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 | d1x9ga_ | Ribonuclease MAR1 | Isochorismatase-like hydrolases | Isochorismatase-like hydrolases | 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 <-- 1.396 --> HitDALI alignment (Z-score: 4.0 Raw score:356.50) d1nhpa2 1 ----------------------------------------ipGKDL-----DNIYLMRG- 14 :::: :::::::: d1x9ga_ 1 msrlmphyskgktaflcvdlqeafskrienfancvfvanrlaRLHEvvpenTKYIVTEHy 60 d1nhpa2 15 -------------------------rqwAIKLKQKTVDpeVNNVVVIGSG--YIGIEAAE 47 :::::::::: :::::::::: :::::::: d1x9ga_ 61 pkglgrivpeitlpktahliektrfscvVPQVEELLED--VDNAVVFGIEghACILQTVA 118 d1nhpa2 48 AFAKAGKKVTVIDILdrpLGVYldKEFTDVLTEEMEAN--NITIATgetveryegdgrvq 105 ::::::::::::::: :::: :::::::::::::: :::::: d1x9ga_ 119 DLLDMNKRVFLPKDG--lGSQK--KTDFKAAIKLMSSWgpNCEITT-------------- 160 d1nhpa2 106 kvVTDKNA--------------ydadlvvvav 123 :::::: d1x9ga_ 161 seSILLQMtkdamdpnfkriskllkeeppipl 192 FAST alignment (Normalized score: 3.90 Raw score:600.10) d1nhpa2 1 IPGKDLD----------------------------------------------------N 8 : d1x9ga_ 1 -------MSRLMPHYSKGKTAFLCVDLQEAFSKRIENFANCVFVANRLARLHEVVPENTK 53 d1nhpa2 9 IYLM-------------------------------RGRQWAIKLKQKTVDPEVNNVVVI- 36 ::: :::::::::: :::::::: d1x9ga_ 54 YIV-TEHYPKGLGRIVPEITLPKTAHLIEKTRFSCVVPQVEELLE------DVDNAVVFG 106 d1nhpa2 37 -GSGYIGIEAAEAFAKAGKKVTVIDILDRPLGVY-----LDKEFTDVLTEEMEA--NNIT 88 :::::::::::::::::::::::: ::::::::::::::: :::: d1x9ga_ 107 IEGHACILQTVADLLDMNKRVFLPK---------DGLGSQKKTDFKAAIKLMSSWGPNCE 157 d1nhpa2 89 IATGETVERYEGDGRVQKVVTDKNAYDADLVVVAV------------------------- 123 :: d1x9ga_ 158 IT---------------------------------TSESILLQMTKDAMDPNFKRISKLL 184 d1nhpa2 124 -------- 124 d1x9ga_ 185 KEEPPIPL 192 TMalign alignment (TM-score: 0.53 Raw score:65.37) d1nhpa2 1 --------------------------------------I---PGKD--L--DNIYLMR-- 13 : :::: : ::::::: d1x9ga_ 1 MSRLMPHYSKGKTAFLCVDLQEAFSKRIENFANCVFVANRLARLHEVVPENTKYIVTEHY 60 d1nhpa2 14 --------------------GR----QW-AIKLKQKTVDPEVNNVVVIGS-G-YIGIEAA 46 :: : :::::::: : :::::::::: : ::::::: d1x9ga_ 61 PKGLGRIVPEITLPKTAHLIEKTRFS-CVVPQVEELL-E-DVDNAVVFGIEGHACILQTV 117 d1nhpa2 47 EAFAKAGKKVTVIDILDRPLGV-YLDKEFTDVLTEEMEANNITIATGETVERYEGDGRVQ 105 :::::::::::::::: ::::: :::: ::::::::::: ::::: : d1x9ga_ 118 ADLLDMNKRVFLPKDG-LGSQKKTDFK-AAIKLMSSWGP-NCEIT--T------------ 160 d1nhpa2 106 KVVTDKNA-YD------------------------ADLVVVAV 123 ::::: :: d1x9ga_ 161 ---SESILLQMTKDAMDPNFKRISKLLKEEPPIPL-------- 192 HHsearch alignment (Probability: 0.11 E-value:0.04) d1nhpa2 24 KTVDPEVNNVVVIGSGYIGIE--AAEAFAKAGKKVTVIDILDRPLGVYLDKEFTDVLTEE 81 ::::::::::::::::::::: :::::::::::::::::::: ::::::::::::: d1x9ga_ 93 EELLEDVDNAVVFGIEGHACILQTVADLLDMNKRVFLPKDGLG----SQKKTDFKAAIKL 148 d1nhpa2 82 MEANN--ITIATG 92 ::::: :::::: d1x9ga_ 149 MSSWGPNCEITTS 161