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 <-- 0.786 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1ptma_) 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 d1ptma_ 4-​hydroxythreonine-​4-​phosphate dehydrogenase PdxAIsocitrate/​Isopropylmalate dehydrogenase-​likeIsocitrate/​Isopropylmalate dehydrogenase-​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 <-- 0.786 --> Hit
DALI alignment (Z-score: 3.1 Raw score:387.90) d1jzta_ 1 lkvvssklaaeidkelmgpqigftlqqlmelagfsvaqavcrqfplrgktETEKgKHVFV 60 :::: ::::: d1ptma_ 1 --------------------------------------------------MVKT-QRVVI 9 d1jzta_ 61 IAG-PGNNGGDGLVCARHlkLFGYNPVVFYPkrsertEFYKQL--vHQLN---------- 107 ::: :::::::::::::: ::::::::::: :::::: :::: d1ptma_ 10 TPGePAGIGPDLVVQLAQ-rEWPVELVVCAD--atllTNRAAMlglPLTLrpyspnspaq 66 d1jzta_ 108 ---fFKVPVLSQD---------------------egNWLEYLKPEKTLCIVDAIFgfsFK 143 ::::::::: ::::::::::::::::::: :: d1ptma_ 67 pqtaGTLTLLPVAlrapvtagqlavenghyvvetlaRACDGCLNGEFAALITGPV---HK 123 d1jzta_ 144 PPMR---epfKGIVEELCKV---------------------------------------- 160 :::: :::::::::: d1ptma_ 124 GVINdagipfTGHTEFFEERsqakkvvmmlateelrvalatthlplrdiadaitpallhe 183 d1jzta_ 161 ------------------------------------------------------------ 161 d1ptma_ 184 viailhhdlrtkfgiaeprilvcglnphagegghmgteeidtiipvlnelraqgmklngp 243 d1jzta_ 161 -------------------------------------------qNIIPIVSVDVptgwdv 177 :::::::::: d1ptma_ 244 lpadtlfqpkyldnadavlamyhdqglpvlkyqgfgrgvnitlgLPFIRTSVDH------ 297 d1jzta_ 178 dkgpisqpsinpavlvsltvpkpcsshirenqtthyvggrfiprdfankfgfepfgyest 237 d1ptma_ 298 ----------------------------------gtalelagrgkadvgsfitalnlaik 323 d1jzta_ 238 dqilkl 243 d1ptma_ 324 mivntq 329 FAST alignment (Normalized score: 1.84 Raw score:519.30) d1jzta_ 1 LK---------------------------------------------------------- 2 d1ptma_ 1 --MVKTQRVVITPGEPAGIGPDLVVQLAQREWPVELVVCADATLLTNRAAMLGLPLTLRP 58 d1jzta_ 3 ------------------------------------------------------------ 3 d1ptma_ 59 YSPNSPAQPQTAGTLTLLPVALRAPVTAGQLAVENGHYVVETLARACDGCLNGEFAALIT 118 d1jzta_ 3 -----------------------------------------------VVSSKLAAEIDKE 15 ::::::::: d1ptma_ 119 GPVHKGVINDAGIPFTGHTEFFEERSQAKKVVMMLATEELRVALATTHLPLRDIAD---- 174 d1jzta_ 16 LMGPQIGFT--LQQLMELAGFSVAQAVCRQFPLRGKTETEK---GKHVFVIA-------- 62 :::::::::::::::::::: ::::::: d1ptma_ 175 ---------AITPALLHEVIAILHHDLRTKF----------GIAEPRILVC-GLNPHAGE 214 d1jzta_ 63 -------GPGNNGGDGLVCARHLKLFGYNPVVFYPKRSERTEFYKQLVHQLNFFKVPVLS 115 :::::::::::::: :::::: :::: d1ptma_ 215 GGHMGTEEIDTIIPVLNELRA----QGMKLN-------------------------GPLP 245 d1jzta_ 116 QDEGNWLEYL-----KPEKTLCIVDAIFGFSFKPPMREPFKG------IVEELCKVQNII 164 ::: ::::::::: ::::::: d1ptma_ 246 ADT-------LFQPKYLDNADAVL------------------AMYHDQGLPVLKY----- 275 d1jzta_ 165 PIVSVDVPTGWDVDKGPISQPSINPAVLVSLTVPKPCSSHIREN------QTTHYVGGRF 218 :::: d1ptma_ 276 --------------------------------------------QGFGRGVNIT------ 285 d1jzta_ 219 IPRDFANKFGFEPFGYESTDQILKL----------------------------------- 243 d1ptma_ 286 -------------------------LGLPFIRTSVDHGTALELAGRGKADVGSFITALNL 320 d1jzta_ 244 --------- 244 d1ptma_ 321 AIKMIVNTQ 329 TMalign alignment (TM-score: 0.36 Raw score:87.59) d1jzta_ 1 LKVVSSKLAAEIDKELMGPQIGFTLQQLMELAGFSVAQAVCRQFPLRGKTETEKGKHVFV 60 ::: :::::: d1ptma_ 1 -------------------------------------------------MVK--TQRVVI 9 d1jzta_ 61 IAG-P-GNNGGDGLVCARHLKLFGYNPVVFYP-KRSERTEFYKQLVHQLN---------- 107 ::: : ::::::::::::: ::::::::::: :::::::::::: :::: d1ptma_ 10 TPGEPAGIGPDLVVQLAQR--EWPVELVVCADATLLTNRAAMLGL-PLTLRPYSPNSPAQ 66 d1jzta_ 108 ---FFKVPVLSQDE-------------------G-NWL-EYLKPEKTLCIVDAIFGFSFK 143 ::::::::::: : ::: :::::::::::::::: :: d1ptma_ 67 PQTAGTLTLLPVALRAPVTAGQLAVENGHYVVETLARACDGCLNGEFAALITGPV---HK 123 d1jzta_ 144 PPMR-EPFKG-IV-EELC-KVQN-IIPIVSVD--------VPTGWDVDKGPIS------- 183 :::: ::::: :: :::: :::: :::::::: ::::: d1ptma_ 124 GVINDAGIPFTGHTEFFEERSQAKKVVMMLATEELRVALA--------TTHLPLRDIADA 175 d1jzta_ 184 -----------QPSIN---PA---V----------------------------------- 191 : : : d1ptma_ 176 ITPALLHEVIA----ILHH-DLRTKFGIAEPRILVCGLNPHAGEGGHMGTEEIDTIIPVL 230 d1jzta_ 192 ----------------------------------LVSLTVPKPCSSHI----RENQTTHY 213 :::::: :: d1ptma_ 231 NELRAQGMKLNGPLPADTLFQPKYLDNADAVLAM--------YHDQGLPVLK------YQ 276 d1jzta_ 214 VGGR----------------------------------FIPRDFANKFGFEPFGYESTDQ 239 :::: : d1ptma_ 277 GFGRGVNITLGLPFIRTSVDHGTALELAGRGKADVGSF---------------------I 315 d1jzta_ 240 I---LK---------L 243 : : d1ptma_ 316 TALN-LAIKMIVNTQ- 329 HHsearch alignment (Probability: 0.03 E-value:0.12) d1jzta_ 164 IPIVSVDVPTGWDVDKGP 181 :::::: ::::::::: d1ptma_ 200 EPRILV---CGLNPHAGE 214