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 <-- 1.100 --> Intermediate <-- 1.157 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1rkda_) through the intermediate protein (d1l7da1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1l7da1 Nicotinamide nucleotide transhydrogenase dI componentNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β
Hit d1rkda_ RibokinaseRibokinase-​likeRibokinase-​likeα/β

Supporting Alignments

Query <-- 1.100 --> Intermediate
DALI alignment (Z-score: 5.1 Raw score:345.40) query 1 ---------------GMEN----------KKMNLLLfsgdydkALASLIIANAAREMEIE 35 :::: ::::::: ::::::::::::::::: d1l7da1 1 agyravidgayefarAFPMmmtaagtvppARVLVFG------vGVAGLQAIATAKRLGAV 54 query 36 VTIFCafwgLLLLrdpekasqedkslyeqafssltpreaeelplskmnlggigkkmllem 95 ::::: :::: d1l7da1 55 VMATD----VRAA----------------------------------------------- 63 query 96 mkeekapklsdllSGARKKEVKFYAXQLsveimgfkkeelfpevqimDVKEYLKNALESD 155 ::::::::::::::: ::::::::::::: d1l7da1 64 -----------tkEQVESLGGKFITVKK-------------------QAEAVLKELVKTD 93 query 156 LQLFI------------------------------------------------------- 160 ::::: d1l7da1 94 IAITTalipgkpapvliteemvtkmkpgsviidlaveaggncplsepgkivvkhgvkivg 153 query 161 ------- 161 d1l7da1 154 htnvpsr 160 FAST alignment (Normalized score: 3.90 Raw score:624.80) query 1 GME----------------------------NKKMNLLLFSGDYDK---ALASLIIANAA 29 :::::: ::::::::::: d1l7da1 1 ---AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLV---------FGVGVAGLQAIATA 48 query 30 REMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGK 89 :::::::::: d1l7da1 49 KRLGAVVMAT-------------------------------------------------- 58 query 90 KMLLEMMKEEKAPKLSD-----LLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIM-- 142 :::::::::::::: d1l7da1 59 -----------------DVRAATKEQVESLGGKFIT----------------------VK 79 query 143 -DVKEYLKNALESDLQLFI----------------------------------------- 160 :::::::::::::::: d1l7da1 80 KQAEAVLKELVKTDIAI--TTALIPGKPAPVLITEEMVTKMKPGSVIIDLAVEAGGNCPL 137 query 161 ----------------------- 161 d1l7da1 138 SEPGKIVVKHGVKIVGHTNVPSR 160 TMalign alignment (TM-score: 0.23 Raw score:37.44) query 1 ------------------------------GMENKKMNLLLFSGDYDKALASLIIANAAR 30 d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPA------------------------------ 30 query 31 EMEIEVTIFCAFWGLLLLRDPEK--AS--QEDKSLYEQAFSSLTPREAE----------- 75 :: ::: ::::: :: :::::: : :: :: ::: d1l7da1 31 -----------RV-LVF-GVGVAGLQAIATAKRLG-A--VV--MA-TDVRAATKEQVESL 71 query 76 ---ELPL-SK-----------------MNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKK 114 :::: :: ::::::: d1l7da1 72 GGKFITVKKQAEAVLKELVKTDIAITT--------------------------ALIPGKP 105 query 115 EVKFYA---X----QLSVEIMGFKKEELFPE---V----Q----IMDVKEY--------- 147 :::::: : :::: : : :::: : : ::::::: d1l7da1 106 APVLITEEMVTKMKPGSV----I-I--DLAVEAGGNCPLSEPGKIVVKHGVKIVGHTNVP 158 query 148 --LKNALESDLQLFI 160 d1l7da1 159 SR------------- 160 HHsearch alignment (Probability: 0.09 E-value:0.01) query 21 ASLIIANAAREMEIEVTIF 39 ::::::::::::::::::: d1l7da1 40 AGLQAIATAKRLGAVVMAT 58
Intermediate <-- 1.157 --> Hit
DALI alignment (Z-score: 5.6 Raw score:560.30) d1l7da1 1 agyravidgayefarafpmmmtaagtvpPARVLVFGVG---------------------- 38 :::::::::: d1rkda_ 1 ----------------------------AGSLVVLGSInadhilnlqsfptpgetvtgnh 32 d1l7da1 39 ------VAGLQAIATAKRLGAVVMATDVR------aATKEQVESLGGKFIT--------- 77 ::::::::::::::::::::::: ::::::::::::::: d1rkda_ 33 yqvafgGKGANQAVAAGRSGANIAFIACTgddsigeSVRQQLATDNIDITPvsvikgest 92 d1l7da1 78 -------------------------vkKQAEAVLKELVKTDIAITTALipgkpaPVLIT- 111 ::::::::::::::::::::: ::::: d1rkda_ 93 gvalifvngegenvigihaganaalspALVEAQRERIANASALLMQLE----spLESVMa 148 d1l7da1 112 -eEMVTKMKpgSVIIDLA-vEAGGncPLSEpgkivvkhgvKIVGHTN------------- 156 ::::::: ::::::: :::: :::: ::::::: d1rkda_ 149 aaKIAHQNK--TIVALNPapARELpdELLA---------lVDIITPNeteaekltgirve 197 d1l7da1 157 ---------------------VPSR----------------------------------- 160 :::: d1rkda_ 198 ndedaakaaqvlhekgirtvlITLGsrgvwasvngegqrvpgfrvqavdtiaagdtfnga 257 d1l7da1 161 ------------------------------------------------- 161 d1rkda_ 258 litalleekplpeairfahaaaaiavtrkgaqpsvpwreeidafldrqr 306 FAST alignment (Normalized score: 4.11 Raw score:908.90) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVG---------------------- 38 :::::: d1rkda_ 1 ----------------------------AGSLVV----LGSINADHILNLQSFPTPGETV 28 d1l7da1 39 ----------VAGLQAIATAKRLGAVVMATDV-------RAATKEQVESLGGKFITVK-- 79 ::::::::::::::::::::: :::::::::::::: d1rkda_ 29 TGNHYQVAFGGKGANQAVAAGRSGANIAFIA-CTGDDSIGESVRQQLATDNID-----IT 82 d1l7da1 80 -------------------------------------KQAEAVLKELVKTDIAITTALIP 102 :::::::::::::::::: d1rkda_ 83 PVSVIKGESTGVALIFVNGEGENVIGIHAGANAALSPALVEAQRERIANASALLM----- 137 d1l7da1 103 GKPAPVLI--------TEEMVTKMK---PGSVIIDLAVEAGGNCPLSEPGKIVVKHG--- 148 ::::::: ::::::: d1rkda_ 138 --------QLESPLESVMAAAKI--AHQNKTIVAL----------------------NPA 165 d1l7da1 149 -------------VKIVGHTNVPSR----------------------------------- 160 ::::::: d1rkda_ 166 PARELPDELLALVDIITPNE-----TEAEKLTGIRVENDEDAAKAAQVLHEKGIRTVLIT 220 d1l7da1 161 ------------------------------------------------------------ 161 d1rkda_ 221 LGSRGVWASVNGEGQRVPGFRVQAVDTIAAGDTFNGALITALLEEKPLPEAIRFAHAAAA 280 d1l7da1 161 -------------------------- 161 d1rkda_ 281 IAVTRKGAQPSVPWREEIDAFLDRQR 306 TMalign alignment (TM-score: 0.49 Raw score:78.46) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGV-G--------------------- 38 :: ::::::::: : d1rkda_ 1 -----------------AG---------SLVVLGSINADHILNLQSFPTPGETVTGNHYQ 34 d1l7da1 39 ---VAG-LQAIATAKR--LGAVVMATDVRA-A-TKE-QVE-SL----G-G-KF------- 75 ::: ::::::::: :::::::: :: : :: ::: :: : : :: d1rkda_ 35 VAFGGKGANQAVAAGRSGANIAFIAC--TGDDS-IGESVRQQLATDNIDITPVSVIKGES 91 d1l7da1 76 ----------------------I--TVKK---------------------QAEAVLKELV 90 : :::: :::::::::: d1rkda_ 92 TGVALIFVNGEGENVIGIHAGANAALSPALVEAQRERIANASALLMQLESPLESVMAAAK 151 d1l7da1 91 -K-----TDIAITTALIPGKPAPVLITEEMVTKMKPGSVIIDLAVEAGGNCPLSE-P--G 141 : :::::::: : ::::::::::: ::::: ::::::::::: : : d1rkda_ 152 IAHQNKTIVALNPAP------A-RELPDELLALV---DIITP--NETEAEKLTGIRVEND 199 d1l7da1 142 --KI--V---VK-HGVKIVGHTNVPS-------------R-------------------- 160 :: : :: ::::::::::::: : d1rkda_ 200 EDAAKAAQVLHEKGIRTVLITLGSRGVWASVNGEGQRVPGFRVQAVDTIAAGDTFNGALI 259 d1l7da1 161 ----------------------------------------------- 161 d1rkda_ 260 TALLEEKPLPEAIRFAHAAAAIAVTRKGAQPSVPWREEIDAFLDRQR 306 HHsearch alignment (Probability: 0.03 E-value:0.09) d1l7da1 35 FGVGVAGLQAIATAKRLGAVVMATD 59 ::::::::::::::::::::::::: d1rkda_ 35 VAFGGKGANQAVAAGRSGANIAFIA 59