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
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1ujpa_ | Trp synthase alpha-subunit | Ribulose-phoshate binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1qkka_ | Transcriptional regulatory protein DctD, receiver domain | CheY-like | Flavodoxin-like | α/β |
Query <-- 1.022 --> IntermediateDALI 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 <-- 1.114 --> HitDALI alignment (Z-score: 3.5 Raw score:361.40) d1ujpa_ 1 mttleafakarsegraALIPYLT--------------------agFPSREGFLQAVEevL 40 ::::::: :::::::::::: : d1qkka_ 1 ----------------PSVFLIDddrdlrkamqqtlelagftvssFASATEALAGLS--A 42 d1ujpa_ 41 PYADLLEIGLPysdgpviqraSELAlrkgmsvqGALELVREVRALT-EKPLFLMTYLNPV 99 ::::::::::: :::: ::::::::::::: ::::::::::::: d1qkka_ 43 DFAGIVISDIR----------MPGM--------DGLALFRKILALDpDLPMILVTGHGDI 84 d1ujpa_ 100 lawgpeRFFGLFKQAGATGVILPDlppdedpglvrlaqeigletvFLLAptstdariatv 159 :::::::::::::::::: :::: d1qkka_ 85 ------PMAVQAIQDGAYDFIAKP---------------------FAAD----------- 106 d1ujpa_ 160 vrhatgfVYAVsvevkdlvrrikartalpvavgfgvsgkataaqaavadgvvvgsalvra 219 :::: d1qkka_ 107 -------RLVQ--------------------------------------------sarra 115 d1ujpa_ 220 leegrslapllqeirqglqrlplp 243 d1qkka_ 116 eekrrlvmenrslrraaeaasegl 139 FAST alignment (Normalized score: 3.03 Raw score:556.10) d1ujpa_ 1 MTTLEAFAKARSEGR-----------------------AALIPYLTAGFPSREGFLQAVE 37 ::::::: ::::::::: d1qkka_ 1 ---------------PSVFLIDDDRDLRKAMQQTLELAGFTVSSF----ASATEALAG-- 39 d1ujpa_ 38 EVLPYA------DLLEIGLPYSDGPVIQRASELALRKGMSVQ------GALELVREVRAL 85 :::::: :::::::::::: d1qkka_ 40 ------LSADFAGIVISD------------------------IRMPGMDGLALFRKILAL 69 d1ujpa_ 86 -TEKPLFLMTYLNPVLAWGP-ERFFGLFKQAGATGVILPDLPPDEDPGLVRLAQEIGLET 143 :::::::::::: :::::::::::::::::::: d1qkka_ 70 DPDLPMILVTGHG-------DIPMAVQAIQDGAYDFIAKPF------------------- 103 d1ujpa_ 144 VFLLAPTSTDARIATVVRHATGFVYAVSVEVKDLVRRIKARTALPVAVGFGVSGKATAAQ 203 d1qkka_ 104 ------------------------------------------------------------ 104 d1ujpa_ 204 AAVADGVVVGSALVRALEEGRSLAPLLQEIRQGLQRLPLP-------------------- 243 d1qkka_ 104 ----------------------------------------AADRLVQSARRAEEKRRLVM 123 d1ujpa_ 244 ---------------- 244 d1qkka_ 124 ENRSLRRAAEAASEGL 139 TMalign alignment (TM-score: 0.30 Raw score:73.93) d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAGFPSREGFLQAVEEVLPYADLLEIGLPYSDGPVIQ- 59 : :::::::::::::: d1qkka_ 1 ------------------------------------------P--SVFLIDDDRDLRKAM 16 d1ujpa_ 60 RA-----------SELALRKGMSVQGALELVREVRALTEKPLFLMTYLNPVLAWGPERFF 108 : :: ::::::::::: :::: :::::::::: :::::::: d1qkka_ 17 -QQTLELAGFTVS---SF---ASATEALAGLS--ADFA--GIVISDIRMP--GMDGLALF 63 d1ujpa_ 109 GLFKQAG--ATGVILPDLPPDEDPGLVRLAQEIGLETVFLLAPTSTDARIATVVRHATGF 166 ::::::: :::::: ::: ::::::::::::::::::::: d1qkka_ 64 RKILALDPDLPMILV-TGH--GDIPMAVQAIQDGAYDFIAKP------------------ 102 d1ujpa_ 167 VYAVSVEVKDLVRRIKARTALPVAVG-FGVSGKATAAQAAVADG---------------- 209 ::: : :::: :: d1qkka_ 103 -FAA-------D----------RLVQS---------------ARRAEEKRRLVMENRSLR 129 d1ujpa_ 210 ----------VVVGSALVRALEEGRSLAPLLQEIRQGLQRLPLP 243 d1qkka_ 130 RAAEAASEGL---------------------------------- 139 HHsearch alignment (Probability: 0.43 E-value:0.00) d1ujpa_ 21 YLTAGFPSREGFLQAVEEVLPYADLLEIGLPYSDGPVIQRASELALRKGMSVQGALELVR 80 ::::::::::::::::::::::::::::::::::: ::::: d1qkka_ 25 FTVSSFASATEALAGLSADFAGIVISDIRMPGMDG--------------------LALFR 64 d1ujpa_ 81 EVRA-LTEKPLFLMTYLNPVLAWGPERFFGLFKQAGATGVILPDLPPDEDPGLVRL 135 :::: :::::::::::::: ::::::::::::::::::::::::::::::: d1qkka_ 65 KILALDPDLPMILVTGHGD------IPMAVQAIQDGAYDFIAKPFAADRLVQSARR 114