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 <-- 1.256 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1js1x2) 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 d1js1x2 Transcarbamylase-​like proteinAspartate/​ornithine carbamoyltransferaseATC-​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 <-- 1.256 --> Hit
DALI alignment (Z-score: 8.1 Raw score:647.40) d1vi2a1 1 dgtghiraikesgfdiKGKTMVLLG-------aGGASTAIGAQGAIEGLkEIKLFNRRDe 53 ::::::::: :::::::::::::::: ::::::::: d1js1x2 1 ---------------tARPKVVMTWaphprplpQAVPNSFAEWMNATDY-EFVITHPEG- 43 d1vi2a1 54 FFDKaLAFAQrvnentdcVVTVTDladqqAFAEALASADILTNGT-------kvgmkple 106 :::: ::::: :::::: :::::::::::::::: d1js1x2 44 YELD-PKFVG--------NARVEY-----DQMKAFEGADFIYAKNwaaytgdnygqilst 89 d1vi2a1 107 nESLVnDISLLH--pGLLVTECVYnpHMTK--LLQQAQQAGcKTIDgYGMLLWQGAEQFT 162 :::: :::::: ::::::::: :::: ::::::::: :::: ::::::::::::: d1js1x2 90 dRNWTvGDRQMAvtnNAYFMHCLP--VRRNmiVTDDVIESP-QSIV-IPEAANREISATV 145 d1vi2a1 163 LWTGKdfpleyvkqvmgfga 182 ::::: d1js1x2 146 VLKRL----lenlphhhhhh 161 FAST alignment (Normalized score: 5.19 Raw score:888.40) d1vi2a1 1 DGTGHIRAIKESGFDI-KGKTMVLLGA----------GGASTAIGAQGAIEGLKEIKLFN 49 ::::::: ::::::::::::::: ::::::: d1js1x2 1 ----------------TARPKVVM---TWAPHPRPLPQAVPNSFAEWMNATD-YEFVITH 40 d1vi2a1 50 RRDEFFDK-----ALAFAQRVNENTD-CVVTVTDLADQQ-AFAEALASADILTNGTKVGM 102 : :::: :::::: :::::::::::::: d1js1x2 41 P-------EGYELDPKF---------VGNARVE------YDQMKAFEGADFIYA------ 72 d1vi2a1 103 KPLENESLVNDISLLHP--------------------------------GLLVTECVYNP 130 ::::::: d1js1x2 73 -----------------KNWAAYTGDNYGQILSTDRNWTVGDRQMAVTNNAYFMHC---- 111 d1vi2a1 131 HM----------TKLLQQAQQAGCKTI----DGYGMLLWQGAEQFTLWTGKDFPLEYVKQ 176 ::::: :::::::::::::::::: d1js1x2 112 --LPVRRNMIVTDDVIE----------SPQSIVIPEAANREISATVVLK----------- 148 d1vi2a1 177 VMGFGA------------- 182 d1js1x2 149 ------RLLENLPHHHHHH 161 TMalign alignment (TM-score: 0.54 Raw score:97.58) d1vi2a1 1 DGTGHIRAIKESGFDIKGKTMVLLG-------AGGASTAIGAQGAIEGLKEIKLFNRRDE 53 : ::::::::: ::::::::::::::::: ::::::::: d1js1x2 1 --------------T-ARPKVVMTWAPHPRPLPQAVPNSFAEWMNATDY-EFVITHPEG- 43 d1vi2a1 54 FFDKALAFAQRVNENTDCVVTVTDLADQQAFAEALASADILTNGTKV------------- 100 :::: :::: : : ::::: :::::::::::::::::: d1js1x2 44 YELD-PKFV-G-N------ARVEY-----DQMKAFEGADFIYAKNWAAYTGDNYGQILST 89 d1vi2a1 101 -GMKPLENESLVNDISLLH--PGLLVTECVYNPHMTK---LLQQAQQAGCKTID-GYGML 153 ::::::::::: ::::::::: :: :: :::::::::::::: ::::: d1js1x2 90 D-------RNWTVGDRQMAVTNNAYFMHCL-PV--RRNMIVTDDVIESPQSIVIPEAANR 139 d1vi2a1 154 LWQGAEQFTLWTG---------KDFPLEYVKQVMGFGA 182 ::::::::::::: d1js1x2 140 EISATVVLKRLLENLPHHHHHH---------------- 161 HHsearch alignment (Probability: 0.05 E-value:0.02) d1vi2a1 27 GGASTAIGAQGAIEGLKEIKLFNRRDEFFDKALAFAQRVNENTDCVVTVTDLADQQAFAE 86 :::::::::::::::: ::::::::: :::::::::: ::::::::: d1js1x2 19 QAVPNSFAEWMNATDY-EFVITHPEG--YELDPKFVGN-------------ARVEYDQMK 62 d1vi2a1 87 ALASADILTNGTKVGMK 103 ::::::::::::::::: d1js1x2 63 AFEGADFIYAKNWAAYT 79