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 | d1nu0a_ | Hypothetical protein YqgF (RuvX) | Ribonuclease H-like | Ribonuclease H-like motif | 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 <-- 0.887 --> HitDALI alignment (Z-score: 2.0 Raw score:277.30) d1ujpa_ 1 mttleafakarsegRAALIPYLTAG------------------------fpSREGfLQAV 36 ::::::::::: :::: :::: d1nu0a_ 1 --------------MSGTLMAFDFGtksigvavgqritgtarplpaikaqdGTPD-WNII 45 d1ujpa_ 37 EEVLP--YADLLEIGLPYSDgpviqraselalrkgmSVQGALELVREVRALTEKPLFLMT 94 ::::: ::::::::::::: :::::::::::::::::::::::: d1nu0a_ 46 ERLLKewQPDEIIVGLPLNM----------dgteqpLTARARKFANRIHGRFGVEVKLHD 95 d1ujpa_ 95 YLNpvlawgperffglfkqagatgvilpdlppdedpglvrlaqeigletVFLLaptstda 154 ::: :::: d1nu0a_ 96 ERL------------------stveaggyralnkgkvdsasaviilesyMEQG------- 130 d1ujpa_ 155 riatvvrhatgfvyavsvevkdlvrrikartalpvavgfgvsgkataaqaavadgvvvgs 214 d1nu0a_ 131 ------------------------------------------------------------ 131 d1ujpa_ 215 alvraleegrslapllqeirqglqrlplp 243 d1nu0a_ 131 ----------------------------y 131 FAST alignment (Normalized score: 2.56 Raw score:457.20) d1ujpa_ 1 MTTLEAFAKARSEGRA--ALIPYLTAGFP------------------------------- 27 ::::::: d1nu0a_ 1 ----------------MSGTLMAFD----FGTKSIGVAVGQRITGTARPLPAIKAQDGTP 40 d1ujpa_ 28 SREGFLQAVEEVLPYADLLEIGLPYSDGPVIQRASELALRKGM-------SVQGALELVR 80 ::::::::::: ::::::::::::: :::::::::: d1nu0a_ 41 DWNIIERLLKE--WQPDEIIVGLPLN-----------------MDGTEQPLTARARKFAN 81 d1ujpa_ 81 EVRALTEKPLFLMTYLNPVLAWGPERFFGLFKQAGATGVILPDLPPDEDPGLVRLAQEIG 140 :::::::::::: d1nu0a_ 82 RIHGRFGVEVKL------------------------------------------------ 93 d1ujpa_ 141 LETVFLLAPTSTDARIATVVRHATGFVYAVSVEVKDLVRRIKARTALPVAVGFGVSGKAT 200 d1nu0a_ 94 ------------------------------------------------------------ 94 d1ujpa_ 201 AAQAAVADGVVVGSALVRALEEGRSLAPLLQEIRQGLQRLPLP----------------- 243 d1nu0a_ 94 -------------------------------------------HDERLSTVEAGGYRALN 110 d1ujpa_ 244 --------------------- 244 d1nu0a_ 111 KGKVDSASAVIILESYMEQGY 131 TMalign alignment (TM-score: 0.25 Raw score:61.86) d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAG-FP--------------------S--REGFLQAVE 37 : : ::::::::: :: : ::::::::: d1nu0a_ 1 ------M--S------GTLMAFDFGTKSIGVAVGQRITGTARPLPAIKAQDGTPDWNIIE 46 d1ujpa_ 38 EVLP-Y-ADLLEIGLPYSD----GPVIQRASELALRKGMSVQGALELVREVRALTEKPLF 91 :::: : :::::::::::: ::::::::::::::::::::::: d1nu0a_ 47 RLLKEWQPDEIIVGLPLNMDGTE--------------QPLTARARKFANRIHGRFGVEVK 92 d1ujpa_ 92 LMTYLNP----------VLAWGPERFFGLFKQAGATGVILPDLPPDEDPGLVRLAQEIGL 141 :::: :: d1nu0a_ 93 LHDE-RLSTVEAGGYRA------------------------------------------- 108 d1ujpa_ 142 ETVFLLAPTSTDARIATVVRHATGFVYAVSVEVKDLVRRIKARTALPVAVGFGVSGKATA 201 d1nu0a_ 109 ------------------------------------------------------------ 109 d1ujpa_ 202 AQAAVADGVVVGSA-LVRALEE---------------GRSLAPLLQEIRQGLQRLPLP 243 : :::::: d1nu0a_ 109 -------------LN-KGKVDSASAVIILESYMEQGY--------------------- 131 HHsearch alignment (Probability: 0.16 E-value:0.03) d1ujpa_ 41 PYADLLEIGLPYS-DGPVIQRASELALRKGMSVQGALELVREVRALTEKPLFLM 93 ::::::::::::: :::: ::::::::::::::::::::::::: d1nu0a_ 52 WQPDEIIVGLPLNMDGTE-----------QPLTARARKFANRIHGRFGVEVKLH 94