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: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1nhpa2 | NADH peroxidase | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | α/β |
| Hit | d1b8pa1 | Malate dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
Query <-- 1.215 --> IntermediateDALI alignment (Z-score: 4.1 Raw score:328.10) query 1 --------------------------GMENKKMNLLLfsgdydkALASLIIANAAREMEI 34 ::::::::::: :::::::::::::::: d1nhpa2 1 ipgkdldniylmrgrqwaiklkqktvDPEVNNVVVIG------sGYIGIEAAEAFAKAGK 54 query 35 EVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreAEELPlskmnlggigkkmlle 94 ::::::: :::: ::::: d1nhpa2 55 KVTVIDI---LDRP------------------------lGVYLD---------------- 71 query 95 mmkeekapKLSDLLSGARKKEVKFYAXqlsveimgfkkeelfpevqimDVKEyLKNAleS 154 ::::::::::::::::::: :::: :::: : d1nhpa2 72 ------keFTDVLTEEMEANNITIATG------etveryegdgrvqkvVTDK-NAYD--A 116 query 155 DLQLF-i 160 ::::: d1nhpa2 117 DLVVVav 123 FAST alignment (Normalized score: 4.27 Raw score:599.40) query 1 -------------------------GMEN-KKMNLLLFSGDYDK---ALASLIIANAARE 31 :::: ::::: ::::::::::::: d1nhpa2 1 IPGKDLDNIYLMRGRQWAIKLKQKTVDPEVNNVVV---------IGSGYIGIEAAEAFAK 51 query 32 MEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKM 91 :::::::: d1nhpa2 52 AGKKVTVI---------------------------------------------------- 59 query 92 LLEMMKEEKAP--------------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFP 137 ::::::::::::::::: d1nhpa2 60 -----------DILDRPLGVYLDKEFTDVLTEEMEANNITIA------------------ 90 query 138 EVQIMDVKEYLKNA------------------LESDLQLFI-- 160 ::::: :::::::: d1nhpa2 91 --TGETV-------ERYEGDGRVQKVVTDKNAYDADLVVV-AV 123 TMalign alignment (TM-score: 0.33 Raw score:53.16) query 1 ------------------------GMENKK-MNLLLFSGDYDKALASLIIANAAREMEIE 35 :::::: ::::: ::: :::::::::::::: : d1nhpa2 1 IPGKDLDNIYLMRGRQWAIKLKQKTVDPEVNNVVVI-GSG-YIGIEAAEAFAKAG----K 54 query 36 VTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKK--MLL 93 ::::: ::: : :: :::: :: : d1nhpa2 55 KVTVI---DIL------------------------D-RP-LGVY---------LDKE--F 74 query 94 --EMMKEEKAPKLS-DLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVKE--YL 148 ::: ::::::: : ::::: :: ::::: :: d1nhpa2 75 TD---------VLTEEMEANNI---T-IATGE-TV----------------ERYEGDGRV 104 query 149 KNA--------LESDLQLFI- 160 ::: :: ::::: d1nhpa2 105 QKVVTDKNAYD-AD-LVVVAV 123 HHsearch alignment (Probability: 0.05 E-value:0.02) query 20 LASLIIANAAREMEIEVTIF 39 :::::::::::::::::::: d1nhpa2 40 YIGIEAAEAFAKAGKKVTVI 59
Intermediate <-- 1.106 --> HitDALI alignment (Z-score: 2.9 Raw score:258.00) d1nhpa2 1 ipgkdldniylmrgrqwaiklkqktvdPEVNNVVVIGS-GYIGIEAAEAFAKA------- 52 ::::::::::: :::::::::::::: d1b8pa1 1 ---------------------------KTPMRVAVTGAaGQICYSLLFRIANGdmlgkdq 33 d1nhpa2 53 GKKVTVIDI-----LDRPlgvyldkeftdvLTEEMEAN------NITIAtgETVEryegd 101 ::::::::: :::: :::::::: ::::: :::: d1b8pa1 34 PVILQLLEIpnekaQKAL----------qgVMMEIDDCafpllaGMTAH--ADPM----- 76 d1nhpa2 102 grvqkvvtdknaYDADLVVVAV-------------------------------------- 123 :::::::::: d1b8pa1 77 ---------tafKDADVALLVGarprgpgmerkdlleanaqiftvqgkaidavasrnikv 127 d1nhpa2 124 ----------------------------- 124 d1b8pa1 128 lvvgnpantnayiamksapslpaknftam 156 FAST alignment (Normalized score: 2.18 Raw score:301.40) d1nhpa2 1 IPGKDL------------------------------------DNIYLMRGRQWAI----- 19 :::::::::: d1b8pa1 1 ------KTPMRVAVTGAAGQICYSLLFRIANGDMLGKDQPVILQLLEIPNEK---AQKAL 51 d1nhpa2 20 ----------------------KLKQKTVDP-EVNNVVVIGS-------------GYIGI 43 :::::: ::::::::: ::::: d1b8pa1 52 QGVMMEIDDCAFPLLAGMTAHADPMTAF---KDADVALLVG-ARPRGPGMERKDLLEANA 107 d1nhpa2 44 EAAEAFAKA--------GKKVTVIDILDRPLGVYLDKEF----TDVLTEEMEA------- 84 :::::::: :::::: :::::::::: d1b8pa1 108 QIFTVQGK-AIDAVASRNIKVLV----------------VGNPANTNAYIAMKSAPSLPA 150 d1nhpa2 85 NNITIATGETVERYEGDGRVQKVVTDKNAYDADLVVVAV-- 123 :::: d1b8pa1 151 KNFT-----------------------------------AM 156 TMalign alignment (TM-score: 0.39 Raw score:48.32) d1nhpa2 1 IPGKDLDNIYLMRGRQWAIKLKQKTVDPEVNNVVVIG-S----GYIGIEAAE--A-FAKA 52 : :::::::: : ::::::::: : :::: d1b8pa1 1 ---------------------------K-TPMRVAVTGAAGQICYSLLFRIANGDMLGKD 32 d1nhpa2 53 GKKVTVIDI------LDRPLGVYLDKEFTDVLTEEMEANNITIATGETVERYEGDGRVQK 106 ::::::::: :::: : : :::::::::::::::::::::: d1b8pa1 33 QPVILQLLEIPNEKAQKAL-Q----G-VMMEIDDCAFPLLAGMTAHADP----------- 75 d1nhpa2 107 VVTDKNAYDADLVVVAV------------------------------------------- 123 :: :::::::::::: d1b8pa1 76 -MT--AFKDADVALLVGARPRGPGMERKDLLEANAQIFTVQGKAIDAVASRNIKVLVVGN 132 d1nhpa2 124 ------------------------ 124 d1b8pa1 133 PANTNAYIAMKSAPSLPAKNFTAM 156 HHsearch alignment (Probability: 0.89 E-value:0.00) d1nhpa2 28 PEVNNVVVIGS-GYIGIEAAEAFAKAGK-------KVTVIDILD 63 ::::::::::: :::::::::::::::: ::::::::: d1b8pa1 1 KTPMRVAVTGAAGQICYSLLFRIANGDMLGKDQPVILQLLEIPN 44