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 | d1e0ta3 | Pyruvate kinase, C-terminal domain | PK C-terminal domain-like | Pyruvate kinase C-terminal domain-like | 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 <-- 0.949 --> HitDALI alignment (Z-score: 4.4 Raw score:359.40) d1saya1 1 ----AGRLSVQFGARFLerqqggrgvllggvpgvkpGKVVILG-gGVVGTEAAKMavGLG 55 ::::::::::::: ::::::: :::::::::: ::: d1e0ta3 1 iteaVCRGAVETAEKLD------------------aPLIVVATqgGKSARAVRKY--FPD 40 d1saya1 56 AQVQIFDINVERLSYLETLFgsRVELLYSN--------sAEIETAVAE--------aDLL 99 :::::::::::::::::::: :::::::: ::::::::: ::: d1e0ta3 41 ATILALTTNEKTAHQLVLSK--GVVPQLVKeitstddfyRLGKELALQsglahkgdvVVM 98 d1saya1 100 IGaVLVPGrrapilvpaslveqmrtgsvivdvavdqggcvetlhptshtqptyevfgvvh 159 :: ::::: d1e0ta3 99 VS-GALVP-------------------------------------------------sgt 108 d1saya1 160 ygvpnmpga 168 d1e0ta3 109 tntasvhvl 117 FAST alignment (Normalized score: 3.87 Raw score:542.50) d1saya1 1 A-----GRLSVQFGARFLERQQGGRGVLLGGVPGVKP---GKVVILGGGVVG----TEAA 48 :::::::::: ::::: :::: d1e0ta3 1 -ITEAVCRGAVETAEK---------------------LDAPLIVV-------ATQGGKSA 31 d1saya1 49 KMAVGL--GAQVQIFDINVERLSYLETLFGSRVELLYS------NSAEIETAVAEADLLI 100 :::::: ::::::::::::::::::: :::::::: :::::::::: d1e0ta3 32 RAVRKYFPDATILALTTNEKTAHQLVL--SKGVVPQL-VKEITSTDDFYRLGKE------ 82 d1saya1 101 GAVLVPGRRAPILVPASLVEQ-------MRTGSVIVDVAVDQGGCVETLHPTSHTQPTYE 153 ::::::::: d1e0ta3 83 ---------------------LALQSGLAHKGDVVVM----------------------- 98 d1saya1 154 VFGVVHYGVPNMPGA------------------- 168 d1e0ta3 99 ---------------VSGALVPSGTTNTASVHVL 117 TMalign alignment (TM-score: 0.42 Raw score:71.26) d1saya1 1 AGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVILGGGVVGTEAAKMAVGLGAQVQI 60 :::::::::::::: :::: ::::::::::::::::::: :::::::: d1e0ta3 1 ITEAVCRGAVETAE------KLDA--------PLIVVATQGGKSARAVRKY-FPDATILA 45 d1saya1 61 FDINVERLSYLETLFGSRVELLYSNS--------AEIETAVA----E----ADLLIGAV- 103 ::::::::::::::: ::::::::: :::::::: : :::::::: d1e0ta3 46 LTTNEKTAHQLVLSK--GVVPQLVKEITSTDDFYRLGKELALQSGLAHKGDVVVMVSGAL 103 d1saya1 104 LVP--GRRAPILVPASLVEQMRTGSVIVDVAVDQGGCVETLHPTSHTQPTYEVFGVV--H 159 ::: :: : : : :: d1e0ta3 104 VPSGT-----------------------TN-T-----A--S--------------VHVL- 117 d1saya1 160 YGVPNMPGA 168 d1e0ta3 118 --------- 118 HHsearch alignment (Probability: 0.11 E-value:0.03) d1saya1 43 VGTEAAKMAVGLGAQ-VQIFDINVERLSYLETLFGSRVELLYSNSAEIETAV 93 ::::::::::::::: :::::::::::::::::::::::::::::::::::: d1e0ta3 5 VCRGAVETAEKLDAPLIVVATQGGKSARAVRKYFPDATILALTTNEKTAHQL 56