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 <-- 1.919 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1spxa_) 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 d1spxa_ Glucose dehydrogenase (5l265)NAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/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 <-- 1.919 --> Hit
DALI alignment (Z-score: 9.4 Raw score:774.00) d1l7da1 1 agyravidgayefaRAFPmmmtaagtvpPARVLVFGV-GVAGLQAIATAKRLGAVVMATD 59 :::: ::::::::: :::::::::::::::::::::: d1spxa_ 1 --------------TRFA----------EKVAIITGSsNGIGRATAVLFAREGAKVTITG 36 d1l7da1 60 VRAATKEQVESLG---------GKFIT----vkKQAEAVLKELV----KTDIAITTAL-- 100 ::::::::::::: ::::: ::::::::::: :::::::::: d1spxa_ 37 RHAERLEETRQQIlaagvseqnVNSVVadvttdAGQDEILSTTLgkfgKLDILVNNAGqs 96 d1l7da1 101 ---iPGKP---APVL--ITEEMVTKM-KPGSVIIDLA-----------------vEAGGn 134 :::: :::: ::::::::: :::::::::: :::: d1spxa_ 97 iesyDATLnlnLRSViaLTKKAVPHLsSTKGEIVNISsiasglhatpdfpyysiaKAAI- 155 d1l7da1 135 cPLSEpgkIVVK--HGVKIVGHTN------------------------------------ 156 :::: :::: :::::::::: d1spxa_ 156 dQYTR-ntAIDLiqHGIRVNSISPglvatgfystmatmkecvpagvmgqpqdiaeviafl 214 d1l7da1 157 --------------VPSR----- 160 :::: d1spxa_ 215 adrktssyiighqlVVDGgssli 237 FAST alignment (Normalized score: 5.41 Raw score:1053.00) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVP----PARVLVF-GVGVAGLQAIATAKRLGAVV 55 ::::::: :::::::::::::::::::: d1spxa_ 1 ----------------------------TRFAEKVAIITGSSNGIGRATAVLFAREGAKV 32 d1l7da1 56 MATDVRAATKEQVESL----------GGKFITV-----KKQAEAVLKELV------KTDI 94 ::::::::::::::: :::::: :::::::::: :::: d1spxa_ 33 TITGRHAERLEETRQ-QILAAGVSEQNVNSVV-ADVTTDAGQDEILST--TLGKFGKLDI 88 d1l7da1 95 AITTALIPGKPAPVLI------------------------TEEMVTKMK-PGSVIIDLAV 129 ::::: :::::: ::::::: d1spxa_ 89 LVNNA-----------GQSIESYDATLNLNLRSVIALTKKAVPHLS---STKGEIVN--- 131 d1l7da1 130 EAGGNCPLSEPGKIV-----------------------------------VKHGVKIVGH 154 :::::::::: d1spxa_ 132 ---------------ISSIASGLHATPDFPYYSIAKAAIDQYTRNTAIDLIQHGIRVNSI 176 d1l7da1 155 TNVPSR------------------------------------------------------ 160 d1spxa_ 177 ------SPGLVATGFYSTMATMKECVPAGVMGQPQDIAEVIAFLADRKTSSYIIGHQLVV 230 d1l7da1 161 ------- 161 d1spxa_ 231 DGGSSLI 237 TMalign alignment (TM-score: 0.65 Raw score:104.28) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGV-GVAGLQAIATAKRLGAVVMATD 59 : ::: ::::::::: :::::::::::::::::::::: d1spxa_ 1 ---------T-----RFA----------EKVAIITGSSNGIGRATAVLFAREGAKVTITG 36 d1l7da1 60 VRAATKEQVESLG---------GKFITV---K-KQAEAVLK-EL---VKTDIAITTAL-- 100 ::::::::::::: :::::: : :::::::: :: ::::::::::: d1spxa_ 37 RHAERLEETRQQILAAGVSEQNVNSVVADVTTDAGQDEILSTTLGKFGKLDILVNNAGQS 96 d1l7da1 101 --IPG--KP--AP-VLIT-EEMVTKMKP--GSVIIDLAV--E--------------A-GG 133 :: :: :: :::: ::::::::: ::::::::: : : :: d1spxa_ 97 IE-SYDATLNLNLRSVIALTKKAVPHLSSTKGEIVNISSIASGLHATPDFPYYSIAKAAI 155 d1l7da1 134 NCPLSEPGKIVVK--HGVKIVG-------------------------------------- 153 :::::: ::::: ::::::: d1spxa_ 156 -DQYTRN-TAIDLIQHGIRVNSISPGLVATGFYSTMATMKECVPAGVMGQPQDIAEVIAF 213 d1l7da1 154 -------------HTNVPSR---- 160 ::::::: d1spxa_ 214 LADRKTSSYIIGHQLVVDGGSSLI 237 HHsearch alignment (Probability: 0.97 E-value:0.00) d1l7da1 27 VPPARVLVFG-VGVAGLQAIATAKRLGAVVMATDVRAATKEQVESLG----G---KF--- 75 :::::::::: :::::::::::::::::::::::::::::::::::: : :: d1spxa_ 3 FAEKVAIITGSSNGIGRATAVLFAREGAKVTITGRHAERLEETRQQILAAGVSEQNVNSV 62 d1l7da1 76 ITVKKQAEAVLKELV-------KTDIAITTALIP----------GKPAPVLITEEMVTKM 118 ::::::::::::::: :::::::::::: :::::::::::::::: d1spxa_ 63 VADVTTDAGQDEILSTTLGKFGKLDILVNNAGQSIESYDATLNLNLRSVIALTKKAVPHL 122 d1l7da1 119 K-PGSVIIDLAVEAGG 133 : :::::::::::::: d1spxa_ 123 SSTKGEIVNISSIASG 138