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 <-- 0.733 --> Intermediate <-- 0.707 --> Hit

SVM
score
SVM
score

The query (T517_A.pdb A) is transitively linked to the hit (d1knxa1) through the intermediate protein (d1fw8a_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1fw8a_ Phosphoglycerate kinasePhosphoglycerate kinasePhosphoglycerate kinaseα/β
Hit d1knxa1 HPr kinase/​phoshatase HprK N-​terminal domainHPr kinase/​phoshatase HprK N-​terminal domainMurF and HprK N-​domain-​likeα/β

Supporting Alignments

Query <-- 0.733 --> Intermediate
DALI alignment (Z-score: 5.0 Raw score:484.70) query 1 ------------------------------------------------------------ 1 d1fw8a_ 1 skyslapvakelqsllgkdvtflndcvgpeveaavkasapgsvillenlryhieeegsrk 60 query 1 ------------------------------------------------------------ 1 d1fw8a_ 61 vdgqkvkaskedvqkfrhelssladvyindafgtahrahssmvgfdlpqraagfllekel 120 query 1 -------gMENKKMNLLLFS-GDYDKaLASLIIANAAremeiEVTIFCAFWGLL-LLRDp 51 :::::::::::: ::::: :::::::::: :::::::::::: :::: d1fw8a_ 121 kyfgkaleNPTRPFLAILGGaKVADK-IQLIDNLLDK-----VDSIIIGGGMAFtFKKV- 173 query 52 ekasqedkslyeqafSSLTPReAEELplskmnlggigkkmllemmkeekapKLSDLLSGA 111 :::::: :::: ::::::::: d1fw8a_ 174 ----------lenteIGDSIF-DKAG-----------------------aeIVPKLMEKA 199 query 112 RKKEVKFYAXQlsVEIM-------------gFKKE----elfpevqimDVKEYLKNALES 154 ::::::::::: :::: :::: :::::::::::: d1fw8a_ 200 KAKGVEVVLPV--DFIIadafsadantktvtDKEGipagwqgldngpeSRKLFAATVAKA 257 query 155 DLQLFI------------------------------------------------------ 160 :::::: d1fw8a_ 258 KTIVWNgppgvfefekfaagtkalldevvkssaagntviigggdtatvakkygvtdkish 317 query 161 ------------------------------------------------------------ 161 d1fw8a_ 318 vstgggaslellegkelpgvaflsekkslssklsvqdldlkdkrvfirvdfnvpldgkki 377 query 161 -------------------------------------- 161 d1fw8a_ 378 tsnqrivaalptikyvlehhpryvvlashlgrpngern 415 FAST alignment (Normalized score: 2.52 Raw score:648.60) query 1 GM---------------------------------------------------------- 2 d1fw8a_ 1 --SKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGS 58 query 3 ------------------------------------------------------------ 3 d1fw8a_ 59 RKVDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEK 118 query 3 -----------ENKKMNLLLFSGDYDKALASLIIANAAREMEIE---VTIFCAFWGLLLL 48 ::::::::::::::::::::::::: :::::::::: d1fw8a_ 119 ELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLL--------DKVDSIIIGGGMA--- 167 query 49 RDPEKASQEDKSLYEQAF-----------SSLTPREAEELPLSKMNLGGIGKKMLLEMMK 97 ::::: d1fw8a_ 168 ------------------FTFKKVLENTEIGDSI-------------------------- 183 query 98 EEKAP-------KLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIM-------- 142 :::::::::::::::::::: d1fw8a_ 184 -----FDKAGAEIVPKLMEKAKAKGVEVVLPV--------------------DFIIADAF 218 query 143 ---------------------------DVKEYLKNALESDLQLFI--------------- 160 :::::::::::::::: d1fw8a_ 219 SADANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKAKTIV--WNGPPGVFEFEKFAA 276 query 161 ------------------------------------------------------------ 161 d1fw8a_ 277 GTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPG 336 query 161 ------------------------------------------------------------ 161 d1fw8a_ 337 VAFLSEKKSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEH 396 query 161 ------------------- 161 d1fw8a_ 397 HPRYVVLASHLGRPNGERN 415 TMalign alignment (TM-score: 0.39 Raw score:62.58) query 1 ------------------------------------------------------------ 1 d1fw8a_ 1 SKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGSRK 60 query 1 ------------------------------------------------------------ 1 d1fw8a_ 61 VDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKEL 120 query 1 ---------GMENKKMNLLL-----------------------FS--------------- 13 :::::::::: :: d1fw8a_ 121 KYFGKALEN-PTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEI 179 query 14 ------------------------------------------------------------ 14 d1fw8a_ 180 GDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVTDKEGIPAGWQG 239 query 14 -GD-YDKALASLIIANAAREMEIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTP 71 :: ::::::::::::::: :::::::::: : : : ::: d1fw8a_ 240 LDNGPESRKLFAATVAKAK----TIVWNGPPGV-F----------------E--F--EKF 274 query 72 REAEELPLSKMNLGGIGKKMLLEMMKEEKAPKLSDLLSGARKK-EVKFYAXQLSVEIMGF 130 :::::: ::::::::::: :::::::::::: : d1fw8a_ 275 AAGTKA--------------------------LLDEVVKSSAAGNTVIIGGGDTAT---V 305 query 131 KKEELFPE-V--QI-MDVKEYLKNALE--------------------------------- 153 :::::::: : :: :::::::::::: d1fw8a_ 306 AKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKKSLSSKLSVQDLDLKDKRVFIR 365 query 154 --------------------------------------------------SDLQLFI 160 d1fw8a_ 366 VDFNVPLDGKKITSNQRIVAALPTIKYVLEHHPRYVVLASHLGRPNGERN------- 415 HHsearch alignment (Probability: 0.03 E-value:0.09) query 85 GGIGKKMLLEM---------MKEEKAPKLSDLLSGARKKEVKFY 119 ::::::::::: :::::::::::::::::::::::: d1fw8a_ 164 GGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVV 207
Intermediate <-- 0.707 --> Hit
DALI alignment (Z-score: 2.0 Raw score:256.80) d1fw8a_ 1 skyslapvakelqsllgkdvtflndcvgpeveaavkasapgsvillenlryhieeegsrk 60 d1knxa1 1 ------------------------------------------------------------ 1 d1fw8a_ 61 vdgqkvkaskedvqkfrhelssladvyindafgtahrahssmvgfdlpqraagfllekel 120 d1knxa1 1 ------------------mkkllvkelieqfqdcvnlidghtntsnvirvpglkrvvfem 42 d1fw8a_ 121 kyFGKALenptrPFLAILGGAKVADK--------iQLIDNLLD-KVDSIIIGGGmAFTFk 171 ::::: :::::::::::::: :::::::: :::::::::: :::: d1knxa1 43 lgLFSSQ----iGSVAILGKREFGFLsqktlveqqQILHNLLKlNPPAIILTKS-FTDP- 96 d1fw8a_ 172 kvlenteigdsifdkagaeivPKLMEKAKAKGVEVVLPVdfiiadafsadantktvtdke 231 :::::::::::::::::: d1knxa1 97 ---------------------TVLLQVNQTYQVPILKTD--------------------- 114 d1fw8a_ 232 gipagwqgldngpesrklfaatvakaktivwngpPGVFefekfaaGTKALLDEVVKSSaa 291 :::: ::::::::::::: d1knxa1 115 ---------------------------------fFSTE-------LSFTVETYINEQF-- 132 d1fw8a_ 292 gntviigggdtatvakkygvtdkishvstgggaslellegkelpgvaflsekkslsskls 351 d1knxa1 133 ------------------------------------------------------------ 133 d1fw8a_ 352 vqdldlkdkrvfirvdfnvpldgkkitsnqrivaalptikyvlehhpryvvlashlgrpn 411 d1knxa1 133 ------------------------------------------------------------ 133 d1fw8a_ 412 gern 415 d1knxa1 133 ---- 133 FAST alignment (Normalized score: 1.93 Raw score:450.60) d1fw8a_ 1 SKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGSRK 60 d1knxa1 1 ------------------------------------------------------------ 1 d1fw8a_ 61 VDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKEL 120 d1knxa1 1 ------------------------------------------------------------ 1 d1fw8a_ 121 KYFGKAL-----------------------------------------------ENPTRP 133 :::: d1knxa1 1 -------MKKLLVKELIEQFQDCVNLIDGHTNTSNVIRVPGLKRVVFEMLGLFSSQIG-- 51 d1fw8a_ 134 FLAILGGAKV-------------ADKIQLIDNLLD-KVDSIIIGGGMAFTFKKVLENTEI 179 ::::: :::::::::::: :::::::::: d1knxa1 52 SVAIL-----GKREFGFLSQKTLVEQQQILHNLLKLNPPAIILTKS-------------- 92 d1fw8a_ 180 GDSIFDKAGAEI---VPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVTDKEGIPAG 236 :::::::::::::::::: d1knxa1 93 ------------FTDPTVLLQVNQTYQVPILKT--------------------------- 113 d1fw8a_ 237 WQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAA--GTKALL-DEVVKSSAAGN 293 :::::: ::::::::: d1knxa1 114 ----------------------------------------DFFSTELSFTVETYINEQ-- 131 d1fw8a_ 294 TVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKKSLSSKLSVQ 353 d1knxa1 132 ------------------------------------------------------------ 132 d1fw8a_ 354 DLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEHHPRYVVLASHLGRPNGE 413 d1knxa1 132 ------------------------------------------------------------ 132 d1fw8a_ 414 RN- 415 d1knxa1 132 --F 132 TMalign alignment (TM-score: 0.18 Raw score:74.74) d1fw8a_ 1 --------------------------------SKYSLAPVAKELQSLLGKDVTFLNDCVG 28 ::::::::::: d1knxa1 1 MKKLLVKELIEQFQDCVNLIDGHTNTSNVIRV-----------------PGLKRVVFEML 43 d1fw8a_ 29 PEVEAAVKASAPGSVILL--ENLRYHIEEEGSRKVDGQKVKASKEDVQKFRHELSSLADV 86 :::: :: : :::::: ::::: :: : :: ::::::::::::::::: d1knxa1 44 GLFS--SQ-I--GSVAILGK-REFGF--LS-Q--------KT-LVEQQQILHNLLKLNPP 85 d1fw8a_ 87 YINDAFGTAHRAHSSMVGFD--LPQRAAGFLLEKELKYFGKALENPTRPFLAILGGAKVA 144 ::::::::: :::: ::::: ::::::: : : d1knxa1 86 AIILTKSFT-DPTV-LLQVNQTYQVPILK--T--D------------------------- 114 d1fw8a_ 145 DKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGV 204 d1knxa1 115 ------------------------------------------------------------ 115 d1fw8a_ 205 EVVLPVDFIIADAFSADANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNG 264 d1knxa1 115 ------------------------------------------------------------ 115 d1fw8a_ 265 PPGVFEFEKFAAGTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGA 324 : d1knxa1 115 -------------------------------------------------------F---- 115 d1fw8a_ 325 SLELLEGKELPGVAFLSEKKSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIV 384 :: : d1knxa1 116 ------------------------------------------FS-------------T-- 118 d1fw8a_ 385 AAL-PTIKYVLEHHPRYVVLASHLGRPNGERN 415 ::: :::::::::: d1knxa1 119 ELSFTVETYINEQF------------------ 132 HHsearch alignment (Probability: 0.00 E-value:0.87) d1fw8a_ 149 LIDNLLDKVDSIIIGGGMAFTFKK 172 :::::::::::::::::::::::: d1knxa1 42 MLGLFSSQIGSVAILGKREFGFLS 65