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 <-- 0.712 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1od6a_) 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 d1od6a_ Phosphopantetheine adenylyltransferaseNucleotidylyl transferaseAdenine nucleotide alpha hydrolase-​likeα/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 <-- 0.712 --> Hit
DALI alignment (Z-score: 2.6 Raw score:241.40) d1nhpa2 1 ipgkdldniylmrgrqwaiklkqktvdpevNNVVVIG----sgYIGIEAAEAFAKAGKKV 56 ::::::: ::::::::::::::::: d1od6a_ 1 ------------------------------MHVVYPGsfdpltNGHLDVIQRASRLFEKV 30 d1nhpa2 57 TVIDILdrplgVYLD-KEFTDVLTEEMEAN-NITIATGE-TVERyegdgrvqkvvtdknA 113 :::::: :::: :::::::::::::: :::::::: :::: : d1od6a_ 31 TVAVLE---nqYLFSaEERLAIIREATAHLaNVEAATFSgLLVD------------fvrR 75 d1nhpa2 114 YDADLVVVA--------------------------------------------------- 122 ::::::::: d1od6a_ 76 VGAQAIVKGlravsdyeyelqmahlnrqlypgletlfilaatrysfvsstmvkeiarygg 135 d1nhpa2 123 -------------------v 123 d1od6a_ 136 dvsklvppatlralkaklgq 155 FAST alignment (Normalized score: 1.42 Raw score:196.20) d1nhpa2 1 IPGKDLD------------------------------NIYLMRGRQ-------------- 16 ::::: d1od6a_ 1 -------MHVVYPGSFDPLTNGHLDVIQRASRLFEKVTVAVL----ENQYLFSAEERLAI 49 d1nhpa2 17 ---------------WAIKLKQKTVD-------PEVNNVVVIGS-------GYIGIEAAE 47 :::: :::::::: ::::::::: d1od6a_ 50 IREATAHLANVEAATFSGL-------LVDFVRRVGAQAIVK---GLRAVSDYEYELQMAH 99 d1nhpa2 48 AFAK--AGKKVTVIDILDRPLGVYLDKEFTDVLTEEMEANNITIATGETVERYEGDGRVQ 105 :::: ::::::: d1od6a_ 100 LNRQLYPGLETLF----------------------------------------------- 112 d1nhpa2 106 KVVTDKNAYDADLVVVAV------------------------------------------ 123 d1od6a_ 113 ------------------ILAATRYSFVSSTMVKEIARYGGDVSKLVPPATLRALKAKLG 154 d1nhpa2 124 - 124 d1od6a_ 155 Q 155 TMalign alignment (TM-score: 0.45 Raw score:54.84) d1nhpa2 1 IPGKDLDNIYLMRGRQWAIKLKQKTVDPEVNNVVVIG-S--GY-IGIEAAEAFAKAGKKV 56 ::::::: : :: :::::::::::::::: d1od6a_ 1 ------------------------------MHVVYPGSFDPLTNGHLDVIQRASRLFEKV 30 d1nhpa2 57 TVID-I------LDRPLGVYLDKEFT-DVLTEEMEANNITIATGETVERYEGDGRVQKVV 108 :::: : ::::: : : ::::::: ::::::: ::::::: ::: d1od6a_ 31 TVAVLENQYLFSAEERL-----A--IIREATAHL--ANVEAAT-FSGLLVD------FVR 74 d1nhpa2 109 TDKNAYDADLVVVA---------V------------------------------------ 123 :::::::::: : d1od6a_ 75 ----RVGAQAIVKGLRAVSDYEYELQMAHLNRQLYPGLETLFILAATRYSFVSSTMVKEI 130 d1nhpa2 124 ------------------------- 124 d1od6a_ 131 ARYGGDVSKLVPPATLRALKAKLGQ 155 HHsearch alignment (Probability: 0.01 E-value:0.26) d1nhpa2 52 AGKKVTVI 59 :::::::: d1od6a_ 26 LFEKVTVA 33