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 | d1saya1 | L-alanine dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
| Hit | d1jyka_ | CTP:phosphocholine cytidylytransferase LicC | Nucleotide-diphospho-sugar transferases | Nucleotide-diphospho-sugar transferases | α/β |
Query <-- 0.833 --> IntermediateDALI alignment (Z-score: 4.0 Raw score:377.80) query 1 ----------------------GMEN------KKMNLLLfsgdydkALASLIIANAAREM 32 :::: ::::::: :::::::::::::: d1saya1 1 agrlsvqfgarflerqqggrgvLLGGvpgvkpGKVVILG------gGVVGTEAAKMAVGL 54 query 33 EIEVTIFCAfwGLLLLRdpekasqedkslyeqafssltpreaeelplskmnlggigkkml 92 ::::::::: :::::: d1saya1 55 GAQVQIFDI--NVERLS------------------------------------------- 69 query 93 lemmkeekapklsdlLSGARkkEVKFYAXqlsveimgfkkeelfpevqimDVKEYLKNAL 152 ::::: ::::::: :::::::::: d1saya1 70 -------------ylETLFG-sRVELLYS---------------------NSAEIETAVA 94 query 153 ESDLQLFI---------------------------------------------------- 160 :::::::: d1saya1 95 EADLLIGAvlvpgrrapilvpaslveqmrtgsvivdvavdqggcvetlhptshtqptyev 154 query 161 -------------- 161 d1saya1 155 fgvvhygvpnmpga 168 FAST alignment (Normalized score: 3.98 Raw score:652.10) query 1 GME-------------------------------NKKMNLLLFSGDYDK---ALASLIIA 26 :::::: :::::::: d1saya1 1 ---AGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVI---------LGGGVVGTEAA 48 query 27 NAAREMEIEVTIFCAFW-GLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLG 85 :::::::::::::: :::: d1saya1 49 KMAVGLGAQVQIFD---INVER-------------------------------------- 67 query 86 GIGKKMLLEMMKEEKAPKLSDLLS--GARKK----EVKFYAXQLSVEIMGFKKEELFPEV 139 :::: :::::: d1saya1 68 ------------------------LSYLET-LFGSRVELLY------------------- 83 query 140 QIMDVKEYLKNALESDLQLFI--------------------------------------- 160 ::::::::::::::::: d1saya1 84 --SNSAEIETAVAEADLLI--GAVLVPGRRAPILVPASLVEQMRTGSVIVDVAVDQGGCV 139 query 161 ----------------------------- 161 d1saya1 140 ETLHPTSHTQPTYEVFGVVHYGVPNMPGA 168 TMalign alignment (TM-score: 0.40 Raw score:63.78) query 1 ----------------------GME------NKKMNLLLFSGDYDKALASLIIANAAREM 32 ::: :::::::: ::::::::::::::: d1saya1 1 AGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVILG------GGVVGTEAAKMAVGL 54 query 33 EIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKML 92 ::::::::: :::::: : d1saya1 55 GAQVQIFDI--NVERLS------------------------Y------------------ 70 query 93 LEMMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNAL 152 ::::::: ::::::: :::::::::: d1saya1 71 --------------LETLFGS-RVELLYS---------------------NSAEIETAVA 94 query 153 ESDLQLF-I--------------------------------------------------- 160 ::::::: : d1saya1 95 EADLLIGAVLVPGRRAPILVPASLVEQMRTGSVIVDVAVDQGGCVETLHPTSHTQPTYEV 154 query 161 -------------- 161 d1saya1 155 FGVVHYGVPNMPGA 168 HHsearch alignment (Probability: 0.08 E-value:0.01) query 21 ASLIIANAAREMEIEVTIF 39 ::::::::::::::::::: d1saya1 43 VGTEAAKMAVGLGAQVQIF 61
Intermediate <-- 1.001 --> HitDALI alignment (Z-score: 3.2 Raw score:375.10) d1saya1 1 agrlsvqfgarflerqqggrgvllggvpgvKPGKVVILG--------------------- 39 ::::::::: d1jyka_ 1 -----------------------------eIRVKAIILAaglgtrlrpltentpkalvqv 31 d1saya1 40 -ggVVGTEAAKMAVGLGA-QVQIFDIN-VERLSYLETLFgsRVELLYS----------NS 86 ::::::::::::::: :::::::: ::::::::::: ::::::: :: d1jyka_ 32 nqkPLIEYQIEFLKEKGInDIIIIVGYlKEQFDYLKEKY--GVRLVFNdkyadynnfySL 89 d1saya1 87 AEIETAVAEAdLLIGAVL------------------------------------------ 104 :::::::::: ::::::: d1jyka_ 90 YLVKEELANS-YVIDADNylfknmfrndltrstyfsvyredctnewflvygddykvqdii 148 d1saya1 105 -------------------------------vpgrrapilVPASLveqmrtgsvivdvav 133 ::::: d1jyka_ 149 vdskagrilsgvsfwdaptaekivsfidkayvsgefvdlyWDNMV--------------- 193 d1saya1 134 dqggcvetlhptshtqptyevFGVVHYGV-PNMP---------------ga 168 :::::::: :::: d1jyka_ 194 ---------------kdnikeLDVYVEELeGNSIyeidsvqdyrkleeilk 229 FAST alignment (Normalized score: 3.23 Raw score:632.90) d1saya1 1 AGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVILGGG------------------- 41 :::::::: d1jyka_ 1 -----------------------------EIRVKAII----LAAGLGTRLRPLTENTPKA 27 d1saya1 42 -------VVGTEAAKMAVGLG-AQVQIFDI-NVERLSYLETLFGSRVELLYS-------- 84 :::::::::::::: :::::::: :::::::::::: ::::::: d1jyka_ 28 LVQVNQKPLIEYQIEFLKEKGINDIIIIVGYLKEQFDYLKEKY--GVRLVFNDKYADYNN 85 d1saya1 85 --NSAEIETAVAEADLLIGAVLVPGRRAPILVPASLVEQMRT--------------GSVI 128 ::::::::::: :::::: :::: d1jyka_ 86 FYSLYLVKEELAN-SYVIDA----------------------DNYLFKNMFRNDLTRSTY 122 d1saya1 129 VDVAVDQGGCVETLHPTSHTQPTYEV---------------------------------- 154 d1jyka_ 123 --------------------------FSVYREDCTNEWFLVYGDDYKVQDIIVDSKAGRI 156 d1saya1 155 -------------------------------------------FGVVHYGVPNMPGA--- 168 :::::: d1jyka_ 157 LSGVSFWDAPTAEKIVSFIDKAYVSGEFVDLYWDNMVKDNIKELDVYVE--------ELE 208 d1saya1 169 --------------------- 169 d1jyka_ 209 GNSIYEIDSVQDYRKLEEILK 229 TMalign alignment (TM-score: 0.46 Raw score:77.07) d1saya1 1 AGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVILG----------------GG--- 41 :::::::::: :: d1jyka_ 1 -----------------------------EIRVKAIILAAGLGTRLRPLTENTPKALVQV 31 d1saya1 42 ---VVGTEAAKMAVGLGA-QVQIFDIN-VERLSYLETLFGSRVELLYS-N-------S-- 86 ::::::::::::::: :::::::: ::::::::::: ::::::: : : d1jyka_ 32 NQKPLIEYQIEFLKEKGINDIIIIVGYLKEQFDYLKEKY--GVRLVFNDKYADYNNFYSL 89 d1saya1 87 AEIETAVAEADLLIGAVL-----------VPGRRAPILVPASLVEQMRTGSVIVDV-AV- 133 :::::: ::::::::::: :::::::: : d1jyka_ 90 YLVKEE-LANSYVIDADNYLFKNMFRNDL-------------------TRSTYFSVY-RE 128 d1saya1 134 -DQGGCVETLHPTSHTQ-PTYE-------------------------------------- 153 :::: ::::: :: ::: d1jyka_ 129 DCTNE----WFLVY-GDD-YKVQDIIVDSKAGRILSGVSFWDAPTAEKIVSFIDKAYVSG 182 d1saya1 154 --------------V--FGVVHYGV-PNMPG----------------A 168 : :::::::: ::::: d1jyka_ 183 EFVDLYWDNMVKDNIKELDVYVEELEGNSIYEIDSVQDYRKLEEILK- 229 HHsearch alignment (Probability: 0.01 E-value:0.19) d1saya1 17 QGGRGVLLGGVPGVKPGKVVILGGGVVGTEAAKMAVGLGAQVQIFDIN 64 :::::::::::::::::::::::::::::::::::::::::::::::: d1jyka_ 10 AAGLGTRLRPLTENTPKALVQVNQKPLIEYQIEFLKEKGINDIIIIVG 57