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 | d1q7za2 | Cobalamin-dependent methionine synthase MetH, N-terminal domain | Homocysteine S-methyltransferase | TIM beta/alpha-barrel | α/β |
| Hit | d1r2qa_ | Rab5a | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | α/β |
Query <-- 1.075 --> IntermediateDALI alignment (Z-score: 8.8 Raw score:947.40) query 1 mietpyylidkakltrnmeriahvreksGAKALLAlKCFA-------------------- 40 ::::::: :::: d1q7za2 1 ---------------mrnrrevskllseRVLLLDGaYGTEfmkygyddlpeelnikapdv 45 query 41 TWSVFDLMRD-YMDGTTSSS---------------------LFEVRLGRERFG-KETHAY 77 :::::::::: ::::::::: :::::::::::: :::::: d1q7za2 46 VLKVHRSYIEsGSDVILTNTfgatrmklrkhgledkldpivRNAVRIARRAAGeKLVFGD 105 query 78 SV-------------------AYGDnEIDEVVS-HADKIIFN-------SISQLERFADK 110 :: :::: ::::::: :::::::: ::::::::::: d1q7za2 106 IGptgelpyplgstlfeefyeNFRE-TVEIMVEeGVDGIIFEtfsdileLKAAVLAAREV 164 query 111 AAGIARGLRLNPQ--------rlgeWDVPKVERVmdRINGFMIHNNcenkdfglFDRMLG 162 ::::::::::::: ::::::::: :::::::::: :::::: d1q7za2 165 SRDVFLIAHMTFDekgrsltgtdpaNFAITFDEL--DIDALGINCS------lgPEEILP 216 query 163 EIEeRFGALiARVDwVSLGGGI-------------HFTGddYPVDaFSARLRAFSdrygv 209 ::: ::::: :::: ::::::: :::: :::: ::::::::: d1q7za2 217 IFQ-ELSQY-TDKF-LVVEPNAgkpivengktvypLKPH--DFAV-HIDSYYELG----- 265 query 210 QIYLEP-gEASITksttlevtvldtlynknlaivdssieahmldlliyretakvlpnegs 268 :::::: ::::: d1q7za2 266 VNIFGGccGTTPE----------------------------------------------- 278 query 269 hsymicgksclagdvfgefrfaeelkvgdrisfqdaagytmvkknwfngvkmpaiairel 328 d1q7za2 279 ----------------------------------------------------------hv 280 query 329 dgsvrtvreftyadyeqsls 348 d1q7za2 281 klfrkvlgnrkplqrkkkri 300 FAST alignment (Normalized score: 4.75 Raw score:1537.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKS-------------GAKA-LLALKCFA------ 40 :::: :::::: d1q7za2 1 ----------------------------MRNRREVSKLLSERVLLLDGAYGT--EFMKYG 30 query 41 ---------------TWSVFDLMRD-YMDGTTSS-----------------------SLF 61 :::::::::: :::::: ::: d1q7za2 31 YDDLPEELNIKAPDVVLKVHRSYIESGSDVIL--TNTFGATRMKLRKHGLEDKLDPIVRN 88 query 62 EVRLGRERFG-KETHAYSVAY---------------------GDNEIDEVVS-HADKIIF 98 :::::::::: ::::::: :::::::::: :::::: d1q7za2 89 AVRIARRAAGEKLVFGDI---GPTGELPYPLGSTLFEEFYENFRETVEIMVEEGVDGII- 144 query 99 N---------SISQLERFADKAAGIARGLRLNPQRLGEW---------------DVPKVE 134 :::::::::::::::::::::: :::::: d1q7za2 145 -FETFSDILELKAAVLAAREVSRDVFLIAHMT-------FDEKGRSLTGTDPANFAITFD 196 query 135 RVMDRINGFMIHNNCENKDFGLFDRMLGEIEERFGALIARV--DWVSLGGGIHFTGDDYP 192 : :::::::: :::: ::::::::::::::: ::::::: d1q7za2 197 E--LDIDALGI--NCSL-GPEEILPIFQELSQY--------TDKFLVVEP---------- 233 query 193 --------------------VDAFSARLRAFSDRYGVQ---IYLEPGEASITKSTTLEVT 229 :::::::::: :::::::: d1q7za2 234 NAGKPIVENGKTVYPLKPHDFAVHIDSYYE--------LGVNIFGGCCG----------- 274 query 230 VLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRF 289 d1q7za2 275 ------------------------------------------------------------ 275 query 290 AEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQSLS- 348 d1q7za2 275 -----------------------------------------------------------T 275 query 349 ------------------------- 349 d1q7za2 276 TPEHVKLFRKVLGNRKPLQRKKKRI 300 TMalign alignment (TM-score: 0.30 Raw score:104.26) query 1 ---MIETPYYLIDKAKLTRNMERIAHVREKSG-AK---ALLALKCFATWSVFDLMRDYMD 53 :: : : d1q7za2 1 MRN---------------------------RRE-VSKL---------------------L 11 query 54 ---GTTSSSLFEVRLGRERFGKETHAYS-VAYG------------------DNEIDEVVS 91 ::::::: :::: d1q7za2 12 SER------------------VLLLDGAYGTEFMKYGYDDLPEELNIKAPD--------- 44 query 92 HADKIIFNSISQLERFADKAAGIARGLRL-NP----Q--R-----LG-EWDVPKVERVMD 138 :::::::::::::: ::::::: :: : : : :::::::::::: d1q7za2 45 -------VVLKVHRSYIESGS-DVILTNTFGATRMKLRKHGLEDK-LDPIVRNAVRIARR 95 query 139 RI----NGFMIHNNCENK------DFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTG 188 :: :::::::::::: ::::::::::::::::::: ::::::::::::: d1q7za2 96 AAGEKLVFGDIGPTGELPYPLGSTLFEEFYENFRETVEIMVEE--GVDGIIFETFSDI-- 151 query 189 DDYPVDAFSARLRAFSDRYGVQIYLEPGEA--SIT--KST-------------------- 224 ::::::::::::::: ::::::::::: ::: ::: d1q7za2 152 --LELKAAVLAAREVSR--DVFLIAHMTFDEKGRSLTGTDPANFAITFDELDIDALGINC 207 query 225 --------------------------TLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRE 258 d1q7za2 208 SLGPEEILPIFQELSQYTDKFLVVEP---------------------------------- 233 query 259 TAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGY-TMVKKN---- 313 : ::::: d1q7za2 234 ------------------------------------------------NA-GKPIVENGK 244 query 314 --------------------------------------------------------WFNG 317 d1q7za2 245 TVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLGNRKPLQRKKKRI---- 300 query 318 VKMPAIAIRELDGSVRTVREFTYADYEQSLS 348 d1q7za2 301 ------------------------------- 301 HHsearch alignment (Probability: 0.01 E-value:0.30) query 5 PYYLIDKAKLTRNMERIAHVREKSGAKALL 34 :::::::::::::::::::::::::::::: d1q7za2 115 PLGSTLFEEFYENFRETVEIMVEEGVDGII 144
Intermediate <-- 0.629 --> HitDALI alignment (Z-score: 3.6 Raw score:460.00) d1q7za2 1 mrnrrevskllservllldgaygtefmkygyddlpeelnikapdvvlkvhrsyiesgsdv 60 d1r2qa_ 1 ------------------------------------------------------------ 1 d1q7za2 61 iltntfgatrmklrkhgledkldpivrnavriarraaGEKLVFGDIGPTG---------- 110 ::::::::::::: d1r2qa_ 1 ----------------------------------gnkICQFKLVLLGESAvgksslvlrf 26 d1q7za2 111 ------------------------elpyplgstlfeefyenfrETVEIMVEeGVDGIIFE 146 :::::::: :::::::: d1r2qa_ 27 vkgqfhefqestigaafltqtvclddttvkfeiwdtagqeryhSLAPMYYR-GAQAAIVV 85 d1q7za2 147 TFS----DILELKAAVLAAREVS-RDVFLIAHMTF--DEKGRsltGTDPANFAITFDELD 199 ::: :::::::::::::::: ::::::::::: ::::: ::::::::::::::: d1r2qa_ 86 YDItneeSFARAKNWVKELQRQAsPNIVIALSGNKadLANKR---AVDFQEAQSYADDNS 142 d1q7za2 200 IdALGINCSLGPeeilpifqelsqytdkflvvepnagkpivengktvyplkphdfavhid 259 : :::::::::: d1r2qa_ 143 L-LFMETSAKTS------------------------------------------------ 153 d1q7za2 260 syyelgVNIFggccgttpehvklfrkvlgnrkplqrkkkri 300 :::: d1r2qa_ 154 --mnvnEIFM----------------------aiakklpkn 170 FAST alignment (Normalized score: 2.74 Raw score:619.40) d1q7za2 1 MRNRREVSKLLS---ERVLLLDGAYGTEFMKYGYDDLPEELN------------------ 39 :::::: d1r2qa_ 1 ------------GNKICQFKL---------------------VLLGESAVGKSSLVLRFV 27 d1q7za2 40 --------------------------------------IKAPDVVLKVHRSYIESGSDVI 61 ::::::::::: :::::: d1r2qa_ 28 KGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYY-----RGAQAA 82 d1q7za2 62 LTNTFGATRMKLRKHGLE----DKLDPIVRNAVRIARRA-AGEKLVFGDIGPTGELPYPL 116 :::: ::::::::::::::::: ::::::::::::: d1r2qa_ 83 IVVY--------------DITNEESFARAKNWVKELQRQASPNIVIALSGNKA------- 121 d1q7za2 117 GSTLFEEFYE--------NFRETVEIMVEEGVDGIIFETFSDILELKAAVLAAREVSRDV 168 ::::::::::::: ::::: d1r2qa_ 122 ----------DLANKRAVDFQEAQSYADDNS-LLFME----------------------- 147 d1q7za2 169 FLIAHMTFDEKGRSLTGTDPANFAITFDELDIDALGINCSLGPEEILPIFQELSQYTDKF 228 d1r2qa_ 148 ------------------------------------------------------------ 148 d1q7za2 229 LVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSYYELGVNIFGGCCGTTPEHVKLFRKVLG 288 d1r2qa_ 148 ------------------------------------------------------------ 148 d1q7za2 289 NRKPLQRKKKRI----------------------- 300 d1r2qa_ 148 ------------TSAKTSMNVNEIFMAIAKKLPKN 170 TMalign alignment (TM-score: 0.34 Raw score:100.99) d1q7za2 1 -----MRN--------------RREVSKLLSERVLLL-DGAYGTEFM--KYGYDDLPEEL 38 ::: : ::::::: : ::::::: d1r2qa_ 1 GNKICQFKLVLLGESAVGKSSL--------------VLRFVKGQF-HEF----QESTIGA 41 d1q7za2 39 NIKAPDVVLKVHRSYIESG----SDVILTNTFGATRMKLRKHGLEDKLDPIVRNAVRIAR 94 : : :: :: :: ::::::::: :::: : : d1r2qa_ 42 A------F--LT--QT-VCLDDTTVKFEIWDT-AGQE--R----Y--------------- 68 d1q7za2 95 RAAGEKLVFGDIGPTGELPYPLGSTLFEEFYENFRETVEIMVEEGVDGIIFETFS----- 149 : ::: ::::: :::::::: :: d1r2qa_ 69 --------------------------------H-SLA-PMYYR-GAQAAIVV-YDITNEE 92 d1q7za2 150 DILELKAAVLAAREVS-RDVFLIAHMT-F-DEKGRSLTGTDPANFAITFDELDIDALGIN 206 :::::::::::::::: :::::::::: : ::::: :::::::::::::: ::::::: d1r2qa_ 93 SFARAKNWVKELQRQASPNIVIALSGNKADLANKR---AVDFQEAQSYADDN-SLLFMET 148 d1q7za2 207 CSLGPEEILPIFQELSQYTDKFLVVEPNAGKPIVENGKTVYPLKPHDFAVHIDSYYELGV 266 ::::: : ::: : : d1r2qa_ 149 SAKTS--M----------------NVN---------------------------E----I 159 d1q7za2 267 NIFG-GCCGTTPEHVKLFRKVLGNRKP----LQRKKKRI 300 :::: :: d1r2qa_ 160 FMAIA--------------------KKLPKN-------- 170 HHsearch alignment (Probability: 0.03 E-value:0.08) d1q7za2 187 DPANFAITFDELDIDALGINCSLGPEEILPIFQELSQ 223 ::::::::::::::::::::: ::::::::::::::: d1r2qa_ 130 DFQEAQSYADDNSLLFMETSA-KTSMNVNEIFMAIAK 165