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 <-- 1.526 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1ps9a2) 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 d1ps9a2 2,​4-​dienoyl-​CoA reductase,​ C-​terminal domainFAD/​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 <-- 1.526 --> Hit
DALI alignment (Z-score: 4.4 Raw score:372.10) d1nyta1 1 ----------------dgvGLLSDLerlSFIRpgLRILLIGAGGASRGVLLPLLS----- 39 :::::: :::: ::::::::::::::::::::: d1ps9a2 1 vprtppidgidhpkvlsylDVLRDK---APVG--NKVAIIGCGGIGFDTAMYLSQpgest 55 d1nyta1 40 --------------------------------lDCAVTITNRTVSRA---------eelA 58 :::::::::::::: : d1ps9a2 56 sqniagfcnewgidsslqqagglspqgmqiprsPRQIVMLQRKASKPgqglgkttgwihR 115 d1nyta1 59 KLFAHTGsIQAL-SMDE---------------lEGHEFDLIINATSSGisgdipaipssl 102 ::::::: :::: :::: ::::::::::::::: d1ps9a2 116 TTLLSRG-VKMIpGVSYqkidddglhvvingetQVLAVDNVVICAGQE------------ 162 d1nyta1 103 ihpgiycydmfyqkgktpflawceqrgskrnadglgmlvaqaahafllwhgvlpdvepvi 162 d1ps9a2 163 ------------------------------------------------------------ 163 d1nyta1 163 kqlqeels 170 d1ps9a2 163 -------- 163 FAST alignment (Normalized score: 3.19 Raw score:529.60) d1nyta1 1 DGVGLLSDLERLSFIRPG-----------------------------LRILLIGAGGASR 31 ::::::::::::: d1ps9a2 1 ------------------VPRTPPIDGIDHPKVLSYLDVLRDKAPVGNKVAIIGCGGIGF 42 d1nyta1 32 GVLLPLLSL---------------------------------------DCAVTITNRTVS 52 ::::::: :::::::::::: d1ps9a2 43 DTAMYLS--QPGESTSQNIAGFCNEWGIDSSLQQAGGLSPQGMQIPRSPRQIVMLQRKAS 100 d1nyta1 53 RAE------------ELAKLFAHTGSIQALSMDEL---------------------EGHE 79 ::::::::: ::::: :::: d1ps9a2 101 ---KPGQGLGKTTGWIHRTTLLSR-GVKMI-----PGVSYQKIDDDGLHVVINGETQVLA 151 d1nyta1 80 FDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKTPFLAWCEQRGSKRNADGLGM 139 ::::::: d1ps9a2 152 VDNVVIC----------------------------------------------------- 158 d1nyta1 140 LVAQAAHAFLLWHGVLPDVEPVIKQLQEELS---- 170 d1ps9a2 159 -------------------------------AGQE 162 TMalign alignment (TM-score: 0.26 Raw score:44.83) d1nyta1 1 -----------DGVGLLSDLERLSFIRPGLRILLIGAGGASR-GVLLPLLSLDCAVTITN 48 :: : :::: :::: ::: ::: : :::::: d1ps9a2 1 VPRTPPIDGID-------------HP-----K-VLSY-LDVLRDKA-PVG--N-KVAIIG 36 d1nyta1 49 RTVSRAEELAKLFA-H-------------------------------------TGSIQAL 70 ::::::::::::: : ::::::: d1ps9a2 37 -CGGIGFDTAMYLSQPGESTSQNIAGFCNEWGIDSSLQQAGGLSPQGMQIPRSPRQIVML 95 d1nyta1 71 SMD----------------------------ELEGHE-F--DLIINATSSGISGDIPAIP 99 ::: :::::: : :::: :: d1ps9a2 96 QRKASKPGQGLGKTTGWIHRTTLLSRGVKMIPGVSYQKIDDDGLH-------------VV 142 d1nyta1 100 S--SLIH-PGIY-CYD-------MFYQKGKTPFLAWCEQRGSKRNADGLGMLVAQAAHAF 148 : :::: :: :: d1ps9a2 143 INGETQVL--AVD-NVVICAGQE------------------------------------- 162 d1nyta1 149 LLWHGVLPDVEPVIKQLQEELS 170 d1ps9a2 163 ---------------------- 163 HHsearch alignment (Probability: 0.87 E-value:0.00) d1nyta1 14 FIRPGLRILLIGAGGASRGVLLPLLSLDCAVTIT 47 :::::::::::::::::::::::::::::::::: d1ps9a2 25 KAPVGNKVAIIGCGGIGFDTAMYLSQPGESTSQN 58