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 <-- 0.724 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1gr0a1) 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 d1gr0a1 Myo-​inositol 1-​phosphate synthaseNAD(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 <-- 0.724 --> Hit
DALI alignment (Z-score: 5.4 Raw score:534.00) d1nyta1 1 dgvgllsdlerlsfirPGLRILLIGAGGASRGVLLPL----------------------- 37 ::::::::::::::::::::: d1gr0a1 1 ----------------TEVRVAIVGVGNCASSLVQGVeyyynaddtstvpglmhvrfgpy 44 d1nyta1 38 lSLDCAV-TITNRTVSRAEELAKL-------------faHTGSIQALSM----------- 72 :::::: :::::::::::::::: :::::::::: d1gr0a1 45 hVRDVKFvAAFDVDAKKVGFDLSDaifasenntikiadvAPTNVIVQRGptldgigkyya 104 d1nyta1 73 ----------DELEGH----EFDLIINATSsGISGDIP-aipSSLIHpGIYCYDMFYqkg 117 :::::: :::::::::: ::::::: ::::: ::::::::: d1gr0a1 105 dtielsdaepVDVVQAlkeaKVDVLVSYLP-VGSEEADkfyaQCAIDaGVAFVNALP--- 160 d1nyta1 118 kTPFLA--wcEQRG---sKRNAD-GLGM-----------------------lvaqaahaf 148 ::::: :::: ::::: :::: d1gr0a1 161 -VFIASdpvwAKKFtdarVPIVGdDIKSpnsagviidavraakiakdrgiggpvipasay 219 d1nyta1 149 llwhgvlpdVEPVIKQL--qeels 170 :::::::: d1gr0a1 220 lmksppeqlPDDIARAQleefiig 243 FAST alignment (Normalized score: 3.44 Raw score:699.60) d1nyta1 1 DGVGLLSDLERLSFIRP-GLRILLIGAGGASRGVLLPLLS-------------------- 39 :::::::::::::::::::::: d1gr0a1 1 -----------------TEVRVAIVGVGNCASSLVQGVEYYYNADDTSTVPGLMHVRFGP 43 d1nyta1 40 ---LDCA-VTITNRTVSRAEELAKLFAHTG------------------------------ 65 :::: ::::: d1gr0a1 44 YHVRDVKFVAAFD-----------------VDAKKVGFDLSDAIFASENNTIKIADVAPT 86 d1nyta1 66 SIQALSM----------------------DELE----GHEFDLIINATSSGISGDIPAIP 99 :::::: :::: ::::::::::: d1gr0a1 87 NVIVQR-GPTLDGIGKYYADTIELSDAEPVDVVQALKEAKVDVLVSYL------------ 133 d1nyta1 100 SSLIH-----------------PGIYCYDMFYQKGK--------TPFLAWCEQRGSKRNA 134 :::::::: ::::::::::: :::: d1gr0a1 134 -----PVGSEEADKFYAQCAIDAGVAFVNA------LPVFIASDPVWAKKFTDAR-VPIV 181 d1nyta1 135 DGLGMLVAQAAHAFLLWHGVLPD------------------------------------- 157 d1gr0a1 182 -----------------------GDDIKSPNSAGVIIDAVRAAKIAKDRGIGGPVIPASA 218 d1nyta1 158 ----------VEPVIKQLQEELS---- 170 ::::::::::: d1gr0a1 219 YLMKSPPEQLPDDIARAQLEE--FIIG 243 TMalign alignment (TM-score: 0.54 Raw score:92.39) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLL--S------------------- 39 :::::::::::::::::::::: : d1gr0a1 1 ----------------TEVRVAIVGVGNCASSLVQGVEYYYNADDTSTVPGLMHVRFGPY 44 d1nyta1 40 --LD-CAVTITNRTVSRAEELAKL-F------------AHTGSIQALSM----------- 72 :: ::::::::::::::::::: : ::::::::::: d1gr0a1 45 HVRDVKFVAAFDVDAKKVGFDLSDAIFASENNTIKIADVAPTNVIVQRGPTLDGIGKYYA 104 d1nyta1 73 ----------DEL-E--GH-EFDLIINATSSGISGDIP-AIPSSLIHPGIYCYDMFYQKG 117 ::: : :: :::::::::: ::::::: ::::::::::::::::::::: d1gr0a1 105 DTIELSDAEPVDVVQALKEAKVDVLVSYLP-VGSEEADKFYAQCAIDAGVAFVNALPVFI 163 d1nyta1 118 KTP-FLAWCEQ-RGSKRNADGLGMLVAQA-AH-----------------------AFLLW 151 ::: :::::: :::::::::: :::::: : d1gr0a1 164 ASDP-VWAKKFTDARVPIVGDD-IKSPNSA-GVIIDAVRAAKIAKDRGIGGPVIP----- 215 d1nyta1 152 HGVLPDVE-PVIKQL-Q--EE---------------LS 170 : ::::: : :: d1gr0a1 216 -------AS-AYLMKSPPEQLPDDIARAQLEEFIIG-- 243 HHsearch alignment (Probability: 0.06 E-value:0.03) d1nyta1 20 RILLIGAGGASRGVLLPLL 38 ::::::::::::::::::: d1gr0a1 4 RVAIVGVGNCASSLVQGVE 22