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 | d1gpma2 | GMP synthetase | Class I glutamine amidotransferase-like | Flavodoxin-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 <-- 0.956 --> HitDALI alignment (Z-score: 4.8 Raw score:458.40) d1saya1 1 agrlsvqfgarflerqqggrgvllggvpGVKP-GKVVILG-gGVVGTEAAKMAVGLGAQV 58 :::: ::::::: :::::::::::::::::: d1gpma2 1 ----------------------------ENIHkHRILILDfgSQYTQLVARRVRELGVYC 32 d1saya1 59 QIFDinverlsyletlfgsrvellySNSAEIETAvaEADLLIGAVLVPGR----RAPILV 114 :::: ::::::::: :::::::::::::: :::::: d1gpma2 33 ELWA-------------------wdVTEAQIRDF--NPSGIILSGGPESTteenSPRAPQ 71 d1saya1 115 PaslVEQMrtgSVIVDV--AVDQ------------------------------------- 135 : :::: :::::: :::: d1gpma2 72 Y--vFEAG---VPVFGVcyGMQTmamqlgghveasnerefgyaqvevvndsalvrgieda 126 d1saya1 136 ------------------ggcvetlhpTSHT-------qPTYEVfgVVHYGVPNMP---- 166 :::: ::::: :::::::::: d1gpma2 127 ltadgkplldvwmshgdkvtaipsdfiTVAStescpfaiMANEE--KRFYGVQFHPevth 184 d1saya1 167 -------------------ga 168 d1gpma2 185 trqgmrmlerfvrdicqceal 205 FAST alignment (Normalized score: 3.47 Raw score:643.50) d1saya1 1 AGRLSVQFGARFLERQQGGRGVLLGGVPGVK----PGKVVI-LGGGVVGTEAAKMAVGLG 55 :::::: :::::::::::::::::: d1gpma2 1 -------------------------------ENIHKHRILILDFGSQYTQLVARRVRELG 29 d1saya1 56 AQVQIFDINVERLSYLETLFGSRVELLY----SNSAEIETAVAEADLLIGAVLVPGRRAP 111 ::::: :::::::: :::::::: ::::: d1gpma2 30 VYCEL-----------------------WAWDVTEAQIRD--FNPSGIIL-SGGPE---- 59 d1saya1 112 -------ILVPASLVEQMR-TGSVIVDVAVDQGGCVETLHPTS----------------- 146 :::::::: ::::::: d1gpma2 60 STTEENSPRAPQYVF----EAGVPVFG----------------VCYGMQTMAMQLGGHVE 99 d1saya1 147 ------------------------------------------------------------ 147 d1gpma2 100 ASNEREFGYAQVEVVNDSALVRGIEDALTADGKPLLDVWMSHGDKVTAIPSDFITVASTE 159 d1saya1 147 -HTQPTYEVF--GVVHYGVPNMPGA---------------------------- 168 ::::::: :::::::: d1gpma2 160 SCPFAIMA--NEEKRFYGVQ-----FHPEVTHTRQGMRMLERFVRDICQCEAL 205 TMalign alignment (TM-score: 0.50 Raw score:84.15) d1saya1 1 AGRLSVQFGARFLERQQGGRGVLLGGVPGVK-PGKVVILG-GGVVGTEAAKMAVGLGAQV 58 ::: :::::::: ::::::::::::::::::: d1gpma2 1 ----------------------------ENIHKHRILILDFGSQYTQLVARRVRELGVYC 32 d1saya1 59 QIFDINVERLSYLETLFGSRVELLYSNS-AEIETAVAEADLLIGAVLVPGRR----APIL 113 ::::: ::: :::::: :::::::::: :::: :::: d1gpma2 33 ELWAW--------------------DVTEAQIRDF--NPSGIILSGG-PESTTEENSPRA 69 d1saya1 114 VPASLVEQMRTGSVIVDV-AVDQGGCVETLH----------------------------- 143 :: :::: :: :::::: :::::::::::: d1gpma2 70 PQ-YVFE-AG--VPVFGVCYGMQTMAMQLGGHVEASNEREFGYAQVEVVNDSALVRGIED 125 d1saya1 144 ----------------------P----TSHT--------QPTYEVFGVVHYGVPNMP--- 166 : :::: ::::: ::::::::::: d1gpma2 126 ALTADGKPLLDVWMSHGDKVTAIPSDFITVASTESCPFAIMANE--EKRFYGVQFHPEVT 183 d1saya1 167 -GA------------------- 168 :: d1gpma2 184 HTRQGMRMLERFVRDICQCEAL 205 HHsearch alignment (Probability: 0.49 E-value:0.00) d1saya1 30 VKPGKVVILGGGVV-GTEAAKMAVGLGAQVQIFDIN 64 :::::::::::::: ::::::::::::::::::::: d1gpma2 3 IHKHRILILDFGSQYTQLVARRVRELGVYCELWAWD 38