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 | d1nria_ | Hypothetical protein HI0754 | SIS domain | SIS domain | 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 <-- 0.847 --> HitDALI alignment (Z-score: 3.4 Raw score:397.90) d1saya1 1 ----------------------------------------agrlsvqFGARFLErqqgGR 20 ::::::: :: d1nria_ 1 lstliteqrnpnsvdidrqstleivrlmneedklvplaiesclpqisLAVEQIV----QA 56 d1saya1 21 GVllggvpgvkPGKVVILGGGVVGTEAAKMAVGLG-------aQVQIF-DINVERLSYle 72 :: :::::::::::::::::::::::: ::::: ::::::::: d1nria_ 57 FQ--------qGGRLIYIGAGTSGRLGVLDASECPptfgvsteMVKGIiAGGECAIRH-- 106 d1saya1 73 tlfgsrvellySNSAEIETAVAE-aDLLIGAVLVpgrRAPI---LVPAslVEQMrtgsVI 128 :::::::::::: ::::::::: :::: :::: :::: :: d1nria_ 107 -pvegaedntkAVLNDLQSIHFSknDVLVGIAAS--gRTPYviaGLQY-aKSLG---aLT 159 d1saya1 129 VDVA--vDQGGcvetlhptshtqptyevfgvvHYGVPNMPG------------------- 167 :::: :::: ::::::::: d1nria_ 160 ISIAsnpKSEM-----------------aeiaDIAIETIVGpeiltgssrlksgtaqkmv 202 d1saya1 168 ---------------------------------------------a 168 d1nria_ 203 lnmlttasmillgkcyenlmvdvqasneklkaravrivmqatdcnk 248 FAST alignment (Normalized score: 2.82 Raw score:575.70) d1saya1 1 A----------------------------------------------------------- 1 d1nria_ 1 -LSTLITEQRNPNSVDIDRQSTLEIVRLMNEEDKLVPLAIESCLPQISLAVEQIVQAFQQ 59 d1saya1 2 ----------------------------------------------------------GR 3 :: d1nria_ 60 GGRLIYIGAGTSGRLGVLDASECPPTFGVSTEMVKGIIAGGECAIRHPVEGAEDNTKAVL 119 d1saya1 4 LSVQFGARFLERQQGGRGVLLGGVPGVK-----PGKVVI--LGG-GVVGTEAAKMAVGLG 55 ::::: :::::: ::: ::::::::::::::: d1nria_ 120 NDLQS-----------------------IHFSKNDVLVGIAASGRTPYVIAGLQYAKSLG 156 d1saya1 56 AQVQIFDINVERL-SYLETLFGSRVELLYS--------------------NSAEIETAVA 94 :::::::::: ::::::: :::: ::::::: d1nria_ 157 ALTISIASNP---KSEMAEIA---DIAI--ETIVGPEILTGSSRLKSGTAQKMVLNM--- 205 d1saya1 95 EADLLIGAVLVPGRRAPILVPASLVEQMRTGSVIVDVAVDQGGCVETLHPTSHTQPTYEV 154 :::::: d1nria_ 206 -----------------------LTTASM------------------------------- 211 d1saya1 155 FGVVHYGVPNMPGA------------------------------------- 168 d1nria_ 212 --------------ILLGKCYENLMVDVQASNEKLKARAVRIVMQATDCNK 248 TMalign alignment (TM-score: 0.48 Raw score:80.31) d1saya1 1 ----------------------------------A---GRL--S--VQFGARFLERQQGG 19 : : : ::::::: : d1nria_ 1 LSTLITEQRNPNSVDIDRQSTLEIVRLMNEEDKLVPLA--IESCLP--QISLAVE----Q 52 d1saya1 20 RGVLLGGVPGVKPGKVVILGGGVVGTEAAKMAVGLG--------AQVQIFDINVERLSYL 71 ::::: : :: ::::::::::::::::::::::: ::::::::::::: :: d1nria_ 53 IVQAF-Q---QG-GRLIYIGAGTSGRLGVLDASECPPTFGVSTEMVKGIIAGGECAI-RH 106 d1saya1 72 --------ETLFGSRVELLYSNSAEIET--AVAEADLLIGAVLVPGRRAP--ILVPASLV 119 ::::::::: :::::::::::::: :::: :::::::: d1nria_ 107 PVEGAEDN-----------TKAVLNDLQSIHFSKNDVLVGIAAS--GRTPYVIAGLQYAK 153 d1saya1 120 EQMRTGSVIVDVAVDQGGCVETLHPTSHTQPTYEVFGVVHYGVPNM-------------- 165 :::: ::::::::::::::::: :::::::: d1nria_ 154 SLGA--LTISIASNPKSEMAEIA---------------DIAIETIVGPEILTGSSRLKSG 196 d1saya1 166 -P--GA---------------------------------------------- 168 : :: d1nria_ 197 TAQKMVLNMLTTASMILLGKCYENLMVDVQASNEKLKARAVRIVMQATDCNK 248 HHsearch alignment (Probability: 0.78 E-value:0.00) d1saya1 32 PGKVVILGGGVVGTEAAKMA----VGLGAQVQIFDI-----NVERLSYLETLFGSRVELL 82 :::::::::::::::::::: :::::::::::: ::::::::::::::: d1nria_ 60 GGRLIYIGAGTSGRLGVLDASECPPTFGVSTEMVKGIIAGGECAIRHPVEGAEDNT---- 115 d1saya1 83 YSNSAEIET-AVAEADLLIGAVLVPGRRAPILVPASLVEQMRTGSVIVDVAVDQGGCVE 140 ::::::::: :::::::::: :: ::::::::::: ::::::::::::::::::::::: d1nria_ 116 KAVLNDLQSIHFSKNDVLVG-IA-ASGRTPYVIAG-LQYAKSLGALTISIASNPKSEMA 171