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 <-- 1.382 --> Hit

SVM
score
SVM
score

The query (T515_B.pdb B) is transitively linked to the hit (d1nata_) 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 d1nata_ Sporulation response regulator Spo0FCheY-​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 <-- 1.382 --> Hit
DALI alignment (Z-score: 4.7 Raw score:436.00) d1ujpa_ 1 mttleafakarsegrAALIPYLT--------------------agFPSREGFLQAVEEVL 40 :::::::: ::::::::::::::: d1nata_ 1 ---------------NEKILIVDdqygirillnevfnkegyqtfqAANGLQALDIVTKER 45 d1ujpa_ 41 pyADLLEIGLPysdgpviqraselalrKGMSvqgALELVREVRALT-EKPLFLMTYLNPV 99 ::::::::: :::: :::::::::::: ::::::::::::: d1nata_ 46 --PDLVLLDMK---------------iPGMD---GIEILKRMKVIDeNIRVIIMTAYGEL 85 d1ujpa_ 100 lawgpeRFFGLFKQAGATGVILPDlppdedpglvrlaqeigletvFLLAptstdariatv 159 :::::::::::::::::: :::: d1nata_ 86 ------DMIQESKELGALTHFAKP---------------------FDID----------- 107 d1ujpa_ 160 vrhatgfVYAVsvevkdlvrrikartalpvAVGFgvsgkataaqaavadgvvvgsalvra 219 :::: :::: d1nata_ 108 -------EIRD-------------------AVKK-------------------------- 115 d1ujpa_ 220 leegrslapllqeirqglqrlplp 243 d1nata_ 116 --------------------ylpl 119 FAST alignment (Normalized score: 4.70 Raw score:799.60) d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAGF-------------------------PSREGFLQA 35 :::::: ::::::::: d1nata_ 1 ---------------NEKILI-----VDDQYGIRILLNEVFNKEGYQTFQAANGLQALDI 40 d1ujpa_ 36 VEEVLPYADLLEIGLPYSDGPVIQRASELALRKGMSVQ------GALELVREVRALT-EK 88 ::: ::::::::: ::::::::::::: :: d1nata_ 41 VTK--ERPDLVLLD------------------------MKIPGMDGIEILKRMKVIDENI 74 d1ujpa_ 89 PLFLMTYLNPVLAWGPERFFGLFKQAGATGVILPDLPPDEDPGLVRLAQEIGLETVFLLA 148 ::::::::: ::::::::::::::::::::: d1nata_ 75 RVIIMTAYG------ELDMIQESKELGALTHFAKPF------------------------ 104 d1ujpa_ 149 PTSTDARIATVVRHATGFVYAVSVEVKDLVRRIKARTALPVAVGFGVSGKATAAQAAVAD 208 d1nata_ 105 ------------------------------------------------------------ 105 d1ujpa_ 209 GVVVGSALVRALEEGRSLAPLLQEIRQGLQRLPLP--------------- 243 d1nata_ 105 -----------------------------------DIDEIRDAVKKYLPL 119 TMalign alignment (TM-score: 0.32 Raw score:78.57) d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAGFPSREGFLQAVEEVLPYADLLEIGLPYSDGPVIQ- 59 : : :::::::::::::: d1nata_ 1 ---------------------------------------N--E--KILIVDDQYGIRILL 17 d1ujpa_ 60 RA-----------SELALRKGMSVQGALELVREVRALTEKPLFLMTYLNPVLAWGPERFF 108 : :: :::::::::::::: : :::::::::: :::::::: d1nata_ 18 -NEVFNKEGYQTF---QA---ANGLQALDIVTKER--P---DLVLLDMKIP-GMDGIEIL 64 d1ujpa_ 109 GLFKQAG--ATGVILPDLPPDEDPGLVRLAQEIGLETVFL--LAPTSTDARIATVVRHAT 164 ::::::: :::::: ::: ::::::::::::::::::: ::: d1nata_ 65 KRMKVIDENIRVIIM-TAY--GELDMIQESKELGALTHFAKPFDI--------------- 106 d1ujpa_ 165 GFVYAVSVEVKDLVRRIKARTALPVAVGFGVSGKATAAQAAVADGV---VVGSALVRALE 221 ::: ::: ::: d1nata_ 107 ---DEI------------------RDA----------------VKKYLP----------- 118 d1ujpa_ 222 EGRSLAPLLQEIRQGLQRLPLP 243 : d1nata_ 119 ------------L--------- 119 HHsearch alignment (Probability: 0.82 E-value:0.00) d1ujpa_ 21 YLTAGFPSREGFLQAVEEVLPYADLLEIGLPYSDGPVIQRASELALRKGMSVQGALELVR 80 :::::::::::::::::::::::::::::::::::: :::: d1nata_ 26 YQTFQAANGLQALDIVTKERPDLVLLDMKIPGMDGI--------------------EILK 65 d1ujpa_ 81 EVR-ALTEKPLFLMTYLNPVLAWGPERFFGLFKQAGATGVILPDLPPDEDPG 131 ::: ::::::::::::::: ::::::::::::::::::::::::::: d1nata_ 66 RMKVIDENIRVIIMTAYGE------LDMIQESKELGALTHFAKPFDIDEIRD 111