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 <-- 2.198 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1jaxa_) 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 d1jaxa_ Coenzyme F420H2:NADP+ oxidoreductase (FNO)NAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/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 <-- 2.198 --> Hit
DALI alignment (Z-score: 8.2 Raw score:654.50) d1nyta1 1 dgvgllsdlerlsfirpgLRILLIG-AGGASRGVLLPLLSLDCAVTITNRTVSRAEELAK 59 ::::::: :::::::::::::::::::::::::::::::::: d1jaxa_ 1 ------------------MRVALLGgTGNLGKGLALRLATLGHEIVVGSRREEKAEAKAA 42 d1nyta1 60 LFA---HTGSIQALSMDElegHEFDLIINATSSGisgDIPAI---PSSLIHpGIYCYDMF 113 ::: :::::::::::: ::::::::::::: ::::: :::::: :::::::: d1jaxa_ 43 EYRriaGDASITGMKNED-aaEACDIAVLTIPWE---HAIDTardLKNILR-EKIVVSPL 97 d1nyta1 114 YQ------------KGKTPfLAWCEQRGSKRNADGlGMLVA------------------- 142 :: ::::: ::::::::::::::: ::::: d1jaxa_ 98 VPvsrgakgftyssERSAA-EIVAEVLESEKVVSA-LHTIPaarfanldekfdwdvpvcg 155 d1nyta1 143 --------------------------------------------------qAAHAFllwh 152 ::::: d1jaxa_ 156 dddeskkvvmsliseidglrpldagplsnsrlvesltplilnimrfngmgeLGIKF---- 211 d1nyta1 153 gvlpdvepvikqlqeels 170 d1jaxa_ 212 -----------------l 212 FAST alignment (Normalized score: 6.42 Raw score:1219.00) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLI-GAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAK 59 :::::: ::::::::::::::::::::::::::::::::::: d1jaxa_ 1 ------------------MRVALLGGTGNLGKGLALRLATLGHEIVVGSRREEKAEAKAA 42 d1nyta1 60 LFAHT----GSIQALSMDELEGH---EFDLIINATSSGISGDIPAI-----------PSS 101 :::: :::::::::: ::::::::: ::: d1jaxa_ 43 EYRR-IAGDASITGMKNED----AAEACDIAVLTI-----------PWEHAIDTARDLKN 86 d1nyta1 102 LIHPGIYCYDMFY-------------QKGK--TPFLAWCEQRGSKRNADGLG-------- 138 : :::::::::: :::: :::::: ::::::: d1jaxa_ 87 I-LREKIVVSPL-VPVSRGAKGFTYSSERSAAEIVAEV---LESEKVV----SALHTIPA 137 d1nyta1 139 --------------------------------------------------MLVAQAAHAF 148 :::::::::: d1jaxa_ 138 ARFANLDEKFDWDVPVCGDDDESKKVVMSLISEIDGLRPLDAGPLSNSRLVESLTPLILN 197 d1nyta1 149 LLWHGVLPDVEPVIKQLQEELS----------- 170 :::: d1jaxa_ 198 IMRF------------------NGMGELGIKFL 212 TMalign alignment (TM-score: 0.58 Raw score:98.95) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIG-AGGASRGVLLPLLSLDCAVTITNRTVSRAEELAK 59 ::::::: :::::::::::::::::::::::::::::::::: d1jaxa_ 1 ------------------MRVALLGGTGNLGKGLALRLATLGHEIVVGSRREEKAEAKAA 42 d1nyta1 60 L-FA--HTGSIQALSMDELEGHEFDLIINATSSGISGDIP--AIPSSLIHPGIYCYDMFY 114 : :: :::::::::::::: ::::::::::: ::::::: :::::::: :::::::: d1jaxa_ 43 EYRRIAGDASITGMKNEDAA-EACDIAVLTIP-WEHAIDTARDLKNILRE--KIVVSPLV 98 d1nyta1 115 Q-----------K-GKTPFLAWCE-QRGSKRNADGLGMLVAQA-AHA-----FLLWHGVL 155 : : ::: :::::: ::::::::::: : ::: :: ::: d1jaxa_ 99 PVSRGAKGFTYSSERSA-AEIVAEVLESEKVVSALH--T-IPAA-RFANLDE-----KFD 148 d1nyta1 156 PDVE------------------------PVI-K----Q-LQEEL---------------- 169 :::: : : : ::::: d1jaxa_ 149 WDVPVCGDDDESKKVVMSLISEIDGLRP--LDAGPLSNSRLVESLTPLILNIMRFNGMGE 206 d1nyta1 170 ------S 170 d1jaxa_ 207 LGIKFL- 212 HHsearch alignment (Probability: 0.98 E-value:0.00) d1nyta1 20 RILLI-GAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSI--QALSMDELE 76 ::::: ::::::::::::::::::::::::::::::::::::::::::: ::::::::: d1jaxa_ 2 RVALLGGTGNLGKGLALRLATLGHEIVVGSRREEKAEAKAAEYRRIAGDASITGMKNEDA 61 d1nyta1 77 GHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFY 114 :::::::::::::::::::: ::::::::::::::::: d1jaxa_ 62 AEACDIAVLTIPWEHAIDTA-RDLKNILREKIVVSPLV 98