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 <-- 1.058 --> Intermediate <-- 0.776 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1ua4a_) through the intermediate protein (d1jzta_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1jzta_ Hypothetical protein YNL200c (YNU0 YEAST)YjeF N-​terminal domain-​likeYjeF N-​terminal domain-​likeα/β
Hit d1ua4a_ ADP-​dependent glucokinaseRibokinase-​likeRibokinase-​likeα/β

Supporting Alignments

Query <-- 1.058 --> Intermediate
DALI alignment (Z-score: 3.6 Raw score:420.50) query 1 ---------------------------------------------------gmENKKMNL 9 ::::::: d1jzta_ 1 lkvvssklaaeidkelmgpqigftlqqlmelagfsvaqavcrqfplrgkteteKGKHVFV 60 query 10 LLfSGDYdKALASLIIANAAREMEIEVTIFCafwGLLLlrdpekasqedkslyeqafssl 69 :: :::: ::::::::::::::::::::::: :::: d1jzta_ 61 IA-GPGN-NGGDGLVCARHLKLFGYNPVVFY---PKRS---------------------- 93 query 70 tpREAEelplskmnlggigkkmllemmkeekapKLSDLLSGARKKEVKFYAXqlsveimg 129 :::: ::::::::::::::::::: d1jzta_ 94 --ERTE---------------------------FYKQLVHQLNFFKVPVLSQ-------- 116 query 130 fkkeelfpevQIMDvkeYLKNAL--ESDLQLFI--------------------------- 160 :::: :::::: :::::::: d1jzta_ 117 ----------DEGN---WLEYLKpeKTLCIVDAifgfsfkppmrepfkgiveelckvqni 163 query 161 ------------------------------------------------------------ 161 d1jzta_ 164 ipivsvdvptgwdvdkgpisqpsinpavlvsltvpkpcsshirenqtthyvggrfiprdf 223 query 161 -------------------- 161 d1jzta_ 224 ankfgfepfgyestdqilkl 243 FAST alignment (Normalized score: 4.04 Raw score:797.30) query 1 G----------------------------------------------------MENKKMN 8 ::::::: d1jzta_ 1 -LKVVSSKLAAEIDKELMGPQIGFTLQQLMELAGFSVAQAVCRQFPLRGKTETEKGKHVF 59 query 9 LLLFSGDYDKALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSS 68 :::: ::::::::::::::::::::::::::: d1jzta_ 60 VIAG--PGNNGGDGLVCARHLKLFGYNPVVFYP--------------------------- 90 query 69 LTPREAEELPLSKMNLGGIGKKMLLEMMKEEKAP-------KLSDLLSGARKKEVKFYAX 121 :::::::::::::::::: d1jzta_ 91 ----------------------------------KRSERTEFYKQLVHQLNFFKVPVLS- 115 query 122 QLSVEIMGFKKEELFPEVQIMDVK----EYLKNAL---ESDLQLFI-------------- 160 :::::: :::::: d1jzta_ 116 ------------------------QDEGNWLEYL-KPEKTLCIV--DAIFGFSFKPPMRE 148 query 161 ------------------------------------------------------------ 161 d1jzta_ 149 PFKGIVEELCKVQNIIPIVSVDVPTGWDVDKGPISQPSINPAVLVSLTVPKPCSSHIREN 208 query 161 ----------------------------------- 161 d1jzta_ 209 QTTHYVGGRFIPRDFANKFGFEPFGYESTDQILKL 243 TMalign alignment (TM-score: 0.44 Raw score:70.86) query 1 --------------------------------------------GME------N-KKMNL 9 ::: : ::::: d1jzta_ 1 LKVVSSKLAAEIDKELMGPQIGFTLQQLMELAGFSVAQAVCRQFPLRGKTETEKGKHVFV 60 query 10 LLFSGDYDKALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSL 69 :: ::: ::::::::::::::::::::::::: : : d1jzta_ 61 IA-GPG-NNGGDGLVCARHLKLFGYNPVVFYP-K--R----------------------- 92 query 70 TPREAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMG 129 ::::: :::::::::::::::::::: d1jzta_ 93 -SERTE---------------------------FYKQLVHQLNFFKVPVLSQD------- 117 query 130 FKKEELFPEVQIMDVKEYLKNALESDLQLFI----------------------------- 160 ::::::::: :::::::::: d1jzta_ 118 -----------EGNWLEYLK-PEKTLCIVDAIFGFSFKPPMREPFKGIVEELCKVQNIIP 165 query 161 ------------------------------------------------------------ 161 d1jzta_ 166 IVSVDVPTGWDVDKGPISQPSINPAVLVSLTVPKPCSSHIRENQTTHYVGGRFIPRDFAN 225 query 161 ------------------ 161 d1jzta_ 226 KFGFEPFGYESTDQILKL 243 HHsearch alignment (Probability: 0.06 E-value:0.03) query 4 NKKMNLLLFSGDYDKALASLIIANAAREMEIEVTIFCAF 42 ::::::::::::::::::::::::::::::::::::::: d1jzta_ 53 EKGKHVFVIAGPGNNGGDGLVCARHLKLFGYNPVVFYPK 91
Intermediate <-- 0.776 --> Hit
DALI alignment (Z-score: 6.6 Raw score:851.20) d1jzta_ 1 lkvvssklaaeidkelmgpqigftlqqlmelagfsvaqavcrqfpLRGKteteKGKHVFV 60 :::: ::::::: d1ua4a_ 1 --------------------------------ptweelyknaiekAIKS--vpKVKGVLL 26 d1jzta_ 61 IAG--------------------------------------------------------- 63 ::: d1ua4a_ 27 GYNtnidaikyldskdleeriikagkeevikyseelpdkintvsqllgsilwsirrgkaa 86 d1jzta_ 64 -------------------pgnngGDGLVCARHLK-LFGYNPVVFYpKRSErtEFYKQLV 103 ::::::::::: :::::::::: :::: ::::::: d1ua4a_ 87 elfvescpvrfymkrwgwnelrmgGQAGIMANLLGgVYGVPVIVHV-PQLS--RLQANLF 143 d1jzta_ 104 hqlNFFKVPVLS------------------------------------------------ 115 ::::::::: d1ua4a_ 144 ---LDGPIYVPTlengevklihpkefsgdeencihyiyefprgfrvfefeaprenrfigs 200 d1jzta_ 116 ----------QDEG--NWLEYLKpeKTLCIVDAIFGfSFKP-PMREPFKGIVEELCKVQN 162 :::: ::::::: ::::::::::: :::: :::::::::::::::::: d1ua4a_ 201 addynttlfiREEFreSFSEVIK--NVQLAILSGLQ-ALTKeNYKEPFEIVKSNLEVLNE 257 d1jzta_ 163 -IIPIVSVDV--ptgwDVDKgpisqpsiNPAVLVSLT-VPKPC----------------- 201 ::::::::: :::: ::::::::: ::::: d1ua4a_ 258 rEIPVHLEFAftpdekVREE--ilnvlgMFYSVGLNEvELASImeilgekklakellahd 315 d1jzta_ 202 --------------sSHIRenQTTHYVGGRFiprdfankfgfepfgyestdQILKL---- 243 :::: :::::::::: ::::: d1ua4a_ 316 pvdpiavteamlklaKKTG--VKRIHFHTYG--------------------YYLALteyk 353 d1jzta_ 244 ------------------------------------------------------------ 244 d1ua4a_ 354 gehvrdallfaalaaaakamkgnitsleeireatsvpvnekatqveeklraeygikegig 413 d1jzta_ 244 ----------------------------------------- 244 d1ua4a_ 414 evegyqiafiptkivakpkstvgigdtisssafigefsftl 454 FAST alignment (Normalized score: 3.15 Raw score:1046.00) d1jzta_ 1 LKVVSSKLAAEIDKELMGPQIGFTLQQLMELAGFSVAQAVCRQFPLRGK----------- 49 d1ua4a_ 1 -------------------------------------------------PTWEELYKNAI 11 d1jzta_ 50 --TETEKG----KHVFVIAGPGNNG----------------------------------- 68 :::: ::::: d1ua4a_ 12 EKAIKS--VPKVKGVLL--------GYNTNIDAIKYLDSKDLEERIIKAGKEEVIKYSEE 61 d1jzta_ 69 -------------------------------------------------GDGLVCARHL- 78 :::::::::: d1ua4a_ 62 LPDKINTVSQLLGSILWSIRRGKAAELFVESCPVRFYMKRWGWNELRMGGQAGIMANLLG 121 d1jzta_ 79 KLFGYNPVVFYPKRSERTEFYKQLVHQL-NFFKVPVLSQDEG------------------ 119 :::::::::::::: ::::::: :::::::: d1ua4a_ 122 GVYGVPVIVHVPQL------SRLQANL-FLDGPIYVP-----TLENGEVKLIHPKEFSGD 169 d1jzta_ 120 -----------------------------------------------NWLEYLKPE-KTL 131 :::::: ::: d1ua4a_ 170 EENCIHYIYEFPRGFRVFEFEAPRENRFIGSADDYNTTLFIREEFRESFSEVI---KNVQ 226 d1jzta_ 132 CIVDAIFGFSFKPPM------REPFKGIVEELCKVQN-IIPIVSVDVPTGWDVDKGPISQ 184 :::::: :::::: ::::::::::::: :::::: d1ua4a_ 227 LAILSG-LQALTK--ENYKEPFEIVKSNLEVLNE---REIPVHL---------------- 264 d1jzta_ 185 PSI-------------------NPAVLVSLTVP--------------------------- 198 ::::::::: d1ua4a_ 265 ---EFAFTPDEKVREEILNVLGMFYSVGLNE--VELASIMEILGEKKLAKELLAHDPVDP 319 d1jzta_ 199 -------KPCSSHIRENQ---TTHYVGGRFIPRDFANKFGFEPFGYESTDQILKL----- 243 :::::: :::::: d1ua4a_ 320 IAVTEAMLKLAKK-----TGVKRIHFH----------------------------TYGYY 346 d1jzta_ 244 ------------------------------------------------------------ 244 d1ua4a_ 347 LALTEYKGEHVRDALLFAALAAAAKAMKGNITSLEEIREATSVPVNEKATQVEEKLRAEY 406 d1jzta_ 244 ------------------------------------------------ 244 d1ua4a_ 407 GIKEGIGEVEGYQIAFIPTKIVAKPKSTVGIGDTISSSAFIGEFSFTL 454 TMalign alignment (TM-score: 0.52 Raw score:126.36) d1jzta_ 1 ---------LKVVSSKLAAEIDKELMGPQIGFTLQQLMELAGFSVAQAVCR-QFPLRGKT 50 :: :::::: d1ua4a_ 1 PTWEELYKN----------------------------------------AIE-KAIKSV- 18 d1jzta_ 51 ETEKGKHVFVIAGPG-N------------------------------------------- 66 : :::::::::::: : d1ua4a_ 19 P--KVKGVLLGYNTNIDAIKYLDSKDLEERIIKAGKEEVIKYSEELPDKINTVSQLLGSI 76 d1jzta_ 67 ----------N----------------------GGDGLVCARHLK-LFGYNPVVFYPKRS 93 : :::::::::::: :::::::::: ::: d1ua4a_ 77 LWSIRRGKAAELFVESCPVRFYMKRWGWNELRMGGQAGIMANLLGGVYGVPVIVHV-PQL 135 d1jzta_ 94 ERTEFYKQLVHQLNFFKVPVLS-------------------------------------- 115 : :::::::::::::::: d1ua4a_ 136 S-----RLQANLFLDGPIYVPTLENGEVKLIHPKEFSGDEENCIHYIYEFPRGFRVFEFE 190 d1jzta_ 116 --------------------QDEG--NWLEYLKPEKTLCIVDAIFGFSFKP-PMREPFKG 152 :::: ::::::: ::::::::::: :::: :::::::: d1ua4a_ 191 APRENRFIGSADDYNTTLFIREEFRESFSEVIK--NVQLAILSGLQ-ALTKENYKEPFEI 247 d1jzta_ 153 IVEELCKVQN-IIPIVSVDVPT-G-WDVDKGPISQPSIN-PAVLVSLTVPK-PCS----- 202 :::::::::: ::::::::::: : :::::::: ::: ::::::::::: ::: d1ua4a_ 248 VKSNLEVLNEREIPVHLEFAFTPDEKVREEILN---VLGMFYSVGLNEVELASIMEILGE 304 d1jzta_ 203 --------------------S---HIR--ENQTTHYVGG--------------------- 216 : ::: :::::::::: d1ua4a_ 305 KKLAKELLAHDPVDPIAVTEAMLKLAKKTGVKRIHFHTYGYYLALTEYKGEHVRDALLFA 364 d1jzta_ 217 ---R---F-------------------------------------------------IPR 221 : : d1ua4a_ 365 ALAAAAKAMKGNITSLEEIREATSVPVNEKATQVEEKLRAEYGIKEGIGEVEGYQIA--- 421 d1jzta_ 222 DFANKFGFEPFGYESTD--------Q---IL--K---------L 243 ::::::: : :: : d1ua4a_ 422 ----------FIPTKIVAKPKSTVGIGDTISSSAFIGEFSFTL- 454 HHsearch alignment (Probability: 0.03 E-value:0.10) d1jzta_ 68 GGDGLVCARHLKL-FGYNPVVFYPKRSE 94 ::::::::::::: :::::::::::::: d1ua4a_ 110 GGQAGIMANLLGGVYGVPVIVHVPQLSR 137