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 <-- 1.616 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1f4pa_) 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 d1f4pa_ FlavodoxinFlavoproteinsFlavodoxin-​likeα/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 <-- 1.616 --> Hit
DALI alignment (Z-score: 4.5 Raw score:424.60) d1ps9a3 1 intcigcnqacldqifvgkvtsclvnprachetkmpilpavqkKNLAVVG------aGPA 54 ::::::: ::: d1f4pa_ 1 -------------------------------------------PKALIVYgsttgntEYT 17 d1ps9a3 55 GLAFAINAAARGHQVTLFDAHseiggqfniakqipgkeefyetlryyrrmievtgvtlkl 114 ::::::::::::::::::::: d1f4pa_ 18 AETIARELADAGYEVDSRDAA--------------------------------------- 38 d1ps9a3 115 nhTVTADQLQA-FDETILaSGIP--------------nralaqplidSGKTVHLIggcDV 159 ::::::::: :::::: :::: :::::::: :: d1f4pa_ 39 --SVEAGGLFEgFDLVLL-GCSTwgddsielqddfiplfdsleetgaQGRKVACF---GC 92 d1ps9a3 160 AM-------------------------------ELDARRAIAQGTRLALEI---- 179 :: :::::::::::::::::: d1f4pa_ 93 GDssweyfcgavdaieeklknlgaeivqdglriDGDPRAARDDIVGWAHDVrgai 147 FAST alignment (Normalized score: 4.24 Raw score:687.40) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVGA--------- 51 ::::: d1f4pa_ 1 -------------------------------------------PKALI---VYGSTTGNT 14 d1ps9a3 52 GPAGLAFAINAAARGHQVTLFDAHSEIGGQFNIAKQIPGKEEFYETLRYYRRMIEVTGVT 111 ::::::::::::::::::::: d1f4pa_ 15 EYTAETIARELADAGYEVDSR--------------------------------------- 35 d1ps9a3 112 LKLNH---TVTADQL----QAFDETILASGIPN----------RALAQPLID-------S 147 :::: :::::::::: ::::::::: : d1f4pa_ 36 -----DAASVEA---GGLFEGFDLVLLGC----STWGDDSIELQDDFIPLFDSLEETGAQ 83 d1ps9a3 148 GKTVHLIGGCDVAMEL-----------------------------------------DAR 166 ::::::: ::: d1f4pa_ 84 GRKVACF---------GCGDSSWEYFCGAVDAIEEKLKNLGAEIVQDGLRIDGDPRAARD 134 d1ps9a3 167 RAIAQGTRLALEI-- 179 ::::::::::: d1f4pa_ 135 DIVGWAHDVRG--AI 147 TMalign alignment (TM-score: 0.40 Raw score:70.76) d1ps9a3 1 INTCIGCNQACLDQIFVGKVTSCLVNPRACHETKMPILPAVQKKNLAVVG------AGPA 54 : :::::: :::: d1f4pa_ 1 ------------------------------------------P-KALIVYGSTTGNTEYT 17 d1ps9a3 55 GLAFAINAAARGHQVTLFDAHS----------------EIGGQ----------FNIAKQI 88 :::::::::::::::::::::: :: d1f4pa_ 18 AETIARELADAGYEVDSRDAASVEAGGLFEGFDLVLLG---CSTWGDDSIELQ------- 67 d1ps9a3 89 PGKEEFYETLRYYRRMIEVTGVTLKLNHT--VT--ADQLQA-FDETILASGI-------P 136 ::: :: :::::: :::::::::: : d1f4pa_ 68 --------------------------DDFIPLFDSLEETGAQGRKVACFGCGDSSWEYFC 101 d1ps9a3 137 -NR-ALAQPLIDSGKTV-H-LIGGCDVAMEL-DARRAIAQGTRLALE-I 179 :: ::::::::::::: : :::: :::: ::::::::::::::: : d1f4pa_ 102 GAVDAIEEKLKNLGAEIVQDGLRI---DGDPRAARDDIVGWAHDVRGAI 147 HHsearch alignment (Probability: 0.14 E-value:0.02) d1ps9a3 95 YETLRYYRRMIEVTGVTLKLNHTVTA--DQ-LQAFDETILASG 134 :::::::::::::::::::::::::: :: :::::::::::: d1f4pa_ 15 EYTAETIARELADAGYEVDSRDAASVEAGGLFEGFDLVLLGCS 57