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 | d1vlla_ | Archaeal alanine 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 <-- 1.421 --> HitDALI alignment (Z-score: 4.1 Raw score:266.00) d1nhpa2 1 ------------------------------------------------------------ 1 d1vlla_ 1 metliltqeeveslismdeamnaveeafrlyalgkaqmppkvylefekgdlrampahlmg 60 d1nhpa2 1 ------------------------------------ipgkdldniylmrgrqwaIKLKQk 24 ::::: d1vlla_ 61 yaglkwvnshpgnpdkglptvmalmilnspetgfplavmdatyttslrtgaaggIAAKY- 119 d1nhpa2 25 tVDPEVNNVVVIGSGYIGIEAAEAFA-KAGK-KVTVIDILDRPlgvyldkeftdvlTEEM 82 ::::::::::::::::::::::::: :::: ::::::::::: :::: d1vlla_ 120 lARKNSSVFGFIGCGTQAYFQLEALRrVFDIgEVKAYDVREKA---------akkfVSYC 170 d1nhpa2 83 EA--NNITIAtgetveryegdgrvqkvvtdknaYDADLVVVAV----------------- 123 :: :::::: :::::::::: d1vlla_ 171 EDrgISASVQ------------------paeeaSRCDVLVTTTpsrkpvvkaewveegth 212 d1nhpa2 124 ------------------------------------------------------------ 124 d1vlla_ 213 inaigadgpgkqeldveilkkakivvddleqakhggeinvavskgvigvedvhatigevi 272 d1nhpa2 124 ------------------------------------------------- 124 d1vlla_ 273 aglkdgresdeeitifdstglaiqdvavakvvyenalsknvgskikffr 321 FAST alignment (Normalized score: 3.16 Raw score:627.10) d1nhpa2 1 IPGKDLDNIYLMR----------------------------------------------- 13 d1vlla_ 1 -------------METLILTQEEVESLISMDEAMNAVEEAFRLYALGKAQMPPKVYLEFE 47 d1nhpa2 14 -------------------------------------------------------GRQWA 18 ::::: d1vlla_ 48 KGDLRAMPAHLMGYAGLKWVNSHPGNPDKGLPTVMALMILNSPETGFPLAVMDATYTTSL 107 d1nhpa2 19 IKLKQKT------VDPEVNNVVVIGSGYIGIEAAEAFAKAG----KKVTVIDILDRPLGV 68 ::::::: :::::::::::::::::::::::::: :::::::::: d1vlla_ 108 RTGAAGGIAAKYLARKNSSVFGFIGCGTQAYFQLEALRR--VFDIGEVKAYDVRE----- 160 d1nhpa2 69 YLDKEF--TDVLTEEMEA--NNITIATGETVERYEGDGRVQKVVTDKNA------YDADL 118 :::::::::: ::::: ::::: d1vlla_ 161 ------KAAKKFVSYCEDRGISASV------------------------QPAEEASRCDV 190 d1nhpa2 119 VVVAV------------------------------------------------------- 123 :::: d1vlla_ 191 LVTT-TPSRKPVVKAEWVEEGTHINAIGADGPGKQELDVEILKKAKIVVDDLEQAKHGGE 249 d1nhpa2 124 ------------------------------------------------------------ 124 d1vlla_ 250 INVAVSKGVIGVEDVHATIGEVIAGLKDGRESDEEITIFDSTGLAIQDVAVAKVVYENAL 309 d1nhpa2 124 ------------ 124 d1vlla_ 310 SKNVGSKIKFFR 321 TMalign alignment (TM-score: 0.49 Raw score:59.90) d1nhpa2 1 ------------------------------------------------------------ 1 d1vlla_ 1 METLILTQEEVESLISMDEAMNAVEEAFRLYALGKAQMPPKVYLEFEKGDLRAMPAHLMG 60 d1nhpa2 1 -----------------------------------------------IPGKDLDNIYLMR 13 :: d1vlla_ 61 YAGLKWVNSHPGNPDKGLPTVMALMILNSPETGFPLAVMDATYTTSL-----------RT 109 d1nhpa2 14 GRQWAIKLKQKTVDPEVNNVVVIGSGYIGIEAAEAFAK-AGK-KVTVIDILDRPLGVYLD 71 ::::::::::::::: :::::::::::::::::::::: ::: ::::::::::::: d1vlla_ 110 GAAGGIAAKYLARKN-SSVFGFIGCGTQAYFQLEALRRVFDIGEVKAYDVREKAAK---- 164 d1nhpa2 72 KEFTDVLTEEMEA-NNITIATGETVERYEGDGRVQKVVTDKNAY-DADLVVVAV------ 123 : ::::::: ::::::: : : : :: ::::::::: d1vlla_ 165 ---K--FVSYCEDRGISASVQ-P-A------------E----EASRCDVLVTTTPSRKPV 201 d1nhpa2 124 ------------------------------------------------------------ 124 d1vlla_ 202 VKAEWVEEGTHINAIGADGPGKQELDVEILKKAKIVVDDLEQAKHGGEINVAVSKGVIGV 261 d1nhpa2 124 ------------------------------------------------------------ 124 d1vlla_ 262 EDVHATIGEVIAGLKDGRESDEEITIFDSTGLAIQDVAVAKVVYENALSKNVGSKIKFFR 321 HHsearch alignment (Probability: 0.93 E-value:0.00) d1nhpa2 6 LDNIYLMRGRQWAIKLKQKTVDPEVNNVVVIGSGYIGIEAAEAFAK--AGKKVTVIDILD 63 :::::::::::::::::::::::::::::::::::::::::::::: ::::::::::: d1vlla_ 101 ATYTTSLRTGAAGGIAAKYLARKNSSVFGFIGCGTQAYFQLEALRRVFDIGEVKAYDVR- 159 d1nhpa2 64 RPLGVYLDKEFTDVLTEEMEANNITIATGE 93 :::::::::::::::::::::: d1vlla_ 160 --------EKAAKKFVSYCEDRGISASVQP 181