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 | d1tlta1 | Virulence factor MviM | 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 <-- 1.266 --> HitDALI alignment (Z-score: 7.8 Raw score:582.90) d1l7da1 1 agyravidgayefarafpmmmtaagtvpPARVLVFGVGVAGL-QAIATAKRL-GAVV-MA 57 :::::::::::::: ::::::::: :::: :: d1tlta1 1 ----------------------------KLRIGVVGLGGIAQkAWLPVLAAAsDWTLqGA 32 d1l7da1 58 TD-VRAATKEQVESLGGKFITvkkqaeAVLKELVKTDIAITTALipgkpAPVL--ITEEM 114 :: :::::::::::::::::: ::::::::::::::::: :::: ::::: d1tlta1 33 WSpTRAKALPICESWRIPYAD------SLSSLAASCDAVFVHSS-----TASHfdVVSTL 81 d1l7da1 115 VTKMkpgSVIIDLAVEAGgncplsepgkiVVKHGVKIVGHTnVPSR-------------- 160 :::: ::::::::::: :::::::::::: :::: d1tlta1 82 LNAG---VHVCVDKPLAEnlrdaerlvelAARKKLTLMVGF-NRRFrgfvgcarhfiecv 137 d1l7da1 161 ----------------------------- 161 d1tlta1 138 qnqtvpqtageqavlaqrivdkiwrdams 166 FAST alignment (Normalized score: 5.56 Raw score:905.80) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGL-QAIATAKR--LGAV-VM 56 :::::::::::::: ::::::: :::: :: d1tlta1 1 ----------------------------KLRIGVVGLGGIAQKAWLPVLA-AASDWTLQG 31 d1l7da1 57 ATDVR-AATKEQVESLGGKFITVKKQAE--AVLKELVKTDIAITTALIPGKPAPVLI--- 110 ::::: :::::::::::::: ::::::::::::::: d1tlta1 32 AWSPTRAKALPICESWRIPY--------ADSLSSLAASCDAVFVH------------SST 71 d1l7da1 111 ------TEEMVTKMKPGSVIIDLAVEAGGNCPLSEPGKIVV------------------K 146 :::::: :::::::: : d1tlta1 72 ASHFDVVSTLLN---AGVHVCVD------------------KPLAENLRDAERLVELAAR 110 d1l7da1 147 HGVKIVGHTNVPSR---------------------------------------------- 160 :::::::: d1tlta1 111 KKLTLMVG------FNRRFRGFVGCARHFIECVQNQTVPQTAGEQAVLAQRIVDKIWRDA 164 d1l7da1 161 -- 161 d1tlta1 165 MS 166 TMalign alignment (TM-score: 0.57 Raw score:90.64) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGL-QAIATAKRLG--AVVMA 57 : ::::::::::::: :::::::::: ::::: d1tlta1 1 ---------------K-------------LRIGVVGLGGIAQKAWLPVLAAASDWTLQGA 32 d1l7da1 58 TD-VRAATKEQVESLGGKFITVKKQAEAVLKELVKTDIAITTALIPGKPAPV-LITEEMV 115 :: :::::::::::::::::: ::::::::::::::::: :::: ::::::: d1tlta1 33 WSPTRAKALPICESWRIPYAD------SLSSLAASCDAVFVHSS----TASHFDVVSTLL 82 d1l7da1 116 TKMKPGSVIIDLAVEAGG--NC-PLSE-PGKIVVKHGVKIVGHTNVPSR----------- 160 ::: :::::::::::: :: :::: :::::::::::: :::: d1tlta1 83 NAG---VHVCVDKPLAENLRDAERLVEL----AARKKLTLMVGF-NRRFRGFVGCARHFI 134 d1l7da1 161 -------------------------------- 161 d1tlta1 135 ECVQNQTVPQTAGEQAVLAQRIVDKIWRDAMS 166 HHsearch alignment (Probability: 0.96 E-value:0.00) d1l7da1 30 ARVLVFGVGVAGLQA-IATAKRLG-AVVM-ATDVRAATKEQVESLGGKFITVKKQAEAVL 86 ::::::::::::::: :::::::: :::: :::::::::::::::::: ::::::: d1tlta1 2 LRIGVVGLGGIAQKAWLPVLAAASDWTLQGAWSPTRAKALPICESWRI-----PYADSLS 56 d1l7da1 87 KELVKTDIAITTALIPGKPAPVLITEEMVTKMKPG 121 :::::::::::: ::::::: :::::::::: d1tlta1 57 SLAASCDAVFVH--SSTASHF----DVVSTLLNAG 85