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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1nyta1 | Shikimate 5-dehydrogenase AroE | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
| Hit | d1lc0a1 | Biliverdin reductase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
Query <-- 0.853 --> IntermediateDALI 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 <-- 0.605 --> HitDALI alignment (Z-score: 6.7 Raw score:539.40) d1nyta1 1 dgvgllsdlerlsfirPGLRILLIGAGGASRGVLLPLLS----LDCAV-TITNRTVSraE 55 ::::::::::::::::::::::: ::::: :::::::: : d1lc0a1 1 -----------mitnsGKFGVVVVGVGRAGSVRLRDLKDprsaAFLNLiGFVSRREL--G 47 d1nyta1 56 ELAKlfahtgsIQALSMDELEGHE-FDLIINATSSGisgDIPA-IPSSLIhpgIYCYDMF 113 :::: ::::::::::::: ::::::::::: :::: :::::: ::::::: d1lc0a1 48 SLDE-------VRQISLEDALRSQeIDVAYICSESS-shEDYIrQFLQAG---KHVLVEY 96 d1nyta1 114 Y----qkgktpflaWCEQRGSkRNADGLgmLVAQ---------aahafllwhgvlpdvep 160 : ::::::: :::::: :::: d1lc0a1 97 PmtlsfaaaqelweLAAQKGR-VLHEEH--VELLkniflkdqdifvqklldqvsaedlaa 153 d1nyta1 161 vikQLQEELS--------- 170 ::::::: d1lc0a1 154 ekkRIMHCLGlasdiqklc 172 FAST alignment (Normalized score: 5.33 Raw score:911.20) d1nyta1 1 DGVGLLSDLERLSFIRP------GLRILLIGAGGASRGVLLPLLSL------DCAV-TIT 47 ::::::::::::::::::::: :::: ::: d1lc0a1 1 -----------------MITNSGKFGVVVVGVGRAGSVRLRDLK--DPRSAAFLNLIGFV 41 d1nyta1 48 NRTVSRAEELAKLFAHT-----GSIQALSMDELEGH-EFDLIINATSSGISGDIPAIPSS 101 ::: :::::::::::::: ::::::::: d1lc0a1 42 SRR--------------ELGSLDEVRQISLEDALRSQEIDVAYICS-------------- 73 d1nyta1 102 LIH--------------PGIYCYDMFYQKGK----------TPFLAWCEQRGSKRNADGL 137 :::::::: ::::::::::: :::::: d1lc0a1 74 ---ESSSHEDYIRQFLQAGKHVLVE------YPMTLSFAAAQELWELAAQKG-RVLHEE- 122 d1nyta1 138 GMLVAQAAHAFLLWHGVLPD--------------------VEPVIKQLQEELS------- 170 :::: ::::::::::: d1lc0a1 123 ----HVEL------------LKNIFLKDQDIFVQKLLDQVSAEDLAAEKKR--IMHCLGL 164 d1nyta1 171 -------- 171 d1lc0a1 165 ASDIQKLC 172 TMalign alignment (TM-score: 0.53 Raw score:90.93) d1nyta1 1 -----DGVGLLSDLERLSFIRPGLRILLIGAGGASRGVLLPLLS--LD---CAVTITNRT 50 ::::::::::::::::::::::: :: ::::::::: d1lc0a1 1 MITNS----------------GKFGVVVVGVGRAGSVRLRDLKDPRSAAFLNLIGFVSRR 44 d1nyta1 51 VSRAEELAKLFAHTGSIQALSMDELEGHE-FDLIINATSSGISGDIPAIPSSLIHPGIYC 109 :: : ::: : ::::::::::::: ::::::::: ::::::::::::::: ::: d1lc0a1 45 EL--G--SLD-E----VRQISLEDALRSQEIDVAYICSE-SSSHEDYIRQFLQAG--KHV 92 d1nyta1 110 YDMFY-Q-KGKTP-FLAWCEQ-RGSKRNADGLGMLVAQAAHA------------------ 147 ::::: : ::::: :::::: :::::::::: ::::: ::: d1lc0a1 93 LVEYPMTLSFAAAQ-ELWELAAQKGRVLHEEH-VELLK-NIFLKDQDIFVQKLLDQVSAE 149 d1nyta1 148 ---FLLWHGVLPDVEPVIK-QLQE-ELS---------- 170 :: ::: ::: d1lc0a1 150 DLA--------------AEK-KRIMHCLGLASDIQKLC 172 HHsearch alignment (Probability: 0.96 E-value:0.00) d1nyta1 17 PGLRILLIGAGGASRGVLLPLLSLDCAVTITNRTVSRAEELAKLFAHTGSIQALSMDEL- 75 :::::::::::::::::::::::::::::::::::::::::::: ::::::::::: d1lc0a1 6 GKFGVVVVGVGRAGSVRLRDLKDPRSAAFLNLIGFVSRRELGSL----DEVRQISLEDAL 61 d1nyta1 76 EGHEFDLIINATSSGISGDIPAIPSSLIHPGIYCYDMFYQKGKT------PFLAWCEQRG 129 :::::::::::::::::::: :::::::::::: ::::::: :::::::::: d1lc0a1 62 RSQEIDVAYICSESSSHEDY---IRQFLQAGKHVL--VEYPMTLSFAAAQELWELAAQKG 116 d1nyta1 130 SKRNADGLGMLVAQAAHAFLL 150 :: :::::::::::::::::: d1lc0a1 117 RV-LHEEHVELLKNIFLKDQD 136