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 <-- 1.219 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1nhpa1) 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 d1nhpa1 NADH peroxidaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/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 <-- 1.219 --> Hit
DALI alignment (Z-score: 4.7 Raw score:412.60) d1nyta1 1 dgvgllsdlerlsfirpgLRILLIGAGGASRGVLLPLLS--LDCAVTITNRTVSR----- 53 ::::::::::::::::::::: :::::::::::::: d1nhpa1 1 ------------------MKVIVLGSSHGGYEAVEELLNlhPDAEIQWYEKGDFIsflsa 42 d1nyta1 54 ----------------aeELAKLFAHTGsIQAL--SMDE------------------lEG 77 :::::::::: :::: :::: :: d1nhpa1 43 gmqlylegkvkdvnsvryMTGEKMESRG-VNVFsnTEITaiqpkehqvtvkdlvsgeeRV 101 d1nyta1 78 HEFDLIINATSSG-----iSGDI---------------paipsslihpgIYCYDM--FYQ 115 ::::::::::::: :::: :::::: ::: d1nhpa1 102 ENYDKLIISPGAVpfeldgVRPNtawlkgtlelhpngliktdeymrtsePDVFAVgdATL 161 d1nyta1 116 KG--------ktpflawceqrgskrnadglgmlVAQAahafllwhgvlpdvepvikqlqe 167 :: :::: d1nhpa1 162 IKynpadtevnialatnarkqgrfavknleepvKPFP----------------------- 198 d1nyta1 168 els 170 d1nhpa1 199 --- 199 FAST alignment (Normalized score: 3.23 Raw score:592.80) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLS--LDCAVTITNRTVSRAEE-- 56 ::::::::::::::::::::: ::::::::::: d1nhpa1 1 ------------------MKVIVLGSSHGGYEAVEELLNLHPDAEIQWYEKG------DF 36 d1nyta1 57 -------------------------LAKLFAHTGSIQALSMDEL---------------- 75 :::::::: :::: d1nhpa1 37 ISFLSAGMQLYLEGKVKDVNSVRYMTGEKMESR-GVNV------FSNTEITAIQPKEHQV 89 d1nyta1 76 ----------EGHEFDLIINATSSGISGDIPAIPSSLIHPG------------------- 106 :::::::::::: d1nhpa1 90 TVKDLVSGEERVENYDKLIISP-------------------GAVPFELDGVRPNTAWLKG 130 d1nyta1 107 --------------------IYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGMLVAQAAH 146 ::::: d1nhpa1 131 TLELHPNGLIKTDEYMRTSEPDVFA----------------------------------- 155 d1nyta1 147 AFLLWHGVLPDVEPVIKQLQEELS------------------------------------ 170 d1nhpa1 156 ------------------------VGDATLIKYNPADTEVNIALATNARKQGRFAVKNLE 191 d1nyta1 171 ------- 171 d1nhpa1 192 EPVKPFP 198 TMalign alignment (TM-score: 0.45 Raw score:75.92) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLS-L-DCAVTITNRTVSRA---- 54 ::::::::::::::::::::: : :::::::::::::: d1nhpa1 1 ------------------MKVIVLGSSHGGYEAVEELLNLHPDAEIQWYEKGDFISFLSA 42 d1nyta1 55 ------------------EELAKLFAHTGSIQAL-SM-------------DE-----LEG 77 ::::::::::::::: :: :: ::: d1nhpa1 43 GMQLYLEGKVKDVNSVRY-MTGEKMESRGVNVFSNTEITAIQPKEHQVTVKDLVSGEERV 101 d1nyta1 78 HEFDLIINATSSG------ISGDIPAI-PSS------------------LIHPGIYCYDM 112 ::::::::::::: :::::::: :: ::::::: d1nhpa1 102 ENYDKLIISPGAVPFELDGVRPNTAWLK-GTLELHPNGLIKTDEYMRTS----EPDVFAV 156 d1nyta1 113 F--YQ-------KG-KT------PFLAWCEQRGSKRNADG-LGMLVAQ--------AAHA 147 : :: :: : : :::::: d1nhpa1 157 GDATLIKYNPADTEV-NIALATN----------------AR-KQGRFAVKNLEEPV---- 194 d1nyta1 148 FLLWHGVLPDVEPVIKQLQEELS 170 :: :: d1nhpa1 195 ----------KP-FP-------- 198 HHsearch alignment (Probability: 0.90 E-value:0.00) d1nyta1 20 RILLIGAGGASRGVLLPLLSL--DCAVTITNRTV 51 ::::::::::::::::::::: ::::::::::: d1nhpa1 2 KVIVLGSSHGGYEAVEELLNLHPDAEIQWYEKGD 35