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 | d1m6ia2 | Apoptosis-inducing factor (AIF) | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | α/β |
| Hit | d1j2ra_ | Hypothetical protein YecD | Isochorismatase-like hydrolases | Isochorismatase-like hydrolases | α/β |
Query <-- 1.321 --> IntermediateDALI alignment (Z-score: 3.4 Raw score:307.80) query 1 -------------------------------GMEN--KKMNLLLfsgdydkALASLIIAN 27 :::: ::::::: ::::::::: d1m6ia2 1 prslsaidragaevksrttlfrkigdfrsleKISRevKSITIIG------gGFLGSELAC 54 query 28 AAREME----IEVTIFCafwGLLLlrdpekasqedkslyeqafssltpreAEELPlskmn 83 :::::: ::::::: :::: ::::: d1m6ia2 55 ALGRKAralgTEVIQLF---PEKG------------------------nmGKILP----- 82 query 84 lggigkkmllemmkeekapKLSDLLSGARKKEVKFY--AXQLsveimgfkkeelfpevqi 141 ::::::::::::::::: :::: d1m6ia2 83 -----------------eyLSNWTMEKVRREGVKVMpnAIVQ-----svgvssgkllikl 120 query 142 mDVKEYlknalESDLQLF---i 160 ::::: ::::::: d1m6ia2 121 kDGRKV-----ETDHIVAavgl 137 FAST alignment (Normalized score: 3.45 Raw score:510.50) query 1 GME------------------------------------NKKMNLLLFSGDYDKALASLI 24 :::::: ::::::::::::: d1m6ia2 1 ---PRSLSAIDRAGAEVKSRTTLFRKIGDFRSLEKISREVKSITI--IGGGFLGSELACA 55 query 25 IANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNL 84 :::::::::::::::: d1m6ia2 56 LGRKARALGTEVIQLF-------------------------------------------- 71 query 85 GGIGKKMLLEMMKEEKAP-------------KLSDLLSGARKKEVKFYAXQLSVEIMGFK 131 ::::::::::::::::: d1m6ia2 72 ------------------PEKGNMGKILPEYLSNWTMEKVRREGVKVM------------ 101 query 132 KEELFPEVQIMDVKEYLKNA-------------------LESDLQLFI----- 160 ::::: ::::::: d1m6ia2 102 --------PNAIV-------QSVGVSSGKLLIKLKDGRKVETDHIV--AAVGL 137 TMalign alignment (TM-score: 0.37 Raw score:59.83) query 1 -------------GMENK-KMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCAFWGLL 46 : :::::: ::::::::::::::::::::::::::::: d1m6ia2 1 PRSLSAIDRAGAE----VKSRTTLF------RKIGDFRSLEKISREVKSITIIGGGFLGS 50 query 47 LLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSD 106 ::: : : d1m6ia2 51 ELA------------------------C------------------------------A- 55 query 107 LLSGARKK-EVKFYAXQLSV--EI-M-G--FK--KEELFP--EVQIM-DVKEYLKNALE- 153 :::::::: ::::::::::: :: : : :: :::::: ::::: ::: :: ::: d1m6ia2 56 LGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVRREGVKVMPNAIV--QS-VGVS 112 query 154 ---S------------DLQLFI--- 160 : :::::: d1m6ia2 113 SGKLLIKLKDGRKVETDHIVAAVGL 137 HHsearch alignment (Probability: 0.03 E-value:0.11) query 4 NKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIF 39 :::::::::::::::::::::::::::::::::::: d1m6ia2 35 REVKSITIIGGGFLGSELACALGRKARALGTEVIQL 70
Intermediate <-- 0.596 --> HitDALI alignment (Z-score: 3.9 Raw score:378.60) d1m6ia2 1 ----------------------------------prSLSAIDR-AGAEVksRTTLFRKI- 24 ::::::: ::::: :::::::: d1j2ra_ 1 mlelnakttalvvidlqegilpfaggphtadevvnrAGKLAAKfRASGQ--PVFLVRVGw 58 d1m6ia2 25 ------------------------------------------------gdfRSLEKISR- 35 :::::::: d1j2ra_ 59 sadyaealkqpvdapspakvlpenwwqhpaalgttdsdieiikrqwgafygTDLELQLRr 118 d1m6ia2 36 -EVKSITIIG--GGFLGSELACALGRKAralgTEVIQLFPekgnMGKILpeYLSNWTM-E 91 ::::::::: :::::::::::::::: :::::::: ::::: ::::::: : d1j2ra_ 119 rGIDTIVLCGisTNIGVESTARNAWELG----FNLVIAED--acSAASA--EQHNNSInH 170 d1m6ia2 92 KVRReGVKVMpnAIVQsvgvssgkllIKLKdgrkvetdhivaavgl 137 :::: ::::: :::: :::: d1j2ra_ 171 IYPR-IARVR--SVEE----------ILNA---------------l 188 FAST alignment (Normalized score: 3.14 Raw score:503.40) d1m6ia2 1 PRS----------------------------------------LSAIDRAGAEVKS---R 17 :::::: : d1j2ra_ 1 ---MLELNAKTTALVVIDLQEGILPFAGGPHTADEVVNRAGKLAAKFRA-------SGQP 50 d1m6ia2 18 TTLFRKIGDF-------------------------------------------------- 27 :::: d1j2ra_ 51 VFLV------RVGWSADYAEALKQPVDAPSPAKVLPENWWQHPAALGTTDSDIEIIKRQW 104 d1m6ia2 28 -----RSLEKISR--EVKSITIIGGGF-LGSELACALGRKARALGTEVIQLFPEKGNMGK 79 :::::::: ::::::::: ::::::::::::::::::::::: d1j2ra_ 105 GAFYGTDLELQLRRRGIDTIVLCG---ISTNIGVESTARNAWELGFNLVIA--------- 152 d1m6ia2 80 I------LPEYLSNWTME-KVRREGVKVMPNAIVQSVGVSSGKLLIKLKDGRKVETDHIV 132 ::::::::::: :::: :::: d1j2ra_ 153 -EDACSAASAEQHNNSINHIYPR-IARV-------------------------------- 178 d1m6ia2 133 AAVGL---------- 137 d1j2ra_ 179 -----RSVEEILNAL 188 TMalign alignment (TM-score: 0.50 Raw score:68.91) d1m6ia2 1 --------------P-R------------------------------------------- 2 : : d1j2ra_ 1 MLELNAKTTALVVIDLQEGILPFAGGPHTADEVVNRAGKLAAKFRASGQPVFLVRVGWSA 60 d1m6ia2 3 -------------------------SLSAIDRAGAEVKSRTTLFRKI--GD-FRSLEKIS 34 ::::: ::::: :: :: :::: :: :::::::: d1j2ra_ 61 DYAEALKQPVDAPSPAKVLPENWWQHPAAL-GTTDS-DI-EI-IKRQWGAFYGTDLELQL 116 d1m6ia2 35 RE--VKSITIIGGG--FLGSELACALGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTM 90 :: :::::::::: :::::::::::::: ::::::::: ::: :::: :::::: d1j2ra_ 117 RRRGIDTIVLCGISTNIGVESTARNAWELG----FNLVIAEDA-CSA-ASAE--QHNNSI 168 d1m6ia2 91 -EKVRREGVKVMPNAIVQSVGVSSGKLLIKLKDGRK-VETDHIVAAVGL 137 :::::: ::::: : :::: :: d1j2ra_ 169 NHIYPRI-ARVRS-V-----------------EEILNAL---------- 188 HHsearch alignment (Probability: 0.18 E-value:0.03) d1m6ia2 35 REVKSITIIGGGFLGSELACALGRKARALGTEVIQLFPEKGNMGKILPEYLSNWTMEKVR 94 :::::::::::::::::::::::: ::::::::::::: ::: :::::::::::::: d1j2ra_ 119 RGIDTIVLCGISTNIGVESTARNA--WELGFNLVIAEDA--CSA--ASAEQHNNSINHIY 172 d1m6ia2 95 REGVKVMPNAIV 106 :::::::::::: d1j2ra_ 173 PRIARVRSVEEI 184