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 | d1oxbb_ | Response regulator Sin1 | 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 <-- 1.504 --> HitDALI alignment (Z-score: 4.1 Raw score:394.70) d1ujpa_ 1 mttleafakarsegrAALIPYLT---------------------agFPSREGFLQAVEEV 39 :::::::: :::::::::::::: d1oxbb_ 1 ---------------SVKILVVEdnhvnqevikrmlnlegienielACDGQEAFDKVKEL 45 d1ujpa_ 40 L---PYADLLEIGLPysdgpviqraselalrkgmsvqGALELVREVRA--LTEKPLFLMT 94 : ::::::::::: ::::::::::: :::::::::: d1oxbb_ 46 TskgENYNMIFMDVQ------------------mpkvDGLLSTKMIRRdlGYTSPIVALT 87 d1ujpa_ 95 YLnpvlawgPERFFGLFKQAGATGVILPDlppdedpglvrlaqeigletvFLLAptstda 154 :: :::::::::::::::::::: :::: d1oxbb_ 88 AF------aDDSNIKECLESGMNGFLSKP---------------------IKRP------ 114 d1ujpa_ 155 riatvvrhATGFVyavsvevkdlvrrikartalpvavgfgvsgkataaqaavadgvvvgs 214 ::::: d1oxbb_ 115 ------klKTILT----------------------------------------------- 121 d1ujpa_ 215 alvraleegrslapllqeirqglqrlplp 243 d1oxbb_ 122 --------------------------efc 124 FAST alignment (Normalized score: 4.52 Raw score:784.80) d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAGF--------------------------PSREGFLQ 34 :::::: :::::::: d1oxbb_ 1 ---------------SVKILV-----VEDNHVNQEVIKRMLNLEGIENIELACDGQEAFD 40 d1ujpa_ 35 AVEEVLP---YADLLEIGLPYSDGPVIQRASELALRKGMSVQ------GALELVREVRA- 84 ::::::: :::::::: ::::::::::: d1oxbb_ 41 KVKELTSKGENYNMIFMD------------------------VQMPKVDGLLSTKMIRRD 76 d1ujpa_ 85 -LTEKPLFLMTYLNPVLAWG---PERFFGLFKQAGATGVILPDLPPDEDPGLVRLAQEIG 140 :::::::::: ::::::::::::::::::::: ::::::: d1oxbb_ 77 LGYTSPIVALT---------AFADDSNIKECLESGMNGFLSKPI----KRPKLKT----- 118 d1ujpa_ 141 LETVFLLAPTSTDARIATVVRHATGFVYAVSVEVKDLVRRIKARTALPVAVGFGVSGKAT 200 d1oxbb_ 119 ------------------------------------------------------------ 119 d1ujpa_ 201 AAQAAVADGVVVGSALVRALEEGRSLAPLLQEIRQGLQRLPLP------ 243 d1oxbb_ 119 -------------------------------------------ILTEFC 124 TMalign alignment (TM-score: 0.32 Raw score:78.27) d1ujpa_ 1 MTTLEAFAKARSEGRAALIPYLTAGFPSREGFLQAVEEVLPYADLLEIGLPYSDGPVIQR 60 :: ::::::::::::::: d1oxbb_ 1 -----------------------------------------SV--KILVVEDNHVNQEVI 17 d1ujpa_ 61 A------------SELALRKGMSVQGALELVREVRALTEKPLFLMTYLNPVLAWGPERFF 108 : :: ::::::::::::::::::::::::::::::::::: ::: d1oxbb_ 18 KRMLNLEGIENIE---LA---CDGQEAFDKVKELTSKGENYNMIFMDVQMPKVDGL-LST 70 d1ujpa_ 109 GLFK-QAGA-TGVILPD-LPPDEDPGLVRLAQEIGLETVFLL---APTSTDARIATVVRH 162 :::: :::: ::::::: :::::::::::::: :::::: :: d1oxbb_ 71 KMIRRDLGYTSPIVALTAFADDSNIKECLESG----MNGFLSKPIKR------------- 113 d1ujpa_ 163 ATGFVYAVSVEVKDLVRRIKARTALPVAVGFGVSGKATAAQAAVADGVVVGSALVRALEE 222 :::: : ::: ::: d1oxbb_ 114 -----PKLK------T----------ILT---------------EFC------------- 124 d1ujpa_ 223 GRSLAPLLQEIRQGLQRLPLP 243 d1oxbb_ 125 --------------------- 125 HHsearch alignment (Probability: 0.78 E-value:0.00) d1ujpa_ 70 MSVQGALELVREVRA--LTEKPLFLMTYLNPVLAWGPERFFGLFKQAGATGVILPDLPPD 127 ::::::::::::::: ::::::::::::: :::::::::::::::::::::::: d1oxbb_ 61 MPKVDGLLSTKMIRRDLGYTSPIVALTAFA------DDSNIKECLESGMNGFLSKPIKRP 114 d1ujpa_ 128 EDPGLVRLAQEI 139 : :::::::: d1oxbb_ 115 K---LKTILTEF 123