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 <-- 0.883 --> Intermediate <-- 1.112 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1e5da1) through the intermediate protein (d1vi2a1) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1vi2a1 Putative shikimate dehydrogenase YdiBNAD(P)-​binding Rossmann-​fold domainsNAD(P)-​binding Rossmann-​fold domainsα/β
Hit d1e5da1 Rubredoxin oxygen:oxidoreductase (ROO),​ C-​terminal domainFlavoproteinsFlavodoxin-​likeα/β

Supporting Alignments

Query <-- 0.883 --> Intermediate
DALI alignment (Z-score: 4.6 Raw score:365.80) query 1 --------------GMENKKMNLLLfsgdydkALASLIIANAAREMEI-EVTIFCAFWgl 45 ::::::::::: :::::::::::::::: ::::::::: d1vi2a1 1 dgtghiraikesgfDIKGKTMVLLG------aGGASTAIGAQGAIEGLkEIKLFNRRD-- 52 query 46 LLLRdpekasqedkslyeqafssltpreaeelplskmnlggigkkmllemmkeekapkls 105 :::: d1vi2a1 53 EFFD-------------------------------------------------------- 56 query 106 dlLSGARKKE------VKFYAXQlsveimgfkkeelfpevqimDVKEYLKNALESDLQLF 159 :::::::: ::::::: ::::::::::::::::: d1vi2a1 57 kaLAFAQRVNentdcvVTVTDLA--------------------DQQAFAEALASADILTN 96 query 160 ------------------------------------------------------------ 160 d1vi2a1 97 gtkvgmkpleneslvndisllhpgllvtecvynphmtkllqqaqqagcktidgygmllwq 156 query 160 -------------------------i 160 d1vi2a1 157 gaeqftlwtgkdfpleyvkqvmgfga 182 FAST alignment (Normalized score: 4.17 Raw score:711.70) query 1 --------------GMENKKMNLLLFSGDYDK---ALASLIIANAAREME-IEVTIFCA- 41 ::::::::: ::::::::::::::: :::::::: d1vi2a1 1 DGTGHIRAIKESGFDIKGKTMVL---------LGAGGASTAIGAQGAIEGLKEIKLFNRR 51 query 42 FWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKEEKA 101 ::::: d1vi2a1 52 DEFFD------------------------------------------------------- 56 query 102 PK-LSDLLSGARK---KEVKFYAXQLSVEIMGFKKEELFPEVQIM--DVKEYLKNALESD 155 :::::::::: ::::::: ::::::::::::: d1vi2a1 57 --KALAFAQRVNENTDCVVTVTD----------------------LADQQAFAEALASAD 92 query 156 LQLFI------------------------------------------------------- 160 ::: d1vi2a1 93 ILT--NGTKVGMKPLENESLVNDISLLHPGLLVTECVYNPHMTKLLQQAQQAGCKTIDGY 150 query 161 -------------------------------- 161 d1vi2a1 151 GMLLWQGAEQFTLWTGKDFPLEYVKQVMGFGA 182 TMalign alignment (TM-score: 0.31 Raw score:49.46) query 1 ------GMENKKMNL------------LLFSGDYD-KALASLIIAN-AAR--EMEIEVTI 38 :::: ::::: :::::::::: ::: d1vi2a1 1 DGTGHI-----RAIKESGFDIKGKTMV---LLGAGGASTAIGAQGAIEGLKE-------- 44 query 39 FCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKMLLEMMKE 98 ::::::::: : ::::::::::::: d1vi2a1 45 ----------------------------------IKLFNRRDE-F--FDKALAFAQRVNE 67 query 99 EK-APKLS------------DLLSGARKKEVKFYA----XQLS----VEIMG--FKKEEL 135 :: ::::: ::::: : ::: : :::: :::::: d1vi2a1 68 NTDCVVTVTDLADQQAFAEA--LASAD---I-LTNGTKV---GMKPL-ENESLVNDISLL 117 query 136 FPEV-Q---------------IMD-----VKEYLKNALESDLQL---------------- 158 :::: : ::: ::: ::: ::::: d1vi2a1 118 HPGLLVTECVYNPHMTKLLQQAQQAGCKT--IDG-YGM-LLWQGAEQFTLWTGKDFPLEY 173 query 159 ---------FI 160 d1vi2a1 174 VKQVMGFGA-- 182 HHsearch alignment (Probability: 0.01 E-value:0.14) query 102 PKLSDLLSGARKKEVKFY 119 :::::::::::::::::: d1vi2a1 130 PHMTKLLQQAQQAGCKTI 147
Intermediate <-- 1.112 --> Hit
DALI alignment (Z-score: 7.4 Raw score:531.80) d1vi2a1 1 dgtghiraikesgfdikgKTMVLLG------aGGASTAIGAQGAIEGLkEIKLFNRRdef 54 ::::::: :::::::::::::::: :::::::: d1e5da1 1 ----------------ptNKVVIFYdsmwhstEKMARVLAESFRDEGC-TVKLMWCK--- 40 d1vi2a1 55 fdkalafaqrvnentdcvvtvtDLADQqAFAEALASADILTNGTKvgMKPLENE----sL 110 ::::: ::::::::::::::::: ::::::: : d1e5da1 41 ----------------------ACHHS-QIMSEISDAGAVIVGSP--THNNGILpyvagT 75 d1vi2a1 111 VND-ISLLHPGLLVTECV----yNPHMTKLLQQAQQAGCKTIDgygmllwqgaeqftlwt 165 ::: :::::::::::::: :::::::::::::::::::: d1e5da1 76 LQYiKGLRPQNKIGGAFGsfgwsGESTKVLAEWLTGMGFDMPAtpvkvknvpthadyeql 135 d1vi2a1 166 gkdfpleyvkqvmgfga 182 d1e5da1 136 ktmaqtiaralkaklaa 152 FAST alignment (Normalized score: 5.25 Raw score:872.50) d1vi2a1 1 DGTGHIRAIKESGFDIKG--KTMVLLGA--------GGASTAIGAQGAIEGLKEIKLFNR 50 :::::: ::::::::::::::: ::::::: d1e5da1 1 ------------------PTNKVVIF--YDSMWHSTEKMARVLAESFRDEG-CTVKLMW- 38 d1vi2a1 51 RDEFFDKALAFAQRVNENTDCVVTVTDL---ADQQAFAEALASADILTNGTKVGMKPLEN 107 :::::::::::::::::::: d1e5da1 39 ----------------------------CKACHHSQIMSEISDAGAVIVGS--------- 61 d1vi2a1 108 E------------SLVNDISLL------HPGLLVTECVYNPHM---------TKLLQQAQ 140 :::: :::::::::: :::::::: d1e5da1 62 -PTHNNGILPYVAGTLQ-----YIKGLRPQNKIGGAFG-----SFGWSGESTKVLAEWLT 110 d1vi2a1 141 QAGCKTIDGYGMLLWQGAEQFTLWTGKDFPLEYVKQVMGFGA------------------ 182 ::::::: d1e5da1 111 GMGFDMP-----------------------------------ATPVKVKNVPTHADYEQL 135 d1vi2a1 183 ----------------- 183 d1e5da1 136 KTMAQTIARALKAKLAA 152 TMalign alignment (TM-score: 0.50 Raw score:90.42) d1vi2a1 1 -DGTGHIRAIKESGFDIKGKTMVLLG------AGGASTAIGAQGAIEGLKEIKLFNRRDE 53 :::::::: ::::::::::::::::: :::::::: d1e5da1 1 P-----------------TNKVVIFYDSMWHSTEKMARVLAESFRDEGC-TVKLMWCK-- 40 d1vi2a1 54 FFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKVGMKPLEN-E--S- 109 ::: ::::::::::::::::::: :::::: : : d1e5da1 41 -----------------------ACH-HSQIMSEISDAGAVIVGSP--THNNGILPYVAG 74 d1vi2a1 110 LVND-ISLLHPGLLVTECVY----NP-HMTKLLQQAQQAGCKT-IDGYGM-------LLW 155 :::: ::::::::::::::: :: ::: :::::::::::: :::::: ::: d1e5da1 75 TLQYIKGLRPQNKIGGAFGSFGWSGESTKV-LAEWLTGMGFDMPATPVKVKNVPTHADYE 133 d1vi2a1 156 QGAE---------------QFTLWTGKDFPLEYVKQVMGFGA 182 :::: d1e5da1 134 QLKTMAQTIARALKAKLAA----------------------- 152 HHsearch alignment (Probability: 0.55 E-value:0.00) d1vi2a1 82 QAFAEALASADILTNGTKVGMKPLENESLVNDISLLH------PGLLVTECVYNP---HM 132 :::::::::::::::::::::::::::: :::::::: ::::::: :::: :: d1e5da1 45 SQIMSEISDAGAVIVGSPTHNNGILPYV-AGTLQYIKGLRPQNKIGGAFG-SFGWSGEST 102 d1vi2a1 133 TKLLQQAQQAGCKTI-DGY 150 ::::::::::::::: ::: d1e5da1 103 KVLAEWLTGMGFDMPATPV 121