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 | d1o5ka_ | Dihydrodipicolinate synthase | Aldolase | TIM beta/alpha-barrel | α/β |
| Hit | d1ls1a2 | GTPase domain of the signal sequence recognition protein Ffh | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | α/β |
Query <-- 0.660 --> IntermediateDALI alignment (Z-score: 6.3 Raw score:820.90) query 1 ----------mietpYYLIDKAKLTRNMERIAHVReksgAKALLALKCF--------aTW 42 :::::::::::::::::::: :::::::::: :: d1o5ka_ 1 hmfrgvgtaivtpfkNGELDLESYERLVRYQLENG---vNALIVLGTTGesptvnedeRE 57 query 43 SVFDLMRDYM-----DGTTSS------SLFEVRLGRERfGKETHAYSVA--------yGD 83 :::::::::: :::::: ::::::::::: :::::::::: :: d1o5ka_ 58 KLVSRTLEIVdgkipVIVGAGtnstekTLKLVKQAEKL-GANGVLVVTPyynkptqegLY 116 query 84 NEIDEVV--SHADKIIFN---------SISQLERFADKAaGIARGLRL-NPQRlgEWDVp 131 ::::::: ::::::::: :::::::::::: :::::::: :::: :::: d1o5ka_ 117 QHYKYISerTDLGIVVYNvpgrtgvnvLPETAARIAADL-KNVVGIXEaNPDI-dQIDRt 174 query 132 kverVMDR-INGFMIHNNcenkdfglfdrMLGEIEERFgaliarvdwvsLGGGIHFTgdd 190 :::: ::::::::: ::::::::: :::::::: d1o5ka_ 175 vsltKQARsDFMVWSGND----------dRTFYLLCAG--------gdgVISVVSNV--- 213 query 191 yPVDAFSARLRAFSDR---------------------ygvqiylepgeasitKSTTLevt 229 ::::::::::::::: ::::: d1o5ka_ 214 -APKQMVELCAEYFSGnleksrevhrklrplmkalfvetnpipvkaalnlmgFIENE--- 269 query 230 vldtlynknlaivdssieaHMLDLliyretAKVLPnegshsymicgksclagdvfgefrf 289 ::::: ::::: d1o5ka_ 270 ------------------lRLPLV------PASEK------------------------- 280 query 290 aeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1o5ka_ 281 --------------------------------------------tvellrnvlkesgll 295 FAST alignment (Normalized score: 3.73 Raw score:1195.00) query 1 MIETPY----------------YLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSV 44 ::::::::::::::::: d1o5ka_ 1 ------HMFRGVGTAIVTPFKNGELDLESYERLVRYQLE--------------------- 33 query 45 FDLMRD-YMDGTTSS---------------SLFEVRLGRERF--GKETHAYSVAY----- 81 :::::: :::::::::::: ::::::: d1o5ka_ 34 ------NGVNALI--VLGTTGESPTVNEDEREKLVSRTLEIVDGKIPVIVG----AGTNS 81 query 82 ---GDNEIDEVVS-HADKIIFN------------SISQLERFADKAAGIARGLRLNPQRL 125 :::::::::: ::::::: ::::::::::: ::::::::::: d1o5ka_ 82 TEKTLKLVKQAEKLGANGVLV-VTPYYNKPTQEGLYQHYKYISER-TDLGIVVYNVP--- 136 query 126 GE------WDVPKVERV---MDRINGFMIHNNCENKDFGLFDRMLGE--IEERFGALIAR 174 ::::::::: :::::::::: ::::::::::: d1o5ka_ 137 --GRTGVNVLPETAARIAADLKNVVGIXEA-----------------NPDIDQIDRTVSL 177 query 175 V-------DWVSLGGGIHFTGDD-----------------------YPVDAFSARLRAFS 204 ::::: :::::::::::::: d1o5ka_ 178 -TKQARSDFMVWS----------GNDDRTFYLLCAGGDGVISVVSNVAPKQMVELCAEYF 226 query 205 DRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLP 264 d1o5ka_ 227 ------------------------------------------------------------ 227 query 265 NEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIA 324 d1o5ka_ 227 ------------------------------------------------------------ 227 query 325 IRELDGSVRTVREFTYADYEQSLS------------------------------------ 348 d1o5ka_ 227 ------------------------SGNLEKSREVHRKLRPLMKALFVETNPIPVKAALNL 262 query 349 --------------------------------- 349 d1o5ka_ 263 MGFIENELRLPLVPASEKTVELLRNVLKESGLL 295 TMalign alignment (TM-score: 0.41 Raw score:141.40) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSL 60 :::: ::::::::: d1o5ka_ 1 ----------------------------HMFR-------------------GVGTAIVTP 13 query 61 ----------FE-VR-LGRERFGKETHAYS----V--A-Y-G-DNEIDEVVS-H---ADK 95 :: :: :::::::::::::: : : : : ::::::::: : ::: d1o5ka_ 14 FKNGELDLESYERLVRYQLENGVNALIVLGTTGESPTVNEDEREKLVSRTLEIVDGKIPV 73 query 96 II-FN------SISQLERFADKAAGIARGLRLNP--QR---LGEW-DV-PKVERVMDRIN 141 :: :: ::::::::::::: ::::::::: :: :: :: ::::::: ::: d1o5ka_ 74 IVGAGTNSTEKTLKLVKQAEKLGA-NGVLVVTPYYNKPTQE--GLYQHYKYISERT-DLG 129 query 142 GFMIHNNCE--NKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDAFSAR 199 ::::::::: :: :::::::: ::::: ::::::::::::: : ::::: d1o5ka_ 130 IVVYNVPGRTG-----VN-VLPETAAR-IAADL-KNVVGIXEANPDI-----D--QIDRT 174 query 200 LRAFSDRYG-VQIYLEPGEAS--------------I------------------------ 220 ::::::::: ::::::::::: : d1o5ka_ 175 VSLTKQARSDFMVWSGNDDRTFYLLCAGGDGVISVVSNVAPKQMVELCAEYFSGNLEKSR 234 query 221 ---T-KSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGK 276 : :::: d1o5ka_ 235 EVHRKLRPL--------------------------------------------------- 243 query 277 SCLAGDVFGEFRFAEELKVGDRISFQDAAGYT----MVKK---------N-------WFN 316 ::::::: :::: : ::: d1o5ka_ 244 -------------------------MKALFVETNPIPVKAALNLMGFIENELRLPLVPAS 278 query 317 GVKMP-AIAIRELDGSVRTVREFTYADYEQSLS 348 ::::: :::::: ::::: d1o5ka_ 279 EKTVELLRNVLK----ESGLL------------ 295 HHsearch alignment (Probability: 0.03 E-value:0.15) query 1 MIETPYYLI-DKAKLTRNMERIAHVREKSGAKAL---LALKCFATWSVFDLMRD 50 ::::::::: ::::::::::::::::::: :::: ::::::::::::::::: d1o5ka_ 101 LVVTPYYNKPTQEGLYQHYKYISERTDLG-IVVYNVPGRTGVNVLPETAARIAA 153
Intermediate <-- 0.954 --> HitDALI alignment (Z-score: 4.0 Raw score:511.30) d1o5ka_ 1 ---HMFR---------------------------------GVGTAIVTPFK--------- 15 :::: ::::::::::: d1ls1a2 1 earLPVLkdrnlwflvglqgsgktttaaklalyykgkgrrPLLVAADTQRPaareqlrll 60 d1o5ka_ 16 --------ngeldlESYERLVRYQLENG------VNALIVlgttGESPTvNEDEREKLVS 61 :::::::::::::: :::::: ::::: :::::::::: d1ls1a2 61 gekvgvpvlevmdgESPESIRRRVEEKArleardLILVDT----AGRLQ-IDEPLMGELA 115 d1o5ka_ 62 RTLEIVDGkIPVIvGAGT-NSTEKTLKLVKQAEK-LGANGVlVVTPyyNKPTqegLYQHY 119 :::::::: :::: :::: ::::::::::::::: :::::: :::: :::: ::::: d1ls1a2 116 RLKEVLGP-DEVL-LVLDaMTGQEALSVARAFDEkVGVTGL-VLTK-lDGDA---RGGAA 168 d1o5ka_ 120 KYISERTDLGIVVYNVPgrtgvnvlpeTAARIAAdlknvvgixeanpdidqidrtvsltk 179 ::::::::::::::::: ::::::: d1ls1a2 169 LSARHVTGKPIYFAGGL-------epfYPERLAG-------------------------- 195 d1o5ka_ 180 qarsdfmvwsgnddrtfyllcaggdgvisvvsnvapkqmvelcaeyfsgnleksrevhrk 239 d1ls1a2 196 ------------------------------------------------------------ 196 d1o5ka_ 240 lrplmkalfvetnpipvkaalnlmgfienelrlplvpasektvellrnvlkesgll 295 d1ls1a2 196 --------------------------------------------------rilgmg 201 FAST alignment (Normalized score: 2.91 Raw score:709.50) d1o5ka_ 1 HMFRGVGTAIVTPFKNGELDLESYERLVRYQLENGVNALIVLGTTGESPTVNEDEREKLV 60 d1ls1a2 1 ------------------------------------------------------------ 1 d1o5ka_ 61 SRTLEIVDGK-------------------------------------IPVIVGAGT---- 79 :::::: d1ls1a2 1 ----------EARLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLL---VAAD 47 d1o5ka_ 80 ---------------------------NSTEKTLKLVKQAEK-LGANGVLVVTPYYNKPT 111 ::::::::::::::: ::::::::::: d1ls1a2 48 TQRPAAREQLRLLGEKVGVPVLEVMDGESPESIRRRVEEKARLEARDLILVDTA------ 101 d1o5ka_ 112 -----QEGLYQHYKYISERTD--LGIVVYNVPGRTGVNV--------LPETAARIAADLK 156 ::::::::::::::: :::::: :::::::::::: d1ls1a2 102 GRLQIDEPLMGELARLKEVL-GPDEVLLV----------LDAMTGQEALSVARAFDEKV- 149 d1o5ka_ 157 NVVGIAEANPD-------IDQIDRTVSLTKQARSDFMVWSGNDDRTFYLLCAGGDGVISV 209 :::::::: :::::::::: :::: d1ls1a2 150 GVTGLVLT---KLDGDARGGAALSARHV-----TGKP----------------------- 178 d1o5ka_ 210 VSNVAPKQ----------MVELCAEYFSGNLEKSREVHRKLRPLMKALFVETNPIPVKAA 259 ::::::::::: d1ls1a2 179 --------IYFAGGLEPFYPERLAGRILG------------------------------- 199 d1o5ka_ 260 LNLMGFIENELRLPLVPASEKTVELLRNVLKESGLL-- 295 d1ls1a2 200 ------------------------------------MG 201 TMalign alignment (TM-score: 0.36 Raw score:106.69) d1o5ka_ 1 --HMFR-------------------GVGTAIVTPFKNGELDLESYERLVRYQLENGVNAL 39 :::: :::::: :: ::: :: ::: d1ls1a2 1 EARLPVLKDRNLWFLVGLQGSGKTT--TAAKLA-----------LY-YKG--KG---RRP 41 d1o5ka_ 40 IVLG-------T-TGESPTVNEDE--REKLVSRTLEIVDGKIPVIVGAGTNSTEKTLKLV 89 :::: : ::::::: : ::: ::::: ::::::::: d1ls1a2 42 LLVAADTQRPAAR-EQLRLLG--EKV--GVP--------------VLEVM-DGESPESIR 81 d1o5ka_ 90 KQAEK-L----GANGVLVVTPYYNKPTQEGLYQHYKYISERTDLGIVVYNVPGRTGVNVL 144 ::::: : ::::::::::: :::::::::::::::::::::: d1ls1a2 82 RRVEEKARLEARDLILVDTAGR--LQIDEPLMGELARLKEVLGPDE-------------- 125 d1o5ka_ 145 PETAARIAADLKNVVGIAEANPDIDQIDRTVSLTKQARSDFMVWSGNDDRT-FY-LLCAG 202 ::::::::::::::::::::::::::::::::::::: :: ::::: d1ls1a2 126 --------------VLLVLDAMTGQEALSVARAFDEKVGVTGLVLTKLDGDARGGAALSA 171 d1o5ka_ 203 ------GDGVISVVSNVAPKQMVELCAEYFSGNLEKSREVHRKLRPLMKALFVETNPIPV 256 :::::: :: :: :: : : :::::::: :: d1ls1a2 172 RHVTGKPIYFAG-GL------EP--FY-P-E-RLAGRILG-MG----------------- 201 d1o5ka_ 257 KAALNLMGFIENELRLPLVPASEKTVELLRNVLKESGLL 295 d1ls1a2 202 --------------------------------------- 202 HHsearch alignment (Probability: 0.86 E-value:0.01) d1o5ka_ 92 AEKLGANGVLVVTPYYNKPTQEGLYQHYKYISERTD 127 :::::::::::::::::: ::::::::::::::::: d1ls1a2 88 ARLEARDLILVDTAGRLQ-IDEPLMGELARLKEVLG 122