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 <-- 1.503 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1s3ia2) 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 d1s3ia2 10-​formyltetrahydrofolate dehydrogenase domain 2FormyltransferaseFormyltransferaseα/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 <-- 1.503 --> Hit
DALI alignment (Z-score: 6.2 Raw score:490.30) d1l7da1 1 agyravidgayefarafpmmmtaagtvppARVLVFGVGVAGLQAIATAKRLGAVV-MATD 59 :::::::::::::::::::::::::: :::: d1s3ia2 1 -----------------------------MKIAVIGQSLFGQEVYCQLRKEGHEVvGVFT 31 d1l7da1 60 VRA------atKEQVESLGGKFIT----------vKKQAEAVLKElvKTDIAITTAlipg 103 ::: ::::::::::::: :::::::::: ::::::::: d1s3ia2 32 IPDkdgkadpdGLEAEKDGVPVFKfprwrargqalPEVVAKYQAL--GAELNVLPF---- 85 d1l7da1 104 kpAPVLiTEEMVTKMKpgSVIIDLA------------------------veaggnCPLSE 139 :::: ::::::::: ::::::: ::::: d1s3ia2 86 -cSQFI-PMEVINAPR--HGSIIYHpsllprhrgasainwtlihgdkkggftifwADDGL 141 d1l7da1 140 PGKIVvkhgvkivghtnVPSR--------------------------------------- 160 ::::: :::: d1s3ia2 142 DTGDL-----------lLQKEcevlpddtvstlynrflfpegikgmvqavrliaegtapr 190 d1l7da1 161 ------------- 161 d1s3ia2 191 cpqseegatyegi 203 FAST alignment (Normalized score: 4.37 Raw score:788.10) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAV-VMATD 59 ::::::::::::::::::::::::: ::::: d1s3ia2 1 -----------------------------MKIAVIGQSLFGQEVYCQLRKEGHEVVGVFT 31 d1l7da1 60 VR--------AATKEQVESLGGKFITVKKQ---------AEAVLKELV--KTDIAITTAL 100 ::::::::::::::::: ::::::::: ::::::: d1s3ia2 32 --IPDKDGKADPDGLEAEKDGVPVFKF---PRWRARGQALPEVVAKYQALGAELNVL--- 83 d1l7da1 101 IPGKPAPVL------ITEEMVTKMKPG-SVIIDLAVEAGGNCPLSEP------------- 140 ::::::::: ::::: d1s3ia2 84 ---------PFCSQFIPMEVINAP---RHGSII--------------YHPSLLPRHRGAS 117 d1l7da1 141 --------------GKIVVKHGVK----------IVGHT-------------NVPSR--- 160 :::: :::: :::: d1s3ia2 118 AINWTLIHGDKKGGFTIF------WADDGLDTGDLLLQ-KECEVLPDDTVSTLYNR-FLF 169 d1l7da1 161 ---------------------------------- 161 d1s3ia2 170 PEGIKGMVQAVRLIAEGTAPRCPQSEEGATYEGI 203 TMalign alignment (TM-score: 0.51 Raw score:82.20) d1l7da1 1 AGYRAVIDGAYEFARAFPMMMTAAGTVPPARVLVFGVGVAGLQAIATAKRLGAVV-MATD 59 :::::::::::::::::::::::::: :::: d1s3ia2 1 -----------------------------MKIAVIGQSLFGQEVYCQLRKEGHEVVGVFT 31 d1l7da1 60 VRA----AT--KEQVESLGGKFITVKKQ------A-EAVLKELV-KTDIAITTALIPGKP 105 ::: :: ::::::::::::::::: : :::::::: :::::::::: d1s3ia2 32 IPDKDGKADPDGLEAEKDGVPVFKFPRWRARGQALPEVVAKYQALGAELNVLPFC----- 86 d1l7da1 106 APVLITEEMVTKMKPGSVIIDLA---V---EAG------------------G-NCPL-SE 139 :::: :::::: ::: ::::::: : ::: : :::: :: d1s3ia2 87 SQFI-PMEVIN-APR-HGSIIYHPSLLPRHRGASAINWTLIHGDKKGGFTIFWADDGLDT 143 d1l7da1 140 PGKIVVKHGVKIVGHTN----------------V--PS--R------------------- 160 : :: ::::: : :: : d1s3ia2 144 G-DL--------LLQKECEVLPDDTVSTLYNRFLFPEGIKGMVQAVRLIAEGTAPRCPQS 194 d1l7da1 161 --------- 161 d1s3ia2 195 EEGATYEGI 203 HHsearch alignment (Probability: 0.73 E-value:0.00) d1l7da1 31 RVLVFGVGVAGLQAIATAKRLGAVVMATDVR-------AATKEQVESLGGKFIT------ 77 ::::::::::::::::::::::::::::::: :::::::::::::::: d1s3ia2 2 KIAVIGQSLFGQEVYCQLRKEGHEVVGVFTIPDKDGKADPDGLEAEKDGVPVFKFPRWRA 61 d1l7da1 78 VKKQAEAVLKELV--KTDIAITTALIPGKPAPVLITEEMVTKMKPGSVIIDL 127 ::::::::::::: :::::::: :: ::::::::::::::::::::: d1s3ia2 62 RGQALPEVVAKYQALGAELNVLP-FC-----SQFIPMEVINAPRHGSIIYHP 107