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 <-- 0.740 --> Hit

SVM
score
SVM
score

The query (T0542_Ad2+3.pdb) is transitively linked to the hit (d1kbza_) 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 d1kbza_ dTDP-​6-​deoxy-​L-​lyxo-​4-​hexulose reductase (RmlD)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 <-- 0.740 --> Hit
DALI alignment (Z-score: 4.2 Raw score:526.60) d1nyta1 1 dgvgllsdlerlsfirpgLRILLIG-AGGASRGVLLPLLsLDCAVTITNRTVSRaeelak 59 ::::::: ::::::::::::: :::::::::::::: d1kbza_ 1 ------------------MNILLFGkTGQVGWELQRSLA-PVGNLIALDVHSKE------ 35 d1nyta1 60 lfahtgsiqalSMDEL-EGHEFDLIINATS-----------sgISGDI----paipSSLI 103 ::::: ::::::::::::: ::::: :::: d1kbza_ 36 --fcgdfsnpkGVAETvRKLRPDVIVNAAAhtavdkaesepelAQLLNatsveaiaKAAN 93 d1nyta1 104 HPGIYCYDMFY------------------------qkgktPFLAWCEQRgSKRNADGL-- 137 ::::::::::: ::::::::: :::::::: d1kbza_ 94 ETGAWVVHYSTdyvfpgtgdipwqetdatsplnvygktklAGEKALQDN-CPKHLIFRts 152 d1nyta1 138 ------------------------------------------------------------ 138 d1kbza_ 153 wvyagkgnnfaktmlrlakerqtlsvindqygaptgaelladctahairvalnkpevagl 212 d1nyta1 138 GMLVAqaahaflLWHGV----------------------------------lpdvEPVIk 163 ::::: ::::: :::: d1kbza_ 213 YHLVA---ggttTWHDYaalvfdearkagitlaltelnavptsayptpasrpgnsRLNT- 268 d1nyta1 164 QLQEE-----------------------ls 170 ::::: d1kbza_ 269 EKFQRnfdlilpqwelgvkrmltemftttt 298 FAST alignment (Normalized score: 3.32 Raw score:746.90) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIG-AGGASRGVLLPLLSLDCAVTITNRTVSRAEELAK 59 ::::::: :::::::::::::: :::::::::: d1kbza_ 1 ------------------MNILLFGKTGQVGWELQRSLAP-VGNLIALDVH--------- 32 d1nyta1 60 LFAHTGSIQAL---------SMDELE----GHEFDLIINATSSGISGDIPAI-------- 98 :::::: :::::::::: d1kbza_ 33 -----------SKEFCGDFSNPKGVAETVRKLRPDVIVNA------------AAHTAVDK 69 d1nyta1 99 ---------------PSSLIH------PGIYCYDMFYQKGK------------------- 118 :::: :::::::: d1kbza_ 70 AESEPELAQLLNATSVEAI--AKAANETGAWVVHY------STDYVFPGTGDIPWQETDA 121 d1nyta1 119 -----------TPFLAWCEQRGSKRNADGLGMLVAQAAHAFLLWHGVLPDVEPVIKQLQE 167 ::::::::: :::::::: d1kbza_ 122 TSPLNVYGKTKLAGEKALQD-NCPKHLIF------------------------------- 149 d1nyta1 168 ELS--------------------------------------------------------- 170 d1kbza_ 150 ---RTSWVYAGKGNNFAKTMLRLAKERQTLSVINDQYGAPTGAELLADCTAHAIRVALNK 206 d1nyta1 171 ------------------------------------------------------------ 171 d1kbza_ 207 PEVAGLYHLVAGGTTTWHDYAALVFDEARKAGITLALTELNAVPTSAYPTPASRPGNSRL 266 d1nyta1 171 -------------------------------- 171 d1kbza_ 267 NTEKFQRNFDLILPQWELGVKRMLTEMFTTTT 298 TMalign alignment (TM-score: 0.50 Raw score:85.55) d1nyta1 1 DGVGLLSDLERLSFIRPGLRILLIG-AGGASRGVLLPLLSLDCAVTITNRTVSRAEELAK 59 ::::::: ::::::::::::::: ::::::: : : :: d1kbza_ 1 ------------------MNILLFGKTGQVGWELQRSLAPV-GNLIALD-V-H-SK---- 34 d1nyta1 60 LFAHTGSIQALSM------D--EL-EGHEFDLIINATSSG-I---------SG--DIPA- 97 :::: : :: ::::::::::::::: : :: :::: d1kbza_ 35 ---------EFCGDFSNPKGVAETVRKLRPDVIVNAAAHTAVDKAESEPELAQLLNATSV 85 d1nyta1 98 -IP-SSLIHPGIYCYDMFYQ-K--------------G---------KTPFLAWCEQRGSK 131 :: :::::::::::::::: : : :::::::::::::: d1kbza_ 86 EAIAKAANETGAWVVHYSTDYVFPGTGDIPWQETDATSPLNVYGKTKLAGEKALQDNCPK 145 d1nyta1 132 RNADGL---------------------------------------GM------------- 139 :::::: :: d1kbza_ 146 HLIFRTSWVYAGKGNNFAKTMLRLAKERQTLSVINDQYGAPTGAELLADCTAHAIRVALN 205 d1nyta1 140 ---------LVAQA-------------AHAFLLW-------------------------- 151 ::::: : d1kbza_ 206 KPEVAGLYHLVAGGTTTWHDYAALVFD------EARKAGITLALTELNAVPTSAYPTPAS 259 d1nyta1 152 ------HGVLPDVEPVIKQLQ--------------------------EELS 170 ::::::: d1kbza_ 260 RPGNSR--------LNTEKFQRNFDLILPQWELGVKRMLTEMFTTTT---- 298 HHsearch alignment (Probability: 0.91 E-value:0.00) d1nyta1 20 RILLIGA-GGASRGVLLPLLSLDCAVTITNRTVSR 53 ::::::: ::::::::::::::::::::::::::: d1kbza_ 2 NILLFGKTGQVGWELQRSLAPVGNLIALDVHSKEF 36