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 <-- 1.087 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d2dapa1) 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 d2dapa1 Diaminopimelic acid dehydrogenase (DAPDH)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 <-- 1.087 --> Hit
DALI alignment (Z-score: 7.2 Raw score:497.70) d1nyta1 1 dgvgllsdlerlsfirPGLRILLIGAGGASRGVLLPLLSL-DCAV-TITNRTVSraEELA 58 :::::::::::::::::::::::: :::: :::::::: :::: d2dapa1 1 ---------------mTNIRVAIVGYGNLGRSVEKLIAKQpDMDLvGIFSRRAT--LDTK 43 d1nyta1 59 klfahtgsIQALSMDELEGH--EFDLIINATSSGI-sGDIPaipsslihpgIYCYDMFY- 114 :::::::::::: ::::::::::::: :::: :::::::: d2dapa1 44 --------TPVFDVADVDKHadDVDVLFLCMGSATdiPEQA----pkfaqfACTVDTYDn 91 d1nyta1 115 ---QKGKTpfLAWCE-QRGSkRNAD--------------------glgmlvaqaahafll 150 ::::: ::::: :::: :::: d2dapa1 92 hrdIPRHRqvMNEAAtAAGN-VALVstgrnpdftassqiafgraahrmkqqgqsgaftvl 150 d1nyta1 151 whgvlpdvepvikqlqeels 170 d2dapa1 151 evapyllspenlddliardv 170 FAST alignment (Normalized score: 5.04 Raw score:856.60) d1nyta1 1 DGVGLLSDLERLSFIR-PGLRILLIGAGGASRGVLLPLLSL-DCA-VTITNRTVSRAEEL 57 :::::::::::::::::::::::: ::: :::::::: d2dapa1 1 ----------------MTNIRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRA------ 38 d1nyta1 58 AKLFAHTGS-----IQALSMDELEG--HEFDLIINATSSGISGDIPAI-----PSSLIHP 105 ::::::::::: ::::::::: ::::: :::: d2dapa1 39 ---------TLDTKTPVFDVADVDKHADDVDVLFLC--MGSAT-----DIPEQAPKF--- 79 d1nyta1 106 G---IYCYDMFYQKGK---------TPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHG 153 :::::::: ::::::::::: :::: d2dapa1 80 -AQFACTVDTYD----NHRDIPRHRQVMNEAATAAG-NVAL------------------- 114 d1nyta1 154 VLPDVEPVIKQLQEELS------------------------------------------- 170 d2dapa1 115 -----------------VSTGRNPDFTASSQIAFGRAAHRMKQQGQSGAFTVLEVAPYLL 157 d1nyta1 171 ------------- 171 d2dapa1 158 SPENLDDLIARDV 170 TMalign alignment (TM-score: 0.52 Raw score:87.60) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLSL--DCAVTITNRTVSRAEELA 58 ::::::::::::::::::::::::: :::::::::::: ::: d2dapa1 1 ---------------MTNIRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRAT--LDT- 42 d1nyta1 59 KLFAHTGSIQALSMDELEGH-E-FDLIINATSSGIS--GDIPAIPSSLIHPGIYCYDMFY 114 : :::::::::::: : :::::::::: :: :::::::: :: :::::::: d2dapa1 43 K-------TPVFDVADVDKHADDVDVLFLCMGS-ATDIPEQAPKFA-QF---ACTVDTYD 90 d1nyta1 115 ---QKGKTP-FLAWCEQRGSKRNADGLGM-L-VAQA-AH--------------------- 146 :::::: ::::::::::::::::: : : ::: : d2dapa1 91 NHRDIPRHRQVMNEAATAAGNVALVST-GRNP-DFTA-SSQIAFGRAAHRMKQQGQSGAF 147 d1nyta1 147 -AFLLWHGVLPDVEPVIK--------------------QLQEELS 170 :: d2dapa1 148 T---------------VLEVAPYLLSPENLDDLIARDV------- 170 HHsearch alignment (Probability: 0.97 E-value:0.00) d1nyta1 17 PGLRILLIGAGGASRGVLLPLLSL-DCA-VTITNRTVSRAEELAKLFAHTGSIQALSMDE 74 :::::::::::::::::::::::: ::: :::::::::::::: ::::::::: d2dapa1 2 TNIRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRATLDTKT--------PVFDVADVD 53 d1nyta1 75 LEGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMF----YQKGKTPFLA-WCEQRG 129 :::::::::::::::::: :::::::::::::::::: :::::::::: :::::: d2dapa1 54 KHADDVDVLFLCMGSATD---IPEQAPKFAQFACTVDTYDNHRDIPRHRQVMNEAATAAG 110 d1nyta1 130 S 130 : d2dapa1 111 N 111