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 | d1efpa1 | Large, alpha subunit of electron transfer flavoprotein ETFP, N-terminal domain | Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolase-like | α/β |
| Hit | d1pvoa3 | Transcription termination factor Rho, ATPase domain | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | α/β |
Query <-- 0.729 --> IntermediateDALI alignment (Z-score: 4.7 Raw score:461.40) query 1 dadeevysalvvglrayvakngfrSVLIGLS------gGIDSALVAAIACdALGAqnVYG 54 ::::::: :::::::::::: :::: ::: d1efpa1 1 ------------------------AVLLLGEvtngalnRDATAKAVAAVK-ALGD--VTV 33 query 55 VSMPSKyssDHSKGDAAELarRTGLNFRTVSiEPMFdaymaslgltglaeenlQSRL--R 112 :::::: :::::::::: :::::::::: :::: :::: : d1efpa1 34 LCAGAS--aKAAAEEAAKI--AGVAKVLVAE-DALY----------------gHRLAepT 72 query 113 GTTLMAISnQEGHIVLAPGnkselavgysTLYGDSVG----------------------- 149 :::::::: :::::::::: :::::::: d1efpa1 73 AALIVGLA-GDYSHIAAPA----------TTDAKNVMprvaalldvmvlsdvsaildadt 121 query 150 ---------------------AYGPIKDVyktsifrlaewrnraaaergqtpPIPEasit 188 :::::::: :::: d1efpa1 122 ferpiyagnaiqvvkskdakkVFTIRTAS--------------------fdaAGEG---- 157 query 189 kpdypvldailelyvdrdtgadaivaagydrelvvktlrmvdtaeykrrqyppgtkisak 248 d1efpa1 158 ----------------------------------------------------gtapvtet 165 query 249 gfgkdrrlpitnrwregh 266 d1efpa1 166 aaaadpglsswvadevae 183 FAST alignment (Normalized score: 2.23 Raw score:493.20) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGID--------SALVAAIACDALGAQ-- 50 ::::: ::::::::::: d1efpa1 1 ------------------------AVLLL------GEVTNGALNRDATAKAVAA----VK 26 query 51 ---NVYGVSMPSKYSSDH--SKGDAAELARR-TGL-NFRTVSIEPMFDAYMASLGLTGLA 103 ::::::: ::::::::::: ::: ::::::: d1efpa1 27 ALGDVTVLCA--------GASAKAAAEEAAKIAGVAKVLVAED----------------- 61 query 104 EENL------QSRLRGTTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDV 157 :::::::::::::::: ::::: d1efpa1 62 ----ALYGHRLAEPTAALIVGLAGDY-SHIAA---------------------------- 88 query 158 YKTSIFRLAEWRNRAAAERGQTPPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGY 217 d1efpa1 89 ------------------------------------------------------------ 89 query 218 DRELVVKTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH----------- 266 d1efpa1 89 -------------------------------------------------PATTDAKNVMP 99 query 267 ------------------------------------------------------------ 267 d1efpa1 100 RVAALLDVMVLSDVSAILDADTFERPIYAGNAIQVVKSKDAKKVFTIRTASFDAAGEGGT 159 query 267 ------------------------ 267 d1efpa1 160 APVTETAAAADPGLSSWVADEVAE 183 TMalign alignment (TM-score: 0.34 Raw score:89.61) query 1 DADEEVYSALVVGLRAYVAKNGFRSVLIGL-S----GG-IDSALVAAIACDALGAQNVYG 54 :::::: : :: ::::::::::: ::: : ::: d1efpa1 1 ------------------------AVLLLGEVTNGALNRDATAKAVAAVK-ALG-D-VTV 33 query 55 VSMPSKYSSDHSKGDAAELARRTGLNFRTVSIEPMFDAYMASLGLTGLAEENLQSR-LRG 113 :::::: ::: :::::::: :::::::::::: :: :: ::: ::: d1efpa1 34 LCAGAS-AKA-AAEEAAKI--AGVAKVLVAEDA-LY-------------GH--RLAEPTA 73 query 114 TTLMAISNQEGHIVLAPGNKSELAVGYSTLYGDSVG------------------------ 149 ::::::: ::::::::::: :: ::::: d1efpa1 74 ALIVGLA-GDYSHIAAPAT---------TD-AKNVMPRVAALLDVMVLSDVSAILDADTF 122 query 150 --------------------AYGPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPE----- 184 :::::: : :: :: : ::: d1efpa1 123 ERPIYAGNAIQVVKSKDAKKVFTIRT-A---SF--DA---A-----------GEGGTAPV 162 query 185 ---------------------ASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVV 223 d1efpa1 163 TETAAAADPGLSSWVADEVAE--------------------------------------- 183 query 224 KTLRMVDTAEYKRRQYPPGTKISAKGFGKDRRLPITNRWREGH 266 d1efpa1 184 ------------------------------------------- 184 HHsearch alignment (Probability: 0.02 E-value:0.18) query 27 LIGLSGGIDSALVAAIACDALGA--QNVYGVSMPSKYSSDHSKGDAAELARRTGLNF 81 ::::::::::::::::::::::: ::::::::: :::::::::::::::::::: d1efpa1 56 VLVAEDALYGHRLAEPTAALIVGLAGDYSHIAAP---ATTDAKNVMPRVAALLDVMV 109
Intermediate <-- 0.691 --> HitDALI alignment (Z-score: 1.5 Raw score:298.90) d1efpa1 1 --------------------------------------avlllgevtngalNRDATAKAV 22 ::::::::: d1pvoa3 1 nkilfenltplhansrlrmgstedltarvldlaspigrgqrglivappkagKTMLLQNIA 60 d1efpa1 23 AAV-KALG--dVTVLCAgaSAKA-AAEEAAKIAGvAKVLVAE--DALYGhrlaePTAALI 76 ::: :::: :::::: :::: :::::::::: ::::::: ::::: :::::: d1pvoa3 61 QSIaYNHPdcvLMVLLI--DERPeEVTEMQRLVK-GEVVASTfdEPASR---hvQVAEMV 114 d1efpa1 77 VGLAGDY----SHIAA--------------------------pattdaKNVMPRVAalld 106 ::::::: ::::: :::::::: d1pvoa3 115 IEKAKRLvehkKDVIIlldsitrlarayntvvpavltggvdanalhrpKRFFGAAR---- 170 d1efpa1 107 vmvlsdvsaildadtferpiyagnaiqvvkSKDAKKVFTIrtasfdaageggtapvteta 166 :::::::::: d1pvoa3 171 -----------------------------nVEEGGSLTII-------------------- 181 d1efpa1 167 aaadpglsswvADEV--------------------------------------------- 181 :::: d1pvoa3 182 ----atalidtGSKMdeviyeefkgtgnmelhlsrkiaekrvfpaidynrsgtrkeellt 237 d1efpa1 182 -------------------------------------------ae 183 d1pvoa3 238 tqeelqkmwilrkiihpmgeidameflinklamtktnddffemmk 282 FAST alignment (Normalized score: 2.05 Raw score:466.20) d1efpa1 1 AVLLLGEVTNGAL----------------------------------------------- 13 d1pvoa3 1 -------------NKILFENLTPLHANSRLRMGSTEDLTARVLDLASPIGRGQRGLIVAP 47 d1efpa1 14 ----NRDATAKAVAAVKAL------GDVTVLCAGAS---AKAAAEEAA-KIAGVAKVLVA 59 :::::::::::: ::::::: ::::::::: ::: :::::: d1pvoa3 48 PKAGKTMLLQNIAQSI---AYNHPDCVLMVLL----IDERPEEVTEMQRLVK--GEVVAS 98 d1efpa1 60 EDALYGHRLAEPTAALIVGLAGDYSHIAAPA-----------------TTDAKNVMPRVA 102 :: ::::::::::::::::: ::::::::::: d1pvoa3 99 TF----DEPASRHVQVAEMVIEK--------AKRLVEHKKDVIILLDSITRLARAYNTV- 145 d1efpa1 103 ALLDVMVLSDVSAILDADTFERPIYAGNAIQVVKSKDAKKVFTIRTASFDAAGEGGTAPV 162 d1pvoa3 146 ------------------------------------------------------------ 146 d1efpa1 163 TETAAAADPGLSSWVADEVAE--------------------------------------- 183 d1pvoa3 146 ---------------------VPAVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATA 184 d1efpa1 184 ------------------------------------------------------------ 184 d1pvoa3 185 LIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDYNRSGTRKEELLTTQEELQK 244 d1efpa1 184 -------------------------------------- 184 d1pvoa3 245 MWILRKIIHPMGEIDAMEFLINKLAMTKTNDDFFEMMK 282 TMalign alignment (TM-score: 0.38 Raw score:70.05) d1efpa1 1 -------------------------------------AV---LLL-GE--VTN--GALNR 15 : : : :: ::: d1pvoa3 1 NKILFENLTPLHANSRLRMGSTEDLTARVLDLASPIG-RGQR--GL-IVA-PPKA--GKT 53 d1efpa1 16 DATAKAVAAVK-ALG--DVTVLCAGASAKAAAEEAAKIAGVAKVLVAE--DALYGHRLAE 70 ::::::::::: ::: :::::::: :::::::::::: ::::::::: ::::: : d1pvoa3 54 MLLQNIAQSIAYNHPDCVLMVLLID-ERPEEVTEMQRL-VKGEVVASTFDEPASR-H--- 107 d1efpa1 71 P-TAALIVGLA-GD----YSHIAAPATTDAKNV-----------------------MPRV 101 : ::::::::: :: ::::::: : ::::: :::: d1pvoa3 108 VQVAEMVIEKAKRLVEHKKDVIILL-D-SITRLARAYNTVVPAVLTGGVDANALHRPKRF 165 d1efpa1 102 AALLDVM--------------------------------VLSDV---------------- 113 :: :::: ::::: d1pvoa3 166 FG-AARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAID 224 d1efpa1 114 SAILDADTFERPIYAG-NAIQVVK------------------------SKDAKKVFTIRT 148 ::::: :::::: d1pvoa3 225 -----------YNRSGT-RKEELLTTQEELQKMWILRKIIHPMGEIDA------------ 260 d1efpa1 149 A--S------------------FDAAGEGGTAPVTETAAAADPGLSSWVADEVAE 183 : : d1pvoa3 261 MEFLINKLAMTKTNDDFFEMMK--------------------------------- 282 HHsearch alignment (Probability: 0.01 E-value:1.40) d1efpa1 35 CAGASAKAAAEEAAKIAGVAKVLVAEDALYGHRLAEPTAALIVGLA--GDYSHIAAPATT 92 :::::::::::::::::::::::::::::::::::::::::::::: :::::::::::: d1pvoa3 76 LIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSI 135 d1efpa1 93 DAKNVMPR 100 :::::::: d1pvoa3 136 TRLARAYN 143