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 <-- 1.673 --> Intermediate <-- 1.765 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1nhpa1) through the intermediate protein (d1onfa2) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1onfa2 Glutathione reductaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/β
Hit d1nhpa1 NADH peroxidaseFAD/​NAD(P)-​binding domainFAD/​NAD(P)-​binding domainα/β

Supporting Alignments

Query <-- 1.673 --> Intermediate
DALI alignment (Z-score: 4.3 Raw score:336.20) query 1 ------------------GMENKKMNLLLfsgdydkALASLIIANAAREMEIEVTIFCAf 42 ::::::::::: ::::::::::::::::::::::: d1onfa2 1 fppvkgientissdeffnIKESKKIGIVG------sGYIAVELINVIKRLGIDSYIFAR- 53 query 43 wgLLLLrdpekasqedkslyeqafssltprEAEELplskmnlggigkkmllemmkeekap 102 :::: ::::: d1onfa2 54 --GNRI-----------------------lRKFDE------------------------s 64 query 103 KLSDLLSGARKKEVKFY--AXQLsveimgfkkeelfpevqiMDVKEYLknaLESDLQLF- 159 ::::::::::::::::: :::: ::::::: :::::::: d1onfa2 65 VINVLENDMKKNNINIVtfADVV-----eikkvsdknlsihLSDGRIY---EHFDHVIYc 116 query 160 i 160 d1onfa2 117 v 117 FAST alignment (Normalized score: 4.62 Raw score:632.20) query 1 -----------------GMEN-KKMNLLLFSGDYDK---ALASLIIANAAREMEIEVTIF 39 :::: ::::: ::::::::::::::::::::: d1onfa2 1 FPPVKGIENTISSDEFFNIKESKKIGI---------VGSGYIAVELINVIKRLGIDSYIF 51 query 40 CAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEE 99 :: d1onfa2 52 AR---------------------------------------------------------- 53 query 100 KAP-----------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYL 148 ::::::::::::::::: ::::: d1onfa2 54 ---GNRILRKFDESVINVLENDMKKNNINIV--------------------TFADV---- 86 query 149 KN--------------------ALESDLQLFI--- 160 :::::::: d1onfa2 87 --VEIKKVSDKNLSIHLSDGRIYEHFDHVI--YCV 117 TMalign alignment (TM-score: 0.39 Raw score:61.66) query 1 -------------------GMENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCA 41 :: :::::::: : ::::::::::::::::::::::: d1onfa2 1 FPPVKGIENTISSDEFFNIKE-SKKIGIVG-S-----GYIAVELINVIKRLGIDSYIFAR 53 query 42 FWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEEL-PLSKMNLGGIGKKMLLEMMKEEK 100 ::::: : :::: d1onfa2 54 ---GNRIL---------------------R--KFDES----------------------- 64 query 101 APKLS-DLLSGARKKEVKFYAXQLS------------VEIMGFKKEELFPEVQIMDV--K 145 :: ::::::::::::::::::: ::: : d1onfa2 65 ---VINVLENDMKKNNINIVTFADVVEIKKVSDKNLS-----------------IHLSDG 104 query 146 EYLKNALESDLQLFI- 160 :: :: :::::::: d1onfa2 105 RI-YE--HFDHVIYCV 117 HHsearch alignment (Probability: 0.09 E-value:0.01) query 20 LASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPL 79 :::::::::::::::::::::::::::: d1onfa2 32 YIAVELINVIKRLGIDSYIFARGNRILR-------------------------------- 59 query 80 SKMNLGGIGKKMLLEMMKEEKA 101 ::::::::::::::::::: d1onfa2 60 ---KFDESVINVLENDMKKNNI 78
Intermediate <-- 1.765 --> Hit
DALI alignment (Z-score: 7.3 Raw score:536.00) d1onfa2 1 fppvkgientissdeffnikesKKIGIVGSGYIAVELINVIKR--LGIDSYIFARGNRIL 58 ::::::::::::::::::::: ::::::::::::::: d1nhpa1 1 ----------------------MKVIVLGSSHGGYEAVEELLNlhPDAEIQWYEKGDFIS 38 d1onfa2 59 RKF--------------DESVInvLENDMKKNNINIVTFADVVEIKKVSdknLSIHLS-- 102 ::: ::::: ::::::::::::::::::::::::: :::::: d1nhpa1 39 FLSagmqlylegkvkdvNSVRY-mTGEKMESRGVNVFSNTEITAIQPKE---HQVTVKdl 94 d1onfa2 103 ---DGRIYEhFDHVIYCV------------------------------------------ 117 :::::: :::::::: d1nhpa1 95 vsgEERVEN-YDKLIISPgavpfeldgvrpntawlkgtlelhpngliktdeymrtsepdv 153 d1onfa2 118 --------------------------------------------- 118 d1nhpa1 154 favgdatlikynpadtevnialatnarkqgrfavknleepvkpfp 198 FAST alignment (Normalized score: 6.10 Raw score:928.00) d1onfa2 1 FPPVKGIENTISSDEFFNIKESKKIGIVGSGYIAVELINVIKR--LGIDSYIFARGNRIL 58 ::::::::::::::::::::: ::::::::::::::: d1nhpa1 1 ----------------------MKVIVLGSSHGGYEAVEELLNLHPDAEIQWYEKGDFIS 38 d1onfa2 59 RKFDESVINV----------------------LENDMKKNNINIVTFADVVEIKKVSDKN 96 : :::::::::::::::::::::: ::::: d1nhpa1 39 F---------LSAGMQLYLEGKVKDVNSVRYMTGEKMESRGVNVFSNTEITAIQ-PKEHQ 88 d1onfa2 97 LSIHLSDGRIY-------EHFDHVIYCV-------------------------------- 117 :::::: :::::::: d1nhpa1 89 VTVKDL-----VSGEERVENYDKLII--SPGAVPFELDGVRPNTAWLKGTLELHPNGLIK 141 d1onfa2 118 --------------------------------------------------------- 118 d1nhpa1 142 TDEYMRTSEPDVFAVGDATLIKYNPADTEVNIALATNARKQGRFAVKNLEEPVKPFP 198 TMalign alignment (TM-score: 0.63 Raw score:73.52) d1onfa2 1 FPPVKGIENTISSDEFFNIKESKKIGIVGSGYIAVELINVIKR-L-GIDSYIFARGNRIL 58 ::::::::::::::::::::: : :::::::::::::: d1nhpa1 1 ----------------------MKVIVLGSSHGGYEAVEELLNLHPDAEIQWYEKGDFIS 38 d1onfa2 59 RKF-------------DESVINVLENDMKKNNINIVTFADVVEIKKVSDKNLSIHLS--- 102 ::: :::::::::::::::::::::::::::::::: :::::: d1nhpa1 39 FLSAGMQLYLEGKVKDVNSVRYMTGEKMESRGVNVFSNTEITAIQPKE---HQVTVKDLV 95 d1onfa2 103 -DGRIYEHFDHVIYCV-------------------------------------------- 117 ::::::::::::::: d1nhpa1 96 SGEERVENYDKLIISPGAVPFELDGVRPNTAWLKGTLELHPNGLIKTDEYMRTSEPDVFA 155 d1onfa2 118 ------------------------------------------- 118 d1nhpa1 156 VGDATLIKYNPADTEVNIALATNARKQGRFAVKNLEEPVKPFP 198 HHsearch alignment (Probability: 0.99 E-value:0.00) d1onfa2 24 KIGIVGSGYIAVELINVIKRLG--IDSYIFARGNRILR-------------KFDESVINV 68 :::::::::::::::::::::: :::::::::::::: ::::::::: d1nhpa1 2 KVIVLGSSHGGYEAVEELLNLHPDAEIQWYEKGDFISFLSAGMQLYLEGKVKDVNSVRYM 61 d1onfa2 69 LENDMKKNNINIVTFADVVEIKKVSDKNLS--IHLSDGRIYEHFDHVIYCV 117 :::::::::::::::::::::::::::::: ::::::::: ::::::::: d1nhpa1 62 TGEKMESRGVNVFSNTEITAIQPKEHQVTVKDLVSGEERVE-NYDKLIISP 111