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 | d1q1ra2 | Putidaredoxin reductase | FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | α/β |
| Hit | d1otha2 | Ornithine transcarbamoylase | Aspartate/ornithine carbamoyltransferase | ATC-like | α/β |
Query <-- 1.466 --> IntermediateDALI alignment (Z-score: 4.6 Raw score:383.50) query 1 -------------------------------gMENKKMNLLLfsgdydkALASLIIANAA 29 :::::::::: ::::::::::: d1q1ra2 1 rplpvasgavgkannfrylrtledaecirrqlIADNRLVVIG------gGYIGLEVAATA 54 query 30 REMEIEVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreAEELPlskmnlggigk 89 :::::::::::: :::: ::::: d1q1ra2 55 IKANMHVTLLDT---AARV------------------------lERVTA----------- 76 query 90 kmllemmkeekapklSDLLSGARKKEVKFY--AXQLsveimgfkkeelfpevqiMDVKey 147 ::::::::::::::: :::: :::: d1q1ra2 77 -----------ppvsAFYEHLHREAGVDIRtgTQVC---gfemstdqqkvtavlCEDG-- 120 query 148 LKNAleSDLQLFI-- 160 :::: ::::::: d1q1ra2 121 TRLP--ADLVIAGig 133 FAST alignment (Normalized score: 4.48 Raw score:653.70) query 1 -------------------------------GMENKKMNLLLFSGDYDK---ALASLIIA 26 ::::::::: :::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVV---------IGGGYIGLEVA 51 query 27 NAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGG 86 :::::::::::::: d1q1ra2 52 ATAIKANMHVTLLD---------------------------------------------- 65 query 87 IGKKMLLEMMKEEKAP-------------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKE 133 ::::::::::::::::: d1q1ra2 66 ----------------TAARVLERVTAPPVSAFYEHLHREAGVDIR-------------- 95 query 134 ELFPEVQIMDVKEYLKNA----------------------LESDLQLFI---- 160 ::::: ::::::: d1q1ra2 96 ------TGTQV-------CGFEMSTDQQKVTAVLCEDGTRLPADLVI--AGIG 133 TMalign alignment (TM-score: 0.32 Raw score:51.98) query 1 --------------------------------GMENKKMNLLLFSGDYDKALASLIIANA 28 :::::::::::: :::::::::::: d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQL---IADNRLVVIGGG-YIGLEVAATAIK 56 query 29 AREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIG 88 :: ::::: ::: :: :::: : : d1q1ra2 57 AN-----MHVTL---LDT-----------------------AA----RVLE---R--V-- 74 query 89 KK--MLL--EMMKEEKAPKLSDLLSGARKKEV-KF--YA----------------XQLSV 125 :: : ::::::::::: : : : ::::: d1q1ra2 75 TAPP--VSA--------FYEHLHREAGV---DI-RTG-TQVCGFEMSTDQQKVTAVLCED 119 query 126 EIMGFKKEELFPEVQIMDVKEYLKNALESDLQLFI--- 160 : ::: :: : :::: d1q1ra2 120 G--------------TRL--PA---D-----LVIAGIG 133 HHsearch alignment (Probability: 0.05 E-value:0.02) query 20 LASLIIANAAREMEIEVTIF 39 :::::::::::::::::::: d1q1ra2 45 YIGLEVAATAIKANMHVTLL 64
Intermediate <-- 1.595 --> HitDALI alignment (Z-score: 3.9 Raw score:314.50) d1q1ra2 1 rplpvasgavgkannfrylrtledaecirrqlIADNRLVVIG-GGYIGLEVAATAIKANM 59 :::::::::: ::::::::::::::::: d1otha2 1 -------------------------------sLKGLTLSWIGdGNNILHSIMMSAAKFGM 29 d1q1ra2 60 HVTLLDTAARVlervtappvSAFYEHLHREAG------VDIRtgTQVCgfemstdqqkvt 113 ::::::::::: :::::::::::: :::: :::: d1otha2 30 HLQAATPKGYE--------pDASVTKLAEQYAkengtkLLLT--NDPL------------ 67 d1q1ra2 114 avlcedgtrLPADLVIAGIG---------------------------------------- 133 ::::::::::: d1otha2 68 ------eaaHGGNVLITDTWismgreeekkkrlqafqgyqvtmktakvaasdwtflhclp 121 d1q1ra2 134 ------------------------------------------------- 134 d1otha2 122 rkpeevddevfysprslvfpeaenrkwtimavmvslltdyspqlqkpkf 170 FAST alignment (Normalized score: 4.06 Raw score:610.90) d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVV-IGGGYIGLEVAATAIKANM 59 ::::::::: ::::::::::::::::::: d1otha2 1 -------------------------------SLKGLTLSWIGDGNNILHSIMMSAAKFGM 29 d1q1ra2 60 HVTLLDTAARVLERVTAPPV---SAFYEHLHRE------AGVDIRTGTQVCGFEMSTDQQ 110 ::::::::: :::::::::: ::::: d1otha2 30 HLQAATPKG-----------YEPDASVTKLAEQYAKENGTKLLL---------------- 62 d1q1ra2 111 KVTAVLCEDGTR--------LPADLVIAGIG----------------------------- 133 :::::::: d1otha2 63 ------------TNDPLEAAHGGNVLIT---DTWISMGREEEKKKRLQAFQGYQVTMKTA 107 d1q1ra2 134 ------------------------------------------------------------ 134 d1otha2 108 KVAASDWTFLHCLPRKPEEVDDEVFYSPRSLVFPEAENRKWTIMAVMVSLLTDYSPQLQK 167 d1q1ra2 134 --- 134 d1otha2 168 PKF 170 TMalign alignment (TM-score: 0.46 Raw score:60.68) d1q1ra2 1 RPLPVASGAVGKANNFRYLRTLEDAECIRRQLIADNRLVVIG-GGYIGLEVAATAIKANM 59 ::::::::::: ::::::::::::::::: d1otha2 1 -------------------------------SLKGLTLSWIGDGNNILHSIMMSAAKFGM 29 d1q1ra2 60 HVTLLDTAARVLERVTAPPVSAFYEHLHREAG-----VDIRTGTQVCGFEMSTDQQKVTA 114 :::::::::::: :::::::::::: ::::: ::: d1otha2 30 HLQAATPKGYEP--------DASVTKLAEQYAKENGTKLLLT-NDP-------------- 66 d1q1ra2 115 VLCEDGTRLPADLVIAGIG----------------------------------------- 133 :: ::::::::::::: d1otha2 67 -LE---AAHGGNVLITDTWISMGREEEKKKRLQAFQGYQVTMKTAKVAASDWTFLHCLPR 122 d1q1ra2 134 ------------------------------------------------ 134 d1otha2 123 KPEEVDDEVFYSPRSLVFPEAENRKWTIMAVMVSLLTDYSPQLQKPKF 170 HHsearch alignment (Probability: 0.72 E-value:0.00) d1q1ra2 34 ADNRLVVIGGGY-IGLEVAATAIKANMHVTLLDTAARVLERVTAPPVSAFYEHLHREAGV 92 :::::::::::: ::::::::::::::::::::::::: :::::::::::::::::: d1otha2 3 KGLTLSWIGDGNNILHSIMMSAAKFGMHLQAATPKGYE----PDASVTKLAEQYAKENGT 58 d1q1ra2 93 DIRTGTQVCGF 103 ::::::::::: d1otha2 59 KLLLTNDPLEA 69