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 <-- 0.985 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1jmva_) 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 d1jmva_ Universal stress protein A,​ UspAAdenine nucleotide alpha hydrolases-​likeAdenine 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 <-- 0.985 --> Hit
DALI alignment (Z-score: 2.9 Raw score:263.70) d1nhpa2 1 ipgkdldniylmrgrqwaiklkqktvdpEVNNVVVIG----sGYIGIEAAEAFAKA-GKK 55 ::::::::: :::::::::::::: ::: d1jmva_ 1 ----------------------------MYKHILVAVdlseeSPILLKKAVGIAKRhDAK 32 d1nhpa2 56 VTVIDI---------------------------LDRPlgvyldkeftdvLTEEMeANNI- 87 :::::: :::: ::::: :::: d1jmva_ 33 LSIIHVdvnfsdlytglidvnmssmqdristetQKAL----------ldLAESV-DYPIs 81 d1nhpa2 88 TIATG-----eTVERyegdgrvqkvvtdknAYDADLVVVA-------------------- 122 ::::: :::: :::::::::: d1jmva_ 82 EKLSGsgdlgqVLSD------------aieQYDVDLLVTGhhqdfwsklmsstrqvmnti 129 d1nhpa2 123 ----------v 123 d1jmva_ 130 kidmlvvplrd 140 FAST alignment (Normalized score: 3.03 Raw score:397.60) d1nhpa2 1 IPGKDLDNIYLMRGRQWAIKLKQKTVDPEVNNVVVIGS-------GYIGIEAAEAFAK-A 52 ::::::: ::::::::::::: : d1jmva_ 1 ----------------------------MYKHILV---AVDLSEESPILLKKAVGIAKRH 29 d1nhpa2 53 GKKVTVIDILDRPLGVYLDK--------------------------EFTDVLTEEMEANN 86 ::::::: :::::::::::: d1jmva_ 30 DAKLSII-------------HVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAE-- 74 d1nhpa2 87 ------ITIA-TGETVERYEGDGRVQKVVTDKN----------AYDADLVVVAV------ 123 :::: :::: :::::::::: d1jmva_ 75 SVDYPISEKLSGSGD------------------LGQVLSDAIEQYDVDLLVTG-HHQDFW 115 d1nhpa2 124 ------------------------- 124 d1jmva_ 116 SKLMSSTRQVMNTIKIDMLVVPLRD 140 TMalign alignment (TM-score: 0.30 Raw score:37.22) d1nhpa2 1 -----------------------I-PGK-DLDNIYLMR-------------GRQWAIKL- 21 : ::: :::::::: ::::: d1jmva_ 1 MYKHILVAVDLSEESPILLKKAVGIAKRH-DAKLSIIHVDVNFSDLYTGLI---DVNMSS 56 d1nhpa2 22 ---------------------------------KQKTVDPEVNNVVVIGSGYIGIEAAEA 48 : ::: d1jmva_ 57 MQDRISTETQKALLDLAESVDYPISEKLSGSGD----------------------L-GQV 93 d1nhpa2 49 FAKAGK---KVTVIDILDRPLGVYLDKEFTDVLTEEMEANN-ITIATG----ETVERYEG 100 :::::: :::::: :: ::::::::::::::::::: :::::: d1jmva_ 94 LSDAIEQYDVDLLVT----GH-HQDFWSKLMSSTRQVMNTIKIDMLVVPLRD-------- 140 d1nhpa2 101 DGRVQKVVTDKNAYDADLVVVAV 123 d1jmva_ 141 ----------------------- 141 HHsearch alignment (Probability: 0.16 E-value:0.00) d1nhpa2 41 IGIEAAEAFAKA-GKKVTVIDILDR---PLGVYLD-----------KEFTDVLTEEMEAN 85 :::::::::::: :::::::::::: ::::::: :::::::::::::: d1jmva_ 17 ILLKKAVGIAKRHDAKLSIIHVDVNFSDLYTGLIDVNMSSMQDRISTETQKALLDLAESV 76 d1nhpa2 86 NITIATGETVERYEGDGRVQKVVTDKNAYDADLVVVA 122 ::::: :::::::::::::::::::::::::::: d1jmva_ 77 DYPIS----EKLSGSGDLGQVLSDAIEQYDVDLLVTG 109