwslirdcsgklegvtetsvlevllivsrvlgirkedlflkdlgvspteekrilelve 60 d1nyta1 1 ---------------------------------DGVGLLSDLErlSFIR--pGLRILLIG 25 :::::::::: :::: :::::::: d1nv8a_ 61 krasgyplhyilgekefmglsflveegvfvprpETEELVELAL--ELIRkygIKTVADIG 118 d1nyta1 26 AGgasRGVLLPLL-SLDCAVTITNRTVSRAEELAKLFAH---TGSIQALSM---DELEGH 78 :: :::::::: ::::::::::::::::::::::::: ::::::::: :::::: d1nv8a_ 119 TG--sGAIGVSVAkFSDAIVFATDVSSKAVEIARKNAERhgvSDRFFVRKGeflEPFKEK 176 d1nyta1 79 E--FDLIINATsSGIS-----------------------GDIP--aipSSLIhPGIYCYD 111 : :::::::: :::: :::: :::: ::::::: d1nv8a_ 177 FasIEMILSNP-PYVKssahlpkdvlfeppealfggedgLDFYreffgRYDT-SGKIVLM 234 d1nyta1 112 MFYQKGKtpflaWCEQrgskrnaDGLGmlvaqaahafllwhgvlpdvepvIKQL------ 165 ::::::: :::: :::: :::: d1nv8a_ 235 EIGEDQVeelkkIVSD-----tvFLKD-----------------------SAGKyrflll 266 d1nyta1 166 qeels 170 d1nv8a_ 267 nrrss 271 FAST alignment (Normalized score: 4.07 Raw score:873.10) d1nyta1 1 D----------------------------------------------------------- 1 d1nv8a_ 1 -RKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELV 59 d1nyta1 2 ---------------------------------------GVGLLSDLERLSFIRPG-LRI 21 :::::::::::: ::: d1nv8a_ 60 EKRASGYPLHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYG-----IKTV 114 d1nyta1 22 LLIGAGGAS-RGVLLPLL-SLDCAVTITNR---TVSRAEELAKLFAH---TGSIQALS-- 71 :::::: :::::::: ::::::::::: ::::::::::: ::::::: d1nv8a_ 115 ADIGTG---SGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAER---HGVSDRFFVR-KG 167 d1nyta1 72 --MDELEG--HEFDLIINATSSGISGDIPAIPSSLI------------------------ 103 :::::: :::::::::: d1nv8a_ 168 EFLEPFKEKFASIEMILSNP----------------PYVKSSAHLPKDVLFEPPEALFGG 211 d1nyta1 104 ---------------HPGIYCYDMFYQKGK---TPFLAWCEQRGSK--RNADGLGMLVAQ 143 :::::::::::: :::::: ::::: d1nv8a_ 212 EDGLDFYREFFGRYDTSGKIVLMEIGE---DQVEELKKI-------VSDTVFL------- 254 d1nyta1 144 AAHAFLLWHGVLPDVEPVIKQLQEELS----------------- 170 d1nv8a_ 255 ---------------------------KDSAGKYRFLLLNRRSS 271 TMalign alignment (TM-score: 0.59 Raw score:100.51) d1nyta1 1 ------------------------------------------------------------ 1 d1nv8a_ 1 RKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVE 60 d1nyta1 1 --------------------------------D-GVGLLSDLERLSFIR--PGLRILLIG 25 : ::::::::: :::: ::::::::: d1nv8a_ 61 KRASGYPLHYILGEKEFMGLSFLVEEGVFVPRPETEELVELAL--ELIRKYGIKTVADIG 118 d1nyta1 26 AGGASRGVLLPLL-SLDCAVTITNRTVSRAEELAKLFA--HT-GSIQAL-SM--DELEGH 78 ::: :: :::::: :::::::::::::::::::::::: :: :::::: :: :::::: d1nv8a_ 119 TGS-GA-IGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEK 176 d1nyta1 79 E--FDLIINATSSGI----------------------SGDIP-AI-PSSLIHPGIYCYDM 112 : :::::::::::: ::::: :: ::: :::::::::: d1nv8a_ 177 FASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRY-DTSGKIVLME 235 d1nyta1 113 FY--QKGKTPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQ---- 166 :: :::::: :: :: : ::: :: :: : :: :: d1nv8a_ 236 IGEDQVEELK-KI--VS---D-TVF-LK-DS--A----------------GK--YRFLLL 266 d1nyta1 167 -----EELS 170 d1nv8a_ 267 NRRSS---- 271 HHsearch alignment (Probability: 0.22 E-value:0.00) d1nyta1 5 LLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAE---ELAKLF 61 ::::::::::::::::::::::::::::::: ::::::::::::::::::: :::::: d1nv8a_ 98 LVELALELIRKYGIKTVADIGTGSGAIGVSV-AKFSDAIVFATDVSSKAVEIARKNAERH 156 d1nyta1 62 AHTGSIQALSMD--E---LEGHEFDLIINATS 88 :::::::::::: : :::::::::::::: d1nv8a_ 157 GVSDRFFVRKGEFLEPFKEKFASIEMILSNPP 188