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 | d1nt2a_ | Fibrillarin homologue | S-adenosyl-L-methionine-dependent methyltransferases | S-adenosyl-L-methionine-dependent methyltransferases | 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 <-- 1.192 --> HitDALI alignment (Z-score: 6.7 Raw score:587.90) d1saya1 1 ----------------------------------------AGRLsvqfgarflerqqggr 20 :::: d1nt2a_ 1 kelmrnvyllddtlvtkskygshygekvfdgyrewvpwrsKLAA---------milkghr 51 d1saya1 21 gVLLGgvpgvkPGKVVILGGGvvgTEAAKMAVGLG--AQVQIFDINVERLSYLETLFG-- 76 :::: :::::::::: ::::::::::: ::::::::::::::::::::: d1nt2a_ 52 lKLRG------DERVLYLGAA--sGTTVSHLADIVdeGIIYAVEYSAKPFEKLLELVRer 103 d1saya1 77 SRVELLYSN---SAEIETAVAEADLLIGAVLVpgrRAPI-LVPAslVEQM-RTGSVIVDV 131 ::::::::: :::::::::::::::::::: :::: :::: :::: ::::::::: d1nt2a_ 104 NNIIPLLFDaskPWKYSGIVEKVDLIYQDIAQ---KNQIeILKA-nAEFFlKEKGEVVIM 159 d1saya1 132 AVDQG-------gcvetlHPTShtqPTYEVfgvvhygvPNMPGA------------- 168 ::::: :::: ::::: :::::: d1nt2a_ 160 VKARSidstaepeevfksVLKE--mEGDFK-----ivkHGSLMPyhrdhifihayrf 209 FAST alignment (Normalized score: 4.83 Raw score:905.00) d1saya1 1 ----------------------------------------AGRLSVQFGARFLERQQGGR 20 :::: d1nt2a_ 1 KELMRNVYLLDDTLVTKSKYGSHYGEKVFDGYREWVPWRSKLAA---------------- 44 d1saya1 21 GVLLGGVPGVK------------PGKVVILGG--GVVGTEAAKMAVG-LGAQVQIFDINV 65 ::::::::: :::::::::: :::::::::::: d1nt2a_ 45 -----------MILKGHRLKLRGDERVLYLGAASGTTVSHLADI---VDEGIIYAVEYSA 90 d1saya1 66 ERLSYLETLF---GSRVELLYSNSA-------EIETAVA--EADLLIGAVLVPGRRAPIL 113 ::::::::: :::::::: ::::: :::::::::: d1nt2a_ 91 KPFEKLLEL-VRERNNIIPLL----FDASKPWKYSGI--VEKVDLIYQDIA--------- 134 d1saya1 114 V-------PASLVE-QMRTGSVIVDVAVDQGGCVETLHPTSHTQPTYEVFGVV------- 158 :::::: :::::::::: d1nt2a_ 135 -QKNQIEILKANAEFFLKEKGEVVI----------------------------MVKARSI 165 d1saya1 159 -----------------------HYGVPNMPGA----------------- 168 :::: d1nt2a_ 166 DSTAEPEEVFKSVLKEMEGDFKIVKHG------SLMPYHRDHIFIHAYRF 209 TMalign alignment (TM-score: 0.59 Raw score:98.56) d1saya1 1 ----------------------------------------AGRLSVQ--FGARFLERQQG 18 ::::::: :::: d1nt2a_ 1 KELMRNVYLLDDTLVTKSKYGSHYGEKVFDGYREWVPWRSKLAAMILKGHRLK------- 53 d1saya1 19 GRGVLLGGVPGVKPGKVVILGGGVVGTEAAKMAVGL-G-AQVQIFDINVERLSYLETLFG 76 :: : ::::::::::: :::::::::: : ::::::::::::::::::::: d1nt2a_ 54 ---LR-G------DERVLYLGAAS--GTTVSHLADIVDEGIIYAVEYSAKPFEKLLELVR 101 d1saya1 77 -SR-VELLYSN--S--AEIETAVAEADLLIGAVLVPGRRAP-ILVPASLVEQ-MRTGSVI 128 :: ::::::: : :::::: :::::::::::: ::: ::::: :::: ::::::: d1nt2a_ 102 ERNNIIPLLFDASKPWKYSGIV-EKVDLIYQDIAQ---KNQIEILKA-NAEFFLKEKGEV 156 d1saya1 129 VDVAVDQ-G-----------GCVETLHPT-SHTQPTYEVFGVVHYGVPNMPGA------- 168 ::::::: : :::: :::: :::::::::::: d1nt2a_ 157 VIMVKARSIDSTAEPEEVFK-----SVLKE-----MEGD--FKIVKHGSLMPYHRDHIFI 204 d1saya1 169 ----- 169 d1nt2a_ 205 HAYRF 209 HHsearch alignment (Probability: 0.91 E-value:0.00) d1saya1 31 KPGKVVILGGGVVGTEAAKMAVGL-GAQVQIFDINVERLSYLETLFGS--RVELLYSNSA 87 :::::::::::: ::::::::::: ::::::::::::::::::::::: :::::::::: d1nt2a_ 56 GDERVLYLGAAS-GTTVSHLADIVDEGIIYAVEYSAKPFEKLLELVRERNNIIPLLFDAS 114 d1saya1 88 EIETAVA---EADLLIGAVLVPGRRAPILVPASLVEQMRTGSVIV 129 ::::::: :::::::::::: ::: :::::::::::::::::: d1nt2a_ 115 KPWKYSGIVEKVDLIYQDIAQK-NQI-EILKANAEFFLKEKGEVV 157