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 <-- 1.441 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1qp8a1) 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 d1qp8a1 Putative formate dehydrogenaseNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/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 <-- 1.441 --> Hit
DALI alignment (Z-score: 4.3 Raw score:311.40) d1nhpa2 1 ipgkdldniyLMRGrqwaIKLKQKTV-------------------DPEV--NNVVVIGSG 39 :::: :::::::: :::: ::::::::: d1qp8a1 1 -------adaVAEF--alALLLAPYKriiqygekmkrgdygrdveIPLIqgEKVAVLGLG 51 d1nhpa2 40 YIGIEAAEAFAKAGKKVTVIDILDRPlgvyldkeftdvlteemeanNITIAtgETVErye 99 :::::::::::::::::::::::::: ::::: :::: d1qp8a1 52 EIGTRVGKILAALGAQVRGFSRTPKE-------------------gPWRFT--NSLE--- 87 d1nhpa2 100 gdgrvqkvvtdknaYDADLVVVAV------------------------------------ 123 :::::::::: d1qp8a1 88 -----------ealREARAAVCALplnkhtrglvkyqhlalmaedavfvnvgraevldrd 136 d1nhpa2 124 --------------------------------------------- 124 d1qp8a1 137 gvlrilkerpqfifasdvwwgrndfakdaeffslpnvvatpwvag 181 FAST alignment (Normalized score: 3.95 Raw score:589.30) d1nhpa2 1 IPGKDLDNIYLMR----GRQWAIKLKQKTVDPEV-------------------------- 30 :::::::::::: d1qp8a1 1 -------------ADAVAEFALALLLAPY-----KRIIQYGEKMKRGDYGRDVEIPLIQG 42 d1nhpa2 31 NNVVVIGSGYIGIEAAEAFAKAGKKVTVIDILDRPLGVYLDKEFTDVLTEEMEAN---NI 87 ::::::::::::::::::::::::::::::::: :: d1qp8a1 43 EKVAVLGLGEIGTRVGKILAALGAQVRGFSRTP----------------------KEGPW 80 d1nhpa2 88 TIATGETVERYEGDGRVQKVVTDKNA--------YDADLVVVAV---------------- 123 :: ::::::::: d1qp8a1 81 RF------------------------TNSLEEALREARAAVCA-LPLNKHTRGLVKYQHL 115 d1nhpa2 124 ------------------------------------------------------------ 124 d1qp8a1 116 ALMAEDAVFVNVGRAEVLDRDGVLRILKERPQFIFASDVWWGRNDFAKDAEFFSLPNVVA 175 d1nhpa2 124 ------ 124 d1qp8a1 176 TPWVAG 181 TMalign alignment (TM-score: 0.48 Raw score:59.10) d1nhpa2 1 --IPGKDLDNIYLMRGRQWAIKLKQ-KT-------------------VDPEV-NNVVVIG 37 :::::::::::: :: ::::: ::::::: d1qp8a1 1 AD-----------AVAEFALALLLAPYKRIIQYGEKMKRGDYGRDVEIPLIQGEKVAVLG 49 d1nhpa2 38 SGYIGIEAAEAFAKAGKKVTVIDILDRPLGVYLDKEFTDVLTEEMEANNITIATGETVER 97 ::::::::::::::::::::::: :::: : : : ::::: : : d1qp8a1 50 LGEIGTRVGKILAALGAQVRGFS-RTPK-------------E--G--P-WRFTN-S-L-- 86 d1nhpa2 98 YEGDGRVQKVVTDKNAYDADLVVVAV---------------------------------- 123 :: :::::::::::: d1qp8a1 87 ----------EE--ALREARAAVCALPLNKHTRGLVKYQHLALMAEDAVFVNVGRAEVLD 134 d1nhpa2 124 ----------------------------------------------- 124 d1qp8a1 135 RDGVLRILKERPQFIFASDVWWGRNDFAKDAEFFSLPNVVATPWVAG 181 HHsearch alignment (Probability: 0.93 E-value:0.00) d1nhpa2 29 EVNNVVVIGSGYIGIEAAEAFAKAGKKVTVIDILDRPLGVYLDKEFTDVL 78 :::::::::::::::::::::::::::::::::::::::::::::::::: d1qp8a1 41 QGEKVAVLGLGEIGTRVGKILAALGAQVRGFSRTPKEGPWRFTNSLEEAL 90