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 <-- 1.613 --> Intermediate <-- 0.978 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1pfka_) through the intermediate protein (d1ps9a3) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ps9a3 2,​4-​dienoyl-​CoA reductase,​ middle domainNucleotide-​binding domainNucleotide-​binding domainα/β
Hit d1pfka_ ATP-​dependent phosphofructokinasePhosphofructokinasePhosphofructokinaseα/β

Supporting Alignments

Query <-- 1.613 --> Intermediate
DALI alignment (Z-score: 4.1 Raw score:393.70) query 1 ---------------------------------------GMENKKMNLLLfsgdydkALA 21 ::::::::::: ::: d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpAVQKKNLAVVG------aGPA 54 query 22 SLIIANAAREMEIEVTIFCAfwgLLLLrdpekasqedkslyeqafssltpreaeELPLsk 81 :::::::::::::::::::: :::: :::: d1ps9a3 55 GLAFAINAAARGHQVTLFDA---HSEI------------------------ggqFNIA-- 85 query 82 mnlgGIGKKmllemmkeekaPKLSDLLSGARKKEVKFYAXqlsveimgfkkeelfpevqI 141 ::::: :::::::::::::::::::: : d1ps9a3 86 --kqIPGKE--------efyETLRYYRRMIEVTGVTLKLN------------------hT 117 query 142 MDVKEYlknaLESDLQLFI----------------------------------------- 160 :::::: ::::::::: d1ps9a3 118 VTADQL----QAFDETILAsgipnralaqplidsgktvhliggcdvameldarraiaqgt 173 query 161 ------ 161 d1ps9a3 174 rlalei 179 FAST alignment (Normalized score: 3.87 Raw score:654.60) query 1 GME------------------------------------------NKKMNLLLFSGDYDK 18 :::::: d1ps9a3 1 ---INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAV--------- 48 query 19 ---ALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLT-PREA 74 :::::::::::::::::::::: :::: d1ps9a3 49 VGAGPAGLAFAINAAARGHQVTLFD------------------------------AHSEI 78 query 75 EELPLSKMNLGGIGKKMLLEMMKEEKAP------------------KLSDLLSGARKKEV 116 :::::::::::::: d1ps9a3 79 ----------------------------GGQFNIAKQIPGKEEFYETLRYYRRMIEVTGV 110 query 117 KFYAXQLSVEIMGFKKEELFPE-VQIMDVKEYLKNA-LESDLQLFI-------------- 160 ::: :::::::: ::::::: d1ps9a3 111 TLK-------------------LNHTVTADQ-----LQAFDETI--LASGIPNRALAQPL 144 query 161 ----------------------------------- 161 d1ps9a3 145 IDSGKTVHLIGGCDVAMELDARRAIAQGTRLALEI 179 TMalign alignment (TM-score: 0.44 Raw score:70.82) query 1 ---------------------------------------GMENKKMNLLLFSGDYDKALA 21 ::::::::::: :::: d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG------AGPA 54 query 22 SLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREA-EELPLS 80 :::::::::::::::::::: ::::: : :::: d1ps9a3 55 GLAFAINAAARGHQVTLFDA--HSEIG-------------------------GQ-FNIA- 85 query 81 KMNLGGIGKKMLLE-MMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEV 139 : :::::: :: ::::::::::::::::::::: : d1ps9a3 86 --K-QIPGKE--EFY-------ETLRYYRRMIEVTGVTLKLNH-T--------------- 117 query 140 QIMDVKEYLKNALESDLQLFI--------------------------------------- 160 :::::: :::::::::: d1ps9a3 118 ----VTADQL-QAFDETILASGIPNRALAQPLIDSGKTVHLIGGCDVAMELDARRAIAQG 172 query 161 ------- 161 d1ps9a3 173 TRLALEI 179 HHsearch alignment (Probability: 0.10 E-value:0.01) query 2 MENKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIF 39 ::::::::::::: :::::::::::::::::::: d1ps9a3 40 AVQKKNLAVVGAG-----PAGLAFAINAAARGHQVTLF 72
Intermediate <-- 0.978 --> Hit
DALI alignment (Z-score: 5.4 Raw score:542.90) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavQKKNLAVVG-------aGP 53 ::::::::: :: d1pfka_ 1 -----------------------------------------MIKKIGVLTsggdapgmNA 19 d1ps9a3 54 AGLAFAINAAARGHQVTLFDAhseiggqfniakqipgkeefyetlRYYRRmievtgvtlk 113 ::::::::::::::::::::: ::::: d1pfka_ 20 AIRGVVRSALTEGLEVMGIYD---------gylglyedrmvqldrYSVSD--minrggtf 68 d1ps9a3 114 LNHT-----------vtADQLQA---FDETILAsGIPNR-ALAQPLIDSGKTVHLIGG-- 156 :::: :::::: ::::::: ::::: :::::::::::::::::: d1pfka_ 69 LGSArfpefrdeniravAIENLKkrgIDALVVI-GGDGSyMGAMRLTEMGFPCIGLPGti 127 d1ps9a3 157 ---cdvAMEL-------------------------------------------------- 163 :::: d1pfka_ 128 dndikgTDYTigfftalstvveaidrlrdtssshqrisvvevmgrycgdltlaaaiaggc 187 d1ps9a3 164 ------------------------------------------------------------ 164 d1pfka_ 188 efvvvpevefsredlvneikagiakgkkhaivaitehmcdvdelahfieketgretratv 247 d1ps9a3 164 -------------DARRAIAQGTRLALEI------------------------------- 179 :::::::::::::::: d1pfka_ 248 lghiqrggspvpyDRILASRMGAYAIDLLlagyggrcvgiqneqlvhhdiidaienmkrp 307 d1ps9a3 180 ------------- 180 d1pfka_ 308 fkgdwldcakkly 320 FAST alignment (Normalized score: 3.16 Raw score:756.70) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQK--KNLAVVGA------- 51 ::::: d1pfka_ 1 -------------------------------------------MIKKIGV---LTSGGDA 14 d1ps9a3 52 ---GPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVT 108 ::::::::::::::::::::: d1pfka_ 15 PGMNAAIRGVVRSALTEGLEVMGI------------------------------------ 38 d1ps9a3 109 GVTLKLNHTVTADQL--------------------------------------------- 123 d1pfka_ 39 ---------------YDGYLGLYEDRMVQLDRYSVSDMINRGGTFLGSARFPEFRDENIR 83 d1ps9a3 124 ---------QAFDETILASGIPN-RALAQPLID---SGKTVHLIGGCDVAMEL------- 163 :::::::::: ::::::::: :::::::: d1pfka_ 84 AVAIENLKKRGIDALVVIG----GDGSYMGAMRLTEMGFPCIGL---------PGTIDND 130 d1ps9a3 164 ------------------------------------------------------------ 164 d1pfka_ 131 IKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLAAAIAGGCEFV 190 d1ps9a3 164 ------------------------------------------------------------ 164 d1pfka_ 191 VVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHMCDVDELAHFIEKETGRETRATVLGH 250 d1ps9a3 164 ----------DARRAIAQGTRLALEI---------------------------------- 179 ::::::::::::::: d1pfka_ 251 IQRGGSPVPYDRILASRMGAYAIDL-LLAGYGGRCVGIQNEQLVHHDIIDAIENMKRPFK 309 d1ps9a3 180 ----------- 180 d1pfka_ 310 GDWLDCAKKLY 320 TMalign alignment (TM-score: 0.46 Raw score:81.87) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG-------AGP 53 ::::::::: ::: d1pfka_ 1 -----------------------------------------MIKKIGVLTSGGDAPGMNA 19 d1ps9a3 54 AGLAFAINAAARGHQVTLFDAH-----------SEIGGQFNIAKQIPGKEEFYETLRYYR 102 :::::::::::::::::::::: :: d1pfka_ 20 AIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQ-------------------------LD 54 d1ps9a3 103 RMIEV--------TGVTLKLNHT-V--T-----A-DQ--LQA---FDETILASGIP-NRA 139 ::::: ::::: : : : :: ::: ::::::: ::: ::: d1pfka_ 55 RYSVSDMINRGGT-----FLGSARFPEFRDENIRAVAIENLKKRGIDALVVI-GGDGSYM 108 d1ps9a3 140 LAQPLIDSGKTVHLIGGC----DV-AMELD------------------------------ 164 :::::::::::::::::: :: ::::: d1pfka_ 109 GAMRLTEMGFPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVE 168 d1ps9a3 165 ------------------------------------------------------------ 165 d1pfka_ 169 VMGRYCGDLTLAAAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHMCDV 228 d1ps9a3 165 --------------------------------A-RRAIAQGTRLALE-I----------- 179 : ::::::::::::: : d1pfka_ 229 DELAHFIEKETGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQ 288 d1ps9a3 180 -------------------------------- 180 d1pfka_ 289 NEQLVHHDIIDAIENMKRPFKGDWLDCAKKLY 320 HHsearch alignment (Probability: 0.03 E-value:0.08) d1ps9a3 46 LAVVGAGPAGLAFAINAAARGHQVTLFDA 74 ::::::::::::::::::::::::::::: d1pfka_ 97 ALVVIGGDGSYMGAMRLTEMGFPCIGLPG 125