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: T515_B.pdb B
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL


Query <-- 1.022 --> Intermediate <-- 1.198 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1s8na_) through the intermediate protein (d1ujpa_) by significant SVM score (>0.4).

  SCOP Id Protein SCOP Superfamily SCOP Fold SCOP
Class
Intermediate d1ujpa_ Trp synthase alpha-​subunitRibulose-​phoshate binding barrelTIM beta/​alpha-​barrelα/β
Hit d1s8na_ Probable two-​component system transcriptional regulator Rv1626CheY-​likeFlavodoxin-​likeα/β

Supporting Alignments

Query <-- 1.022 --> Intermediate
DALI alignment (Z-score: 9.2 Raw score:936.30) query 1 mietpyylidkakltrnmeriahvrEKSGAKALLALK-----cfaTWSVFDLMRDYMDGT 55 :::::::::::: ::::::::::::::: d1ujpa_ 1 --------------mttleafakarSEGRAALIPYLTagfpsregFLQAVEEVLPYADLL 46 query 56 TSSS-------------------------LFEVRLGRERFGKETHAYSVA------yGDN 84 :::: ::::::::::::::::::::: ::: d1ujpa_ 47 EIGLpysdgpviqraselalrkgmsvqgaLELVREVRALTEKPLFLMTYLnpvlawgPER 106 query 85 EIDEVVS-HADKIIF-NSIS-qlERFADKAA--GIARGLRLNPQrlgeWDVPKVERVMDR 139 ::::::: ::::::: :::: :::::::: ::::::::::: :::::::::::: d1ujpa_ 107 FFGLFKQaGATGVILpDLPPdedPGLVRLAQeiGLETVFLLAPT----STDARIATVVRH 162 query 140 IN-GFMIHNNcenkdfglfdrMLGEIEERFGALIArvDWVSLGGGIHFtgddypvDAFSA 198 :: ::::::: :::::::::::::: ::::::::::: ::::: d1ujpa_ 163 ATgFVYAVSV-----------EVKDLVRRIKARTA--LPVAVGFGVSG-------KATAA 202 query 199 RLRafsdrygvqIYLEPGEASI-TKSTtlevtvldtlynknlaivdssieahmldlliyr 257 ::: :::::::::: :::: d1ujpa_ 203 QAA-------vaDGVVVGSALVrALEE--------------------------------- 222 query 258 etakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqDAAGytmvkknwfng 317 :::: d1ujpa_ 223 ---------------------------------------------GRSL----------- 226 query 318 vkmpaiaireldgsvrtvreftyadyeqsls 348 d1ujpa_ 227 --------------apllqeirqglqrlplp 243 FAST alignment (Normalized score: 5.49 Raw score:1595.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS--------------GAKALLALKCFA------ 40 ::::::: d1ujpa_ 1 ----------------------------MTTLEAFAKARSEGRAALIPY-----LTAGFP 27 query 41 ----TWSVFDLMRDYMDGTTSS--------------------------SLFEVRLGRERF 70 ::::::::::::::::: :::::::::::: d1ujpa_ 28 SREGFLQAVEEVLPYADLLEI-GLPYSDGPVIQRASELALRKGMSVQGALELVREVRALT 86 query 71 GKETHAYSVAY---------GDNEIDEVVS-HADKIIFNSIS--QLERFADKA-----AG 113 :::::::: :::::::::: :::::::: ::::::::: :: d1ujpa_ 87 EKPLFLMT---YLNPVLAWGPERFFGLFKQAGATGVILP---DLPPDEDPGLVRLAQEIG 140 query 114 IARGLRLNPQRLGE-WDVPKVERVMDR-INGFMIHNNCENKDFG--LFDRMLGEIEERFG 169 ::::::::: :::::::::::: ::::::: :::::::::::: d1ujpa_ 141 LETVFLLAP-----TSTDARIATVVRHATGFVYAV---------SVEVKDLVRRIKAR-- 184 query 170 ALIARV--DWVSLGGGIHFTGDDYP-----VDAFSARLRAFSDRYGVQ-IYLEPGEASIT 221 ::::: :::::::::: ::::::::: d1ujpa_ 185 ------TALPVAV------------GFGVSGKATAAQAAV--------ADGVVVGSAL-- 216 query 222 KSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAG 281 d1ujpa_ 217 ------------------------------------------------------------ 217 query 282 DVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYA 341 d1ujpa_ 217 ------------------------------------------------------------ 217 query 342 DYEQSLS--------------------------- 348 d1ujpa_ 217 -------VRALEEGRSLAPLLQEIRQGLQRLPLP 243 TMalign alignment (TM-score: 0.36 Raw score:126.07) query 1 ------------------------------------------------------------ 1 d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAGFPSREGFLQAVEEVLPYADLLEIGLPYSDGPVIQR 60 query 1 ----------MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKC-FAT---WSV-F 45 :::::::::::::::::::::::::: ::: ::: : d1ujpa_ 61 ASELALRKGM------------SVQGALELVREVRALTEKPLFLMTYLNPVLAWGPERFF 108 query 46 DLMRDY-MDGTTSS-SLF-EVRLGRERFG---KETHAYSVA-YGDNEIDEVVSHA-DKII 97 :::::: ::::::: ::: :::::::::: ::::::::: ::::::::::::: :::: d1ujpa_ 109 GLFKQAGATGVILPDLPPDEDPGLVRLAQEIGLETVFLLAPTSTDARIATVVRHATGFVY 168 query 98 FN---SISQLERFADKAAGIARGLRLNPQRLGEWDVPKVERVMDRINGFMIHN-NCENKD 153 :: :::::::::::: ::::::::::: ::::::::: : :::::::: :::: : d1ujpa_ 169 AVSVEVKDLVRRIKART-ALPVAVGFGVS--GKATAAQAA--V--ADGVVVGSALVRA-L 220 query 154 FGLFDRMLGEIEERFGALIAR----VDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGV 209 ::: ::::::::: ::::::: d1ujpa_ 221 EEG-RSLAPLLQE-IRQGLQRLPLP----------------------------------- 243 query 210 QIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSH 269 d1ujpa_ 244 ------------------------------------------------------------ 244 query 270 SYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELD 329 d1ujpa_ 244 ------------------------------------------------------------ 244 query 330 GSVRTVREFTYADYEQSLS 348 d1ujpa_ 244 ------------------- 244 HHsearch alignment (Probability: 0.04 E-value:0.64) query 19 ERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSLFE----VRLGRERFGKET 74 :::::::::::::::::::::::::::::::::::::::::::: :::::::::::: d1ujpa_ 130 PGLVRLAQEIGLETVFLLAPTSTDARIATVVRHATGFVYAVSVEVKDLVRRIKARTALPV 189 query 75 HAYSVAYGDNEIDEVVSHADKII 97 ::::::::::::::::::::::: d1ujpa_ 190 AVGFGVSGKATAAQAAVADGVVV 212
Intermediate <-- 1.198 --> Hit
DALI alignment (Z-score: 3.2 Raw score:333.80) d1ujpa_ 1 mttLEAFakarsegraaLIPYLT---------------------agFPSREGFLQAVEEV 39 :::: :::::: :::::::::::::: d1s8na_ 1 ---AVPR----------RVLIAEdealirmdlaemlreegyeivgeAGDGQEAVELAELH 47 d1ujpa_ 40 LpyADLLEIGLPysdgpviqraselalrkgmsvqGALELVREVRALTEKPLFLMTYLNPV 99 : ::::::::: :::::::::::::::::::::::::: d1s8na_ 48 K--PDLVIMDVK------------------mprrDGIDAASEIASKRIAPIVVLTAFSQR 87 d1ujpa_ 100 lawgpeRFFGLFKQAGATGVILPDlppdedpglvrlaqeigletvFLLAptstdariatv 159 :::::::::::::::::: :::: d1s8na_ 88 ------DLVERARDAGAMAYLVKP---------------------FSIS----------- 109 d1ujpa_ 160 vrhATGFvyavsvevkdlvrrikartalpvavgfgvsgkataaqaavadgvvvgsalvra 219 :::: d1s8na_ 110 ---DLIPaielavsrfreitalegevatlserletrklverakgllqtkhgmtepdafkw 166 d1ujpa_ 220 leegrslapllqeirqglqrlplp 243 d1s8na_ 167 iqraamdrrttmkrvaevvletlg 190 FAST alignment (Normalized score: 2.88 Raw score:619.40) d1ujpa_ 1 MTTLEAFAKARSEGRA---ALIPYLTAGF--------------------------PSREG 31 ::::: ::::: d1s8na_ 1 ----------------AVPRRVLI-----AEDEALIRMDLAEMLREEGYEIVGEAGDGQE 39 d1ujpa_ 32 FLQAVEEVLPYADLLEIGLPYSDGPVIQRASELALRKGMSVQ------GALELVREVRAL 85 ::::::: ::::::::: ::::::::::: d1s8na_ 40 AVELAEL--HKPDLVIMD------------------------VKMPRRDGIDAASEIAS- 72 d1ujpa_ 86 T--EKPLFLMTYLNPVLAWGP-ERFFGLFKQAGA--TGVILPDLPPDEDPGLVRLAQEIG 140 ::::::::::: :::::::::: :::::::: d1s8na_ 73 -KRIAPIVVLTAFS-------QRDLVERARDA--GAMAYLVKPF---------------- 106 d1ujpa_ 141 LETVFLLAPTSTDARIATVVRHATGFVYAVSVEVKDLVRRIKARTALPVAVGFGVSGKAT 200 d1s8na_ 107 ------------------------------------------------------------ 107 d1ujpa_ 201 AAQAAVADGVVVGSALVRALEEGRSLAPLLQEIRQGLQRLPLP----------------- 243 d1s8na_ 107 -------------------------------------------SISDLIPAIELAVSRFR 123 d1ujpa_ 244 ------------------------------------------------------------ 244 d1s8na_ 124 EITALEGEVATLSERLETRKLVERAKGLLQTKHGMTEPDAFKWIQRAAMDRRTTMKRVAE 183 d1ujpa_ 244 ------- 244 d1s8na_ 184 VVLETLG 190 TMalign alignment (TM-score: 0.32 Raw score:78.51) d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAGFPSREGFLQAVEEVLPYADLLEIGLPYSDGPVIQR 60 : : :: ::::::::::::::: d1s8na_ 1 -----A----------V-PR-------------------------RVLIAEDEALIRMDL 19 d1ujpa_ 61 AS----------ELALRKGMSVQGALELVREVRALTEKPLFLMTYLNPVLAWGPERFFGL 110 :: :: ::::::::::::::: ::::::::::: :::::::::: d1s8na_ 20 AEMLREEGYEIV--GE--AGDGQEAVELAELHK-----PDLVIMDVKMP-RRDGIDAASE 69 d1ujpa_ 111 FKQAGATGVILPDLPPDEDPGLVRLAQEIGLETVFL--LAPTS--TDARIATVV--RHAT 164 ::::::::::::::: ::::::::::::::::::: ::::: :: :: d1s8na_ 70 IASKRIAPIVVLTAF--SQRDLVERARDAGAMAYLVKPFSISDLI-------PAIE--LA 118 d1ujpa_ 165 GFV-----------------------------------YAVSVEVKDLVRRIKARTALP- 188 ::: :::::: d1s8na_ 119 VSRFREITALEGEVATLSERLETRKLVERAKGLLQTKH---------------GMTEPDA 163 d1ujpa_ 189 ---------------------------VAVGFGVSGKATAAQAAVADGVVVGSALVRALE 221 d1s8na_ 164 FKWIQRAAMDRRTTMKRVAEVVLETLG--------------------------------- 190 d1ujpa_ 222 EGRSLAPLLQEIRQGLQRLPLP 243 d1s8na_ 191 ---------------------- 191 HHsearch alignment (Probability: 0.68 E-value:0.00) d1ujpa_ 73 QGALELVREVRALTEKPLFLMTYLNPVLAWGPERFFGLFKQAGATGVILPDLPPDEDPGL 132 ::::::::::::::::::::::::: ::::::::::::::::::::::::::::: d1s8na_ 61 RDGIDAASEIASKRIAPIVVLTAFS------QRDLVERARDAGAMAYLVKPFSISDLIPA 114 d1ujpa_ 133 VRLA 136 :::: d1s8na_ 115 IELA 118