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 <-- 0.599 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1sqsa_) 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 d1sqsa_ Hypothetical protein SP1951FlavoproteinsFlavodoxin-​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 <-- 0.599 --> Hit
DALI alignment (Z-score: 5.7 Raw score:522.30) d1l7da1 1 agyravidgayefarafPmmmtaagtvppARVLVFG--------vGVAGLQAIATAKR-L 51 : ::::::: ::::::::::::: : d1sqsa_ 1 -----------------M-----------NKIFIYAgvrnhnsktLEYTKRLSSIISSrN 32 d1l7da1 52 GAVVMATDVRA-------atkeqveslggkfitvKKQAEAVLKELVKTDIAITTALIPGK 104 ::::::::::: :::::::::::::::::::::::::: d1sqsa_ 33 NVDISFRTPFNseleisnsdseelfkkgidrqsnADDGGVIKKELLESDIIIISSPVYLQ 92 d1l7da1 105 PAP---VLITEEM----vtkMKPGSVIIDLA------vEAGGncPLSEpgkivVKHGVKI 151 ::: ::::::: ::::::::::: :::: :::: ::::::: d1sqsa_ 93 NVSvdtKNFIERIggwshlfRLAGKFVVTLDvaesngsDNVS-eYLRD---ifSYMGGQI 148 d1l7da1 152 -VGHTN-------VPSR------------------------------------------- 160 ::::: :::: d1sqsa_ 149 lHQVSItnslkdiAEAQlmeatykiedvlegkikykttdyqerayqtlklilenydsehf 208 d1l7da1 161 ------------------------ 161 d1sqsa_ 209 ekmywekkrlfeansleewyyven 232 FAST alignment (Normalized score: 4.30 Raw score:828.80) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGV-----------GVAGLQAIATAK 49 :::::: :::::::::::: d1sqsa_ 1 ----------------------------MNKIFI---YAGVRNHNSKTLEYTKRLSSIIS 29 d1l7da1 50 -RLGAVVMATDVRAATKEQVESLGGKFITVK--------------------------KQA 82 ::::::::::: ::: d1sqsa_ 30 SRNNVDISFRTP-------------------FNSELEISNSDSEELFKKGIDRQSNADDG 70 d1l7da1 83 EAVLKELVKTDIAITTALIPGKPAPVLI-----------TEEMVTKM---KPGSVIIDLA 128 ::::::::::::::::::::::: :::::: :::::::: d1sqsa_ 71 GVIKKELLESDIIIISSPVYLQN-----VSVDTKNFIERIGGWSH--LFRLAGKFVVT-- 121 d1l7da1 129 VEAGGNCPLSEPGKIV--------------------VKHGVK-IVGHTNVPSR------- 160 :::::: :::: d1sqsa_ 122 ----------------LDVAESNGSDNVSEYLRDIFSYMGGQILHQV------SITNSLK 159 d1l7da1 161 ------------------------------------------------------------ 161 d1sqsa_ 160 DIAEAQLMEATYKIEDVLEGKIKYKTTDYQERAYQTLKLILENYDSEHFEKMYWEKKRLF 219 d1l7da1 161 ------------- 161 d1sqsa_ 220 EANSLEEWYYVEN 232 TMalign alignment (TM-score: 0.39 Raw score:62.56) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFG-------VGVAGLQAIATAKR-L- 51 : :::::::: :::::::::::::: : d1sqsa_ 1 ------------------M---------NKIFIYAGVRNHNSKTLEYTKRLSSIISSRNN 33 d1l7da1 52 GAVVMATDVRAATKEQVESLGGKFITVKK------------------------------- 80 ::::::: : :: :::::: d1sqsa_ 34 VDISFRT---P--FN--------SELEISNSDSEELFKKGIDRQSNADDGGVIKKELLES 80 d1l7da1 81 -------------------Q-AEAVL-K----ELVK-TDIAITTALIPGKPAPV--LITE 112 : ::::: : ::: ::::::::::::::::: :::: d1sqsa_ 81 DIIIISSPVYLQNVSVDTKNFIERIGGWSHLF-RLAGKFVVTLDVAESNGSDNVSEYLRD 139 d1l7da1 113 EMVTKMKPGSVIIDLAV-EA--------------GGNCPLSEPGKI-----------VVK 146 :::::::: :::::::: : : :: d1sqsa_ 140 IFSYMGGQ-ILHQVSITN-SLKDIAEAQLMEATY-----------KIEDVLEGKIKY-KT 185 d1l7da1 147 HGV--------------------------------------------KIVGHTNVPSR 160 ::: d1sqsa_ 186 TDYQERAYQTLKLILENYDSEHFEKMYWEKKRLFEANSLEEWYYVEN----------- 232 HHsearch alignment (Probability: 0.16 E-value:0.02) d1l7da1 42 LQAIATAKRLG-AVVMATDVRAATKE-------QVESLGGKFITVKKQAEAVLKELVKTD 93 ::::::::::: :::::::::::::: ::::::::::::::::::::::::::: d1sqsa_ 22 KRLSSIISSRNNVDISFRTPFNSELEISNSDSEELFKKGIDRQSNADDGGVIKKELLESD 81 d1l7da1 94 IAITTA 99 :::::: d1sqsa_ 82 IIIISS 87