HorA Server Transitive Detail

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


Query <-- 0.833 --> Intermediate <-- 1.134 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1af7a2) through the intermediate protein (d1saya1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1saya1 L-​alanine dehydrogenaseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β
Hit d1af7a2 Chemotaxis receptor methyltransferase CheR,​ C-​terminal domainS-​adenosyl-​L-​methionine-​dependent methyltransferasesS-​adenosyl-​L-​methionine-​dependent methyltransferasesα/β

Supporting Alignments

Query <-- 0.833 --> Intermediate
DALI 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 <-- 1.134 --> Hit
DALI alignment (Z-score: 7.1 Raw score:629.90) d1saya1 1 ------AGRLSVQFGARFLerqqggRGVLlggvpgvKPGKVVILGGGvvgTEAAKMAVGL 54 ::::::::::::: :::: ::::::::::: :::::::::: d1af7a2 1 nltaffREAHHFPILAEHA------RRRH-------GEYRVWSAAAS--tGEEPYSIAIT 45 d1saya1 55 G----------AQVQIFDINVERLSYLETL------------------------------ 74 : ::::::::::::::::::: d1af7a2 46 LadalgmapgrWKVFASDIDTEVLEKARSGiyrlselktlspqqlqryfmrgtgpheglv 105 d1saya1 75 -----fGSRVELLYSN----SAEIetavAEADLLIGA-VLVPGRR--APILVPaSLVEQM 122 :::::::::: :::: ::::::::: ::::::: :::::: :::::: d1af7a2 106 rvrqelANYVEFSSVNllekQYNV---pGPFDAIFCRnVMIYFDKttQEDILR-RFVPLL 161 d1saya1 123 RTGSVIVDVaVDQGG--cveTLHPtshtqptyevfgvvhYGVPnmpga 168 ::::::::: ::::: :::: :::: d1af7a2 162 KPDGLLFAG-HSENFsnlvrEFSL---------------RGQTvyals 193 FAST alignment (Normalized score: 5.39 Raw score:970.70) d1saya1 1 ------AGRLSVQFGARFLERQQGGRGVLLGGVPGV----KPGKVVILGG--GVVGTEAA 48 ::::::::::::: :::::::::: :::::::: d1af7a2 1 NLTAFFREAHHFPILAEHA-----------------RRRHGEYRVWSAAASTGEEPYSIA 43 d1saya1 49 KMAVGL-------GAQVQIFDINVERLSYLETLF-------------------------- 75 ::::: :::::::::::::::::: d1af7a2 44 ITLAD-ALGMAPGRWKVFASDIDTEVLEKAR---SGIYRLSELKTLSPQQLQRYFMRGTG 99 d1saya1 76 ------------GSRVELLYSNSAEIETAV----------AEADLLIGAVLVPGRRAPIL 113 ::::::::: :::::::: d1af7a2 100 PHEGLVRVRQELANYVEFSSV---------NLLEKQYNVPGPFDAIFC------------ 138 d1saya1 114 V--------------PASLVE-QMRTGSVIVDVAVDQGGCV-----------ETLHPTSH 147 :::::: ::::::::: :::: d1af7a2 139 -RNVMIYFDKTTQEDILRRFVPLLKPDGLLF----------AGHSENFSNLVREFS---- 183 d1saya1 148 TQPTYEVFGVVHYGVPNMPGA---------- 168 d1af7a2 184 ---------------------LRGQTVYALS 193 TMalign alignment (TM-score: 0.59 Raw score:98.99) d1saya1 1 ------AGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVILGGGVVGTEAAKMAVG- 53 :::::::::::::: ::: :::::::::::: ::::::::: d1af7a2 1 NLTAFFREAHHFPILAEHAR------RRH-------GEYRVWSAAAST--GEEPYSIAIT 45 d1saya1 54 LG---------AQVQIFDINVERLSYLETL------------------------------ 74 :: ::::::::::::::::::: d1af7a2 46 LADALGMAPGRWKVFASDIDTEVLEKARSGIYRLSELKTLSPQQLQRYFMRGTGPHEGLV 105 d1saya1 75 -F-G--SR-VELLYSN--S-AEIETAVAEADLLIGAVLVPGRRA--PI-LVPASLVEQMR 123 : : :: ::::::: : ::: :: ::::::::::::: ::: :: ::::::::::: d1af7a2 106 RVRQELANYVEFSSVNLLEKQYN-VP-GPFDAIFCRNVMI-YFDKTTQEDILRRFVPLLK 162 d1saya1 124 TGSVIVDVAVDQGG-CVETL-HPTSHTQP--TYEVFGVVHYGVPNMPGA 168 ::::::::: :::: :::: ::: :: ::::: d1af7a2 163 PDGLLFAGH-SENFS-NLVREFSL---RGQTVYALS------------- 193 HHsearch alignment (Probability: 0.93 E-value:0.00) d1saya1 28 PGVKPGKVVILGGGVV--GTEAAKMAVG------LGAQVQIFDINVERLSYLETLF-G-- 76 :::::::::::::::: :::::::::: :::::::::::::::::::::: : d1af7a2 21 RRHGEYRVWSAAASTGEEPYSIAITLADALGMAPGRWKVFASDIDTEVLEKARSGIYRLS 80 d1saya1 77 --------------SRVE----LLYSNSAEIET---------------AVAEADLLIGAV 103 :::: ::::::::::: :::::::::::: d1af7a2 81 ELKTLSPQQLQRYFMRGTGPHEGLVRVRQELANYVEFSSVNLLEKQYNVPGPFDAIFCRN 140 d1saya1 104 L-V--PGRRAPILVPASLVEQMRTGSVIVD 130 : : ::::: ::::::::::::::::::: d1af7a2 141 VMIYFDKTTQ-EDILRRFVPLLKPDGLLFA 169