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 <-- 0.939 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1e5da1) 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 d1e5da1 Rubredoxin oxygen:oxidoreductase (ROO),​ C-​terminal domainFlavoproteinsFlavodoxin-​likeα/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 <-- 0.939 --> Hit
DALI alignment (Z-score: 6.5 Raw score:446.00) d1nyta1 1 dgvgllsdlerlsfirpgLRILLIG------aGGASRGVLLPLLSLDCAVTITNRTVsra 54 ::::::: ::::::::::::::::::::::::: d1e5da1 1 ----------------ptNKVVIFYdsmwhstEKMARVLAESFRDEGCTVKLMWCKA--- 41 d1nyta1 55 eelaklfahtgsiqaLSMDELEG--HEFDLIINATSSGISGD---IPAI---PSSLIHPG 106 :::::::: ::::::::::::::::: :::: :::::::: d1e5da1 42 ---------------CHHSQIMSeiSDAGAVIVGSPTHNNGIlpyVAGTlqyIKGLRPQN 86 d1nyta1 107 IYCYDMF----yqkgkTPFLAWCEQRGSkRNADglgmlvaqaahafllwhgvlpdvepvi 162 ::::::: :::::::::::: :::: d1e5da1 87 KIGGAFGsfgwsgestKVLAEWLTGMGF-DMPA-tpvkvknvpthadyeqlktmaqtiar 144 d1nyta1 163 kqlqeels 170 d1e5da1 145 alkaklaa 152 FAST alignment (Normalized score: 4.92 Raw score:790.50) d1nyta1 1 DGVGLLSDLERLSFIRPG--LRILLIGA-------GGASRGVLLPLLSLDCAVTITNRTV 51 ::::::: ::::::::::::::::::::::: d1e5da1 1 ------------------PTNKVVIFY-DSMWHSTEKMARVLAESFRDEGCTVKLMWC-- 39 d1nyta1 52 SRAEELAKLFAHTGSIQ-ALSMDELEG--HEFDLIINATSS-GISGDIPAIPSSLI---- 103 ::::::::: :::::::::: ::::::: d1e5da1 40 -----------------KACHHSQIMSEISDAGAVIVGS--PTHNNGIL-------PYVA 73 d1nyta1 104 ----------HPGIYCYD-MFYQKGK-----TPFLAWCEQRGSKRNADGLGMLVAQAAHA 147 :::::::: ::::: :::::::::::: d1e5da1 74 GTLQYIKGLRPQNKIGGAFGSFGW--SGESTKVLAEWLTGMGF----------------- 114 d1nyta1 148 FLLWHGVLPDVEPVIKQLQEELS------------------------------------- 170 d1e5da1 115 -----------------------DMPATPVKVKNVPTHADYEQLKTMAQTIARALKAKLA 151 d1nyta1 171 - 171 d1e5da1 152 A 152 TMalign alignment (TM-score: 0.49 Raw score:82.91) d1nyta1 1 -DGVGLLSDLERLSFIRPGLRILLIGA------GGASRGVLLPLLSLDCAVTITNRTVSR 53 ::::::::: ::::::::::::::::::::::::: d1e5da1 1 P-----------------TNKVVIFYDSMWHSTEKMARVLAESFRDEGCTVKLMWCKA-- 41 d1nyta1 54 AEELAKLFAHTGSIQALSMDELEG--HEFDLIINATSSGISGDI--P--AI--PS-SLIH 104 :::::::: :::::::::::::::::: : :: :: :::: d1e5da1 42 ----------------CHHSQIMSEISDAGAVIVGSPTHNNGILPYVAGTLQYIKGLRPQ 85 d1nyta1 105 PGIYCYDMFY----QK-GKTPFLAWCEQRGSKRN-ADGLGM---L-VAQAAHA------- 147 ::::::::: :: ::::::::::::: :: :::::: : :::::: d1e5da1 86 -NKIGGAFGSFGWSGES-TKVLAEWLTGMGF-DMPATPVKVKNVPT-HADYEQLKTMAQT 141 d1nyta1 148 -----------FLLWHGVLPDVEPVIKQLQEELS 170 d1e5da1 142 IARALKAKLAA----------------------- 152 HHsearch alignment (Probability: 0.55 E-value:0.00) d1nyta1 17 PGLRILLIGAG-----GASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALS 71 ::::::::::: ::::::::::::::::::::::::::::::: d1e5da1 2 TNKVVIFYDSMWHSTEKMARVLAESFRDEGCTVKLMWCKACHHSQIM------------- 48 d1nyta1 72 MDELEGHEFDLIINATSSGISGDIPA 97 ::::::::::::::::::::::: d1e5da1 49 ---SEISDAGAVIVGSPTHNNGILPY 71