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 <-- 2.404 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1uxja1) 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 d1uxja1 Malate dehydrogenaseNAD(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 <-- 2.404 --> Hit
DALI alignment (Z-score: 11.7 Raw score:684.90) d1nyta1 1 dgvgllsdlerlsfirpGLRILLIGAGGASRGVLLPLLSLD-CAVTITNRTVSRAEELAK 59 :::::::::::::::::::::::: :::::::::::::::::: d1uxja1 1 -----------------RKKISIIGAGFVGSTTAHWLAAKElGDIVLLDIVEGVPQGKAL 43 d1nyta1 60 LFAHTG-------SIQALSMDELegHEFDLIINATSS---gISGDI---PAIP-SSLIHp 105 :::::: :::::::::: :::::::::::: ::::: :::: ::::: d1uxja1 44 DLYEASpiegfdvRVTGTNNYAD-tANSDVIVVTSGAplikVNADItraCISQaAPLSP- 101 d1nyta1 106 GIYCYDMFYQkgKTPFLAWCEQRGSK--RNADGlgmlvaqaahafllwhgvlpdvepvik 163 :::::::::: :::::::::::::: ::::: d1uxja1 102 NAVIIMVNNP-lDAMTYLAAEVSGFPkeRVIGQ--------------------------- 133 d1nyta1 164 qlqeels 170 d1uxja1 134 ------- 134 FAST alignment (Normalized score: 7.62 Raw score:1145.00) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLD-CAVTITNRTVSRAEELAK 59 :::::::::::::::::::::::: :::::::::::::::::: d1uxja1 1 -----------------RKKISIIGAGFVGSTTAHWLAAKELGDIVLLDIVEGVPQGKAL 43 d1nyta1 60 LFAHT--------GSIQAL-SMDELEGHEFDLIINATSSGISGDIPAIPSSLI------- 103 :::: :::::: ::::: ::::::::: d1uxja1 44 DLYE-ASPIEGFDVRVTGTNNYADT--ANSDVIVVT-----------------SGAPLIK 83 d1nyta1 104 ----------------HPGIYCYDMFYQKGK---TPFLAWCEQRGS------KRNADGLG 138 :::::::::: ::::::::: :::: d1uxja1 84 VNADITRACISQAAPLSPNAVIIMVN-----NPLDAMTYLAAE---VSGFPKERVI---- 131 d1nyta1 139 MLVAQAAHAFLLWHGVLPDVEPVIKQLQEELS-- 170 d1uxja1 132 --------------------------------GQ 133 TMalign alignment (TM-score: 0.57 Raw score:97.73) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSLD-CAVTITNRTVSRAEELAK 59 :::::::::::::::::::::::: :::::::::::::::::: d1uxja1 1 -----------------RKKISIIGAGFVGSTTAHWLAAKELGDIVLLDIVEGVPQGKAL 43 d1nyta1 60 LFAH-T------GSIQALSMDELEGHEFDLIINATSS-GI-S-GD-I--P-AIPSSLIHP 105 :::: : :::::::::::: :::::::::::: :: : :: : : :::::::: d1uxja1 44 DLYEASPIEGFDVRVTGTNNYADT-ANSDVIVVTSGAPLIKVNADITRACISQAAPLSP- 101 d1nyta1 106 GIYCYDMF--YQKGKTPFLAWCEQRGSK-RNADGLGMLVAQAAHAFLLWHGVLPDVEPVI 162 :::::::: :::::::::::: : ::: ::::: d1uxja1 102 NAVIIMVNNPLDAMTYLAAEVS-G-FPKERVIGQ-------------------------- 133 d1nyta1 163 KQLQEELS 170 d1uxja1 134 -------- 134 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 18 GLRILLIGAGGASRGVLLPLLSLDC-AVTITNRTVSRAEELAKLFAHTGSIQ------AL 70 ::::::::::::::::::::::::: :::::::::::::::::::::::::: :: d1uxja1 1 RKKISIIGAGFVGSTTAHWLAAKELGDIVLLDIVEGVPQGKALDLYEASPIEGFDVRVTG 60 d1nyta1 71 SMDELEGHEFDLIINATSSGISGDIPAIPS 100 :::::::::::::::::::::::::::::: d1uxja1 61 TNNYADTANSDVIVVTSGAPLIKVNADITR 90