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 | d1l7da1 | Nicotinamide nucleotide transhydrogenase dI component | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
| Hit | d1vl0a_ | DTDP-4-dehydrorhamnose reductase RfbD | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
Query <-- 1.100 --> IntermediateDALI alignment (Z-score: 5.1 Raw score:345.40) query 1 ---------------GMEN----------KKMNLLLfsgdydkALASLIIANAAREMEIE 35 :::: ::::::: ::::::::::::::::: d1l7da1 1 agyravidgayefarAFPMmmtaagtvppARVLVFG------vGVAGLQAIATAKRLGAV 54 query 36 VTIFCafwgLLLLrdpekasqedkslyeqafssltpreaeelplskmnlggigkkmllem 95 ::::: :::: d1l7da1 55 VMATD----VRAA----------------------------------------------- 63 query 96 mkeekapklsdllSGARKKEVKFYAXQLsveimgfkkeelfpevqimDVKEYLKNALESD 155 ::::::::::::::: ::::::::::::: d1l7da1 64 -----------tkEQVESLGGKFITVKK-------------------QAEAVLKELVKTD 93 query 156 LQLFI------------------------------------------------------- 160 ::::: d1l7da1 94 IAITTalipgkpapvliteemvtkmkpgsviidlaveaggncplsepgkivvkhgvkivg 153 query 161 ------- 161 d1l7da1 154 htnvpsr 160 FAST alignment (Normalized score: 3.90 Raw score:624.80) query 1 GME----------------------------NKKMNLLLFSGDYDK---ALASLIIANAA 29 :::::: ::::::::::: d1l7da1 1 ---AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLV---------FGVGVAGLQAIATA 48 query 30 REMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGK 89 :::::::::: d1l7da1 49 KRLGAVVMAT-------------------------------------------------- 58 query 90 KMLLEMMKEEKAPKLSD-----LLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIM-- 142 :::::::::::::: d1l7da1 59 -----------------DVRAATKEQVESLGGKFIT----------------------VK 79 query 143 -DVKEYLKNALESDLQLFI----------------------------------------- 160 :::::::::::::::: d1l7da1 80 KQAEAVLKELVKTDIAI--TTALIPGKPAPVLITEEMVTKMKPGSVIIDLAVEAGGNCPL 137 query 161 ----------------------- 161 d1l7da1 138 SEPGKIVVKHGVKIVGHTNVPSR 160 TMalign alignment (TM-score: 0.23 Raw score:37.44) query 1 ------------------------------GMENKKMNLLLFSGDYDKALASLIIANAAR 30 d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPA------------------------------ 30 query 31 EMEIEVTIFCAFWGLLLLRDPEK--AS--QEDKSLYEQAFSSLTPREAE----------- 75 :: ::: ::::: :: :::::: : :: :: ::: d1l7da1 31 -----------RV-LVF-GVGVAGLQAIATAKRLG-A--VV--MA-TDVRAATKEQVESL 71 query 76 ---ELPL-SK-----------------MNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKK 114 :::: :: ::::::: d1l7da1 72 GGKFITVKKQAEAVLKELVKTDIAITT--------------------------ALIPGKP 105 query 115 EVKFYA---X----QLSVEIMGFKKEELFPE---V----Q----IMDVKEY--------- 147 :::::: : :::: : : :::: : : ::::::: d1l7da1 106 APVLITEEMVTKMKPGSV----I-I--DLAVEAGGNCPLSEPGKIVVKHGVKIVGHTNVP 158 query 148 --LKNALESDLQLFI 160 d1l7da1 159 SR------------- 160 HHsearch alignment (Probability: 0.09 E-value:0.01) query 21 ASLIIANAAREMEIEVTIF 39 ::::::::::::::::::: d1l7da1 40 AGLQAIATAKRLGAVVMAT 58
Intermediate <-- 1.635 --> HitDALI alignment (Z-score: 4.0 Raw score:472.80) d1l7da1 1 agyravidgayefarafpmmmtaagtvpPARVLVFGV-GVAGLQAIATAKRLGAVVMATD 59 ::::::::: :::::::::::::::::::::: d1vl0a_ 1 ----------------------------HMKILITGAnGQLGREIQKQLKGKNVEVIPTD 32 d1l7da1 60 VRaatkeqveslggkfitvkkQAEAVLKELV--KTDIAITTALIPGK------------p 105 :: :::::::::: :::::::::::::: d1vl0a_ 33 VQ--------------dlditNVLAVNKFFNekKPNVVINCAAHTAVdkceeqydlayki 78 d1l7da1 106 APVLIT--eEMVTKMKpgSVIIDLaVEAG------------------------gncPLSE 139 :::::: ::::::: :::::: :::: :::: d1vl0a_ 79 NAIGPKnlaAAAYSVG--AEIVQI-STDYvfdgeakepitefdevnpqsaygktklEGEN 135 d1l7da1 140 pgkiVVKHGvKIVGHTN------------------------------------------- 156 ::::: ::::::: d1vl0a_ 136 --fvKALNP-KYYIVRTawlygdgnnfvktminlgkthdelkvvhdqvgtptstvdlarv 192 d1l7da1 157 -------------VPSR------------------------------------------- 160 :::: d1vl0a_ 193 vlkvideknygtfHCTCkgicswydfaveifrltgidvkvtpctteefprpakrpkysvl 252 d1l7da1 161 ----------------------------- 161 d1vl0a_ 253 rnymlelttgditrewkeslkeyidllqm 281 FAST alignment (Normalized score: 2.53 Raw score:536.40) d1l7da1 1 --------------------------------------AGYRAVIDGAYEFARAFPMMMT 22 ::::::::::: d1vl0a_ 1 HMKILITGANGQLGREIQKQLKGKNVEVIPTDVQDLDITNVLAVNKFFN----------- 49 d1l7da1 23 AAGTVPP----ARVLVFGV-------------------GVAGLQAIATAKRLGAVVMATD 59 ::::::: ::::::::::::::::::::: d1vl0a_ 50 -------EKKPNVVINCA-AHTAVDKCEEQYDLAYKINAIGPKNLAAAAYSVGAEIVQI- 100 d1l7da1 60 V-----------------------------RAATKEQVES--LGGKFITV---------- 78 :::::::::: ::::::: d1vl0a_ 101 -STDYVFDGEAKEPITEFDEVNPQSAYGKTKLEGENFVKALNPKYYIVR-TAWLYGDGNN 158 d1l7da1 79 ----------------------------KKQAEAVLKELVKTDIAITTALIPGKPAPVLI 110 :::::::::::: d1vl0a_ 159 FVKTMINLGKTHDELKVVHDQVGTPTSTVDLARVVLKVID-------------------- 198 d1l7da1 111 TEEMVTKMKPGSVIIDLAVEAGGNCPLSEPGKIVVKHGVKIVGHTNVPSR---------- 160 d1vl0a_ 199 --------------------------------------------------EKNYGTFHCT 208 d1l7da1 161 ------------------------------------------------------------ 161 d1vl0a_ 209 CKGICSWYDFAVEIFRLTGIDVKVTPCTTEEFPRPAKRPKYSVLRNYMLELTTGDITREW 268 d1l7da1 161 ------------- 161 d1vl0a_ 269 KESLKEYIDLLQM 281 TMalign alignment (TM-score: 0.52 Raw score:83.51) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGV-GVAGLQAIATAKRLGAVVMATD 59 ::::::::: :::::::::::::::::::::: d1vl0a_ 1 ----------------------------HMKILITGANGQLGREIQKQLKGKNVEVIPTD 32 d1l7da1 60 VRAATKEQVESLGGKFIT--VK-KQAEAVLKELVKTDIAITTALI-PG--K------P-- 105 :: ::: : :::::::::: ::::::::::: :: : : d1vl0a_ 33 VQ-------------DLDIT-NVLAVNKFFNEK-KPNVVINCAAHTAVDKCEEQYDLAYK 77 d1l7da1 106 -APVLI-T-EEMVTKMKPGSVIIDLAV--E---------------------A--GG-NCP 136 ::::: : :::::::: :::::::: : : :: ::: d1vl0a_ 78 INAIGPKNLAAAAYSVG--AEIVQISTDYVFDGEAKEPITEFDEVNPQSAYGKTKLEGEN 135 d1l7da1 137 LSEPGKIVVKHGVKIVGHTN---------------------------------------- 156 :: :::: :::::::: d1vl0a_ 136 FV-----KALN-PKYYIVRTAWLYGDGNNFVKTMINLGKTHDELKVVHDQVGTPTSTVDL 189 d1l7da1 157 -----------------VPS---------------------------------------- 159 ::: d1vl0a_ 190 ARVVLKVIDEKNYGTFHCTCKGICSWYDFAVEIFRLTGIDVKVTPCTTEEFPRPAKRPKY 249 d1l7da1 160 ---------------R---------------- 160 : d1vl0a_ 250 SVLRNYMLELTTGDITREWKESLKEYIDLLQM 281 HHsearch alignment (Probability: 0.96 E-value:0.00) d1l7da1 30 ARVLVFGV-GVAGLQAIATAKRLGAVVMATDVRAATKEQVESLGGKFITVKKQAEAVLKE 88 :::::::: :::::::::::::::::::::::::::: ::::::::: d1vl0a_ 2 MKILITGANGQLGREIQKQLKGKNVEVIPTDVQDLDI--------------TNVLAVNKF 47 d1l7da1 89 LVKT--DIAITTALIPGKP----AP-------VLITEEMVTKMKP-GSVIIDLAVEA--- 131 :::: ::::::::::::: :: ::::::::::::: ::::::::::: d1vl0a_ 48 FNEKKPNVVINCAAHTAVDKCEEQYDLAYKINAIGPKNLAAAAYSVGAEIVQISTDYVFD 107 d1l7da1 132 ----GGNCPLSEPGKI 143 :::::::::::: d1vl0a_ 108 GEAKEPITEFDEVNPQ 123