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 <-- 1.215 --> Intermediate <-- 0.965 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1dv1a2) through the intermediate protein (d1nhpa2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1nhpa2 NADH peroxidaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/β
Hit d1dv1a2 Biotin carboxylase (BC),​ N-​terminal domainPreATP-​grasp domainPreATP-​grasp domainα/β

Supporting Alignments

Query <-- 1.215 --> Intermediate
DALI alignment (Z-score: 4.1 Raw score:328.10) query 1 --------------------------GMENKKMNLLLfsgdydkALASLIIANAAREMEI 34 ::::::::::: :::::::::::::::: d1nhpa2 1 ipgkdldniylmrgrqwaiklkqktvDPEVNNVVVIG------sGYIGIEAAEAFAKAGK 54 query 35 EVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreAEELPlskmnlggigkkmlle 94 ::::::: :::: ::::: d1nhpa2 55 KVTVIDI---LDRP------------------------lGVYLD---------------- 71 query 95 mmkeekapKLSDLLSGARKKEVKFYAXqlsveimgfkkeelfpevqimDVKEyLKNAleS 154 ::::::::::::::::::: :::: :::: : d1nhpa2 72 ------keFTDVLTEEMEANNITIATG------etveryegdgrvqkvVTDK-NAYD--A 116 query 155 DLQLF-i 160 ::::: d1nhpa2 117 DLVVVav 123 FAST alignment (Normalized score: 4.27 Raw score:599.40) query 1 -------------------------GMEN-KKMNLLLFSGDYDK---ALASLIIANAARE 31 :::: ::::: ::::::::::::: d1nhpa2 1 IPGKDLDNIYLMRGRQWAIKLKQKTVDPEVNNVVV---------IGSGYIGIEAAEAFAK 51 query 32 MEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKM 91 :::::::: d1nhpa2 52 AGKKVTVI---------------------------------------------------- 59 query 92 LLEMMKEEKAP--------------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFP 137 ::::::::::::::::: d1nhpa2 60 -----------DILDRPLGVYLDKEFTDVLTEEMEANNITIA------------------ 90 query 138 EVQIMDVKEYLKNA------------------LESDLQLFI-- 160 ::::: :::::::: d1nhpa2 91 --TGETV-------ERYEGDGRVQKVVTDKNAYDADLVVV-AV 123 TMalign alignment (TM-score: 0.33 Raw score:53.16) query 1 ------------------------GMENKK-MNLLLFSGDYDKALASLIIANAAREMEIE 35 :::::: ::::: ::: :::::::::::::: : d1nhpa2 1 IPGKDLDNIYLMRGRQWAIKLKQKTVDPEVNNVVVI-GSG-YIGIEAAEAFAKAG----K 54 query 36 VTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKK--MLL 93 ::::: ::: : :: :::: :: : d1nhpa2 55 KVTVI---DIL------------------------D-RP-LGVY---------LDKE--F 74 query 94 --EMMKEEKAPKLS-DLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVKE--YL 148 ::: ::::::: : ::::: :: ::::: :: d1nhpa2 75 TD---------VLTEEMEANNI---T-IATGE-TV----------------ERYEGDGRV 104 query 149 KNA--------LESDLQLFI- 160 ::: :: ::::: d1nhpa2 105 QKVVTDKNAYD-AD-LVVVAV 123 HHsearch alignment (Probability: 0.05 E-value:0.02) query 20 LASLIIANAAREMEIEVTIF 39 :::::::::::::::::::: d1nhpa2 40 YIGIEAAEAFAKAGKKVTVI 59
Intermediate <-- 0.965 --> Hit
DALI alignment (Z-score: 3.4 Raw score:246.10) d1nhpa2 1 ipgkdldniylmrgrqwaiklkqktvdpeVNNVVVIGSGYIGIEAAEAFAKAGKKVTVID 60 ::::::::::::::::::::::::::::::: d1dv1a2 1 -----------------------------LDKIVIANRGEIALRILRACKELGIKTVAVH 31 d1nhpa2 61 I--LDRPLgvyldkeftdvlteemeannITIATG-------ETVERYegdgrvqkvvtdk 111 : ::::: :::::: :::::: d1dv1a2 32 SsaDRDLK---------------hvllaDETVCIgpapsvkSYLNIP-------aiisaa 69 d1nhpa2 112 nAYDADLVVVA--------------------------------v 123 :::::::::: d1dv1a2 70 eITGAVAIHPGygflsenanfaeqversgfifigpkaetirlmg 113 FAST alignment (Normalized score: 3.47 Raw score:409.20) d1nhpa2 1 IPGKDLDNIYLMRGRQWAIKLKQKTVDPEV-NNVVVIGSGYIGIEAAEAFAKAGKKVTVI 59 ::::::::::::::::::::::::::::: d1dv1a2 1 ------------------------------LDKIVIANRGEIALRILRACKELGIKTVAV 30 d1nhpa2 60 DILDRPLGVYLDKEFT----DVLTEEMEANNITIATGE--------------TVERYEGD 101 ::: :::::: :::: d1dv1a2 31 HSS-------------ADRDLKHVLL------------ADETVCIGPAPSVKSYLN---- 61 d1nhpa2 102 GRVQKVVTDKN---------AYDADLVVVAV----------------------------- 123 :::::::::: d1dv1a2 62 -----------IPAIISAAEITGAVAIHPG-YGFLSENANFAEQVERSGFIFIGPKAETI 109 d1nhpa2 124 ---- 124 d1dv1a2 110 RLMG 113 TMalign alignment (TM-score: 0.44 Raw score:54.67) d1nhpa2 1 IPGKDLDNIYLMRGRQWAIKLKQKTVDPEVNNVVVIGSGYIGIEAAEAFAKAGKKVTVID 60 ::::::::::::::::::::::::::::::: d1dv1a2 1 -----------------------------LDKIVIANRGEIALRILRACKELGIKTVAVH 31 d1nhpa2 61 I-LDRPLGVYLDKEFTDVLTEEMEANNITIATGET---------V-ERYEGDGRVQKVVT 109 : ::::: :: :: :: :::: ::: : ::: ::: d1dv1a2 32 SSADRDL--------KH-VL--LA---DETV-CIGPAPSVKSYLNIPAI--------ISA 68 d1nhpa2 110 -DKNAYDADLVVVA--V------------------------------ 123 ::::::::::: : d1dv1a2 69 A--EITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMG 113 HHsearch alignment (Probability: 0.17 E-value:0.01) d1nhpa2 31 NNVVVIGSGYIGIEAAEAFAKAGKKVTVIDI 61 ::::::::::::::::::::::::::::::: d1dv1a2 2 DKIVIANRGEIALRILRACKELGIKTVAVHS 32