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 <-- 0.954 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1f3la_) 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 d1f3la_ Arginine methyltransferase,​ HMT1S-​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 <-- 0.954 --> Hit
DALI alignment (Z-score: 5.4 Raw score:583.30) d1nyta1 1 ----------------------------DGVGLLSDLERLSfIRPGLRILLIGAGgasRG 32 ::::::::::::: ::::::::::::: :: d1f3la_ 1 dlqededgvyfssyghygiheemlkdkvRTESYRDFIYQNPhIFKDKVVLDVGCG--tGI 58 d1nyta1 33 VLLPLLSLDC-AVTITNRTvSRAEELAKLF--AHTG-SIQAL--SMDELE--GHEFDLII 84 :::::::::: :::::::: :::::::::: :::: ::::: :::::: :::::::: d1f3la_ 59 LSMFAAKAGAkKVIAVDQS-EILYQAMDIIrlNKLEdTIVLIkgKIEEVSlpVEKVDVII 117 d1nyta1 85 NATS--sgISGD-IPAI---pSSLIHPGIYCYDMFY------------------------ 114 :::: :::: :::: ::::::::::::::: d1f3la_ 118 SEWMgyflLFESmLDSVlyakSKYLAKGGSVYPDICtislvavsdvskhadriafwddvy 177 d1nyta1 115 -------------------------------qKGKTpFLAW------------------- 124 :::: :::: d1f3la_ 178 gfnmscmkkavipeavvevvdhktlisdpcdiKHID-CHTTsisdlefssdftlrttkta 236 d1nyta1 125 -ceqrgskrnADGL-----GMLVaqaahAFLL---------------------------- 150 :::: :::: :::: d1f3la_ 237 mctavagyfdIYFEknchnRVVFstgpqSTKThwkqtifllekpfpvkagealkgkitvh 296 d1nyta1 151 -----whgvlpdvepvikqlqeels 170 d1f3la_ 297 knkkdprslivtltlnsstqtyslq 321 FAST alignment (Normalized score: 3.61 Raw score:843.70) d1nyta1 1 D-----------------------------GVGLLSDLER-LSFIRPGLRILLIGAGGAS 30 :::::::::: :::: ::::::::::: d1f3la_ 1 -DLQEDEDGVYFSSYGHYGIHEEMLKDKVRTESYRDFIYQNPHIF-KDKVVLDVGCG--- 55 d1nyta1 31 -RGVLLPLLSLD-CAVTITNR--TVSRAEELAKLFAH---TGSIQALSMDELEG------ 77 ::::::::::: :::::::: ::::::::::: ::::::: d1f3la_ 56 TGILSMFAAKAGAKKVIAVDQSEILYQAMDIIRL---NKLEDTIVLI-------KGKIEE 105 d1nyta1 78 -----HEFDLIINATSSGISGDIPAI------------------PSSLIHPGIYCYDMFY 114 ::::::::: ::::::::::: :::: d1f3la_ 106 VSLPVEKVDVIISE------------WMGYFLLFESMLDSVLYAKSKYLAKGGSV-YPDI 152 d1nyta1 115 QKGKTPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS---- 170 d1f3la_ 153 --------------------------------------------------------CTIS 156 d1nyta1 171 ------------------------------------------------------------ 171 d1f3la_ 157 LVAVSDVSKHADRIAFWDDVYGFNMSCMKKAVIPEAVVEVVDHKTLISDPCDIKHIDCHT 216 d1nyta1 171 ------------------------------------------------------------ 171 d1f3la_ 217 TSISDLEFSSDFTLRTTKTAMCTAVAGYFDIYFEKNCHNRVVFSTGPQSTKTHWKQTIFL 276 d1nyta1 171 --------------------------------------------- 171 d1f3la_ 277 LEKPFPVKAGEALKGKITVHKNKKDPRSLIVTLTLNSSTQTYSLQ 321 TMalign alignment (TM-score: 0.57 Raw score:97.17) d1nyta1 1 ----------------------------DGVGLLSDLERLSFIRPGLRILLIGAGGASRG 32 :::::::::::::::::::::::::::: :: d1f3la_ 1 DLQEDEDGVYFSSYGHYGIHEEMLKDKVRTESYRDFIYQNPHIFKDKVVLDVGCGT-GI- 58 d1nyta1 33 VLLPLLSLDC-AVTITNRTVSRAEELAKLFA--HT-GSIQAL-S-M--DELEGHEFDLII 84 :::::::::: :::::::: ::::::::::: :: :::::: : : :::::::::::: d1f3la_ 59 LSMFAAKAGAKKVIAVDQS-EILYQAMDIIRLNKLEDTIVLIKGKIEEVSLPVEKVDVII 117 d1nyta1 85 NATSS--GISGD--IP--AIPSSLIHPGIYCYDMFYQK---------------------- 116 ::::: ::::: :: :::::::::::::::::::: d1f3la_ 118 SEWMGYFLLFESMLDSVLYAKSKYLAKGGSVYPDICTISLVAVSDVSKHADRIAFWDDVY 177 d1nyta1 117 ---------------------------------GKTPFL-AWC-EQ-------------- 127 ::: :: ::: : d1f3la_ 178 GFNMSCMKKAVIPEAVVEVVDHKTLISDPCDIKHID-CHTTSIS-DLEFSSDFTLRTTKT 235 d1nyta1 128 ----------RGSKRNADGL--------GMLV-----AQAAHA----------------- 147 ::: :::: : d1f3la_ 236 AMCTAVAGYF-------DIYFEKNCHNRVVFSTGPQS-----TKTHWKQTIFLLEKPFPV 283 d1nyta1 148 --------------------------------------FLLWHGVLPDVEPVIKQLQEEL 169 d1f3la_ 284 KAGEALKGKITVHKNKKDPRSLIVTLTLNSSTQTYSLQ---------------------- 321 d1nyta1 170 S 170 d1f3la_ 322 - 322 HHsearch alignment (Probability: 0.96 E-value:0.00) d1nyta1 3 VGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTV--SRAEELAKL 60 ::::::::::::::::::::::::::: ::::::::::::::::::::: ::::::::: d1f3la_ 31 ESYRDFIYQNPHIFKDKVVLDVGCGTG-ILSMFAAKAGAKKVIAVDQSEILYQAMDIIRL 89 d1nyta1 61 FAHTGSIQ--ALSMDEL--EGHEFDLIINATSSGISGDIP-AIP------SSLIHPGIYC 109 :::::::: ::::::: :::::::::::: :::::::: ::: :::::::::: d1f3la_ 90 NKLEDTIVLIKGKIEEVSLPVEKVDVIISEW-MGYFLLFESMLDSVLYAKSKYLAKGGSV 148 d1nyta1 110 YD----MFYQKGKTPFLAWCEQRGSKRNADGLGMLVAQA 144 :: :::::::::::::::::::: :::::::::::: d1f3la_ 149 YPDICTISLVAVSDVSKHADRIAFWD-DVYGFNMSCMKK 186