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 | d1geqa_ | Trp synthase alpha-subunit | Ribulose-phoshate binding barrel | TIM beta/alpha-barrel | α/β |
| Hit | d1svia_ | Probable GTPase EngB | P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | α/β |
Query <-- 0.983 --> IntermediateDALI alignment (Z-score: 9.7 Raw score:956.80) query 1 mietpyylidkakltrnmeriahvreksGAKALLALK-----cfaTWSVFDLMRDYMDGT 55 ::::::::: ::::::::::::::: d1geqa_ 1 -------------------------mfkDGSLIPYLTagdpdkqsTLNFLLALDEYAGAI 35 query 56 TSSS--------------------------lFEVRLGRER---fGKETHAYSVA------ 80 :::: ::::::::: :::::::::: d1geqa_ 36 ELGIpfsdpiadgktiqeshyralkngfklrEAFWIVKEFrrhsSTPIVLMTYYnpiyra 95 query 81 yGDNEIDEVVS-HADKIIFNSIS--QLERFADKAA--GIARGLRLNPQrlgeWDVPKVER 135 :::::::::: ::::::::::: :::::::::: ::::::::::: :::::::: d1geqa_ 96 gVRNFLAEAKAsGVDGILVVDLPvfHAKEFTEIAReeGIKTVFLAAPN----TPDERLKV 151 query 136 VMDRIN-GFMIHNNCenkdfgLFDRMLGEIEERFGALIarVDWVSLGGGIHFtgddypvD 194 :::::: :::::::: ::::::::::::::::: :::::::::::: : d1geqa_ 152 IDDMTTgFVYLVSLY------EIPKTAYDLLRRAKRIC--RNKVAVGFGVSK-------R 196 query 195 AFSARLRAFSdrygvqIYLEPGEASITKSTtlevtvldtlynknlaivdssieahmldll 254 :::::::::: :::::::::::::: d1geqa_ 197 EHVVSLLKEG-----aNGVVVGSALVKIIG------------------------------ 221 query 255 iyretakvlpnegshsymicgksclagdvfgefrfaeelkvgdrisfqDAAGytmvkknw 314 :::: d1geqa_ 222 ------------------------------------------------EKGR-------- 225 query 315 fngvkmpaiaireldgsvrtvreftyadyeqsls 348 d1geqa_ 226 ------------------eateflkkkveellgi 241 FAST alignment (Normalized score: 5.72 Raw score:1657.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSG----AKALLALKCFA----------TWSVFD 46 :::::: :::::: d1geqa_ 1 -----------------------------MFKDGSLIPY-----LTAGDPDKQSTLNFLL 26 query 47 LMRDYMDGTTSS------------------------------SLFEVRLGRERFGKETHA 76 ::::::::::: :::::::::::::::::: d1geqa_ 27 ALDEYAGAIEL-GIPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVL 85 query 77 YSVAY---------GDNEIDEVVS-HADKIIFN--SISQLERFADKA---AGIARGLRLN 121 :: :::::::::: :::::::: ::::::::::: :::::::::: d1geqa_ 86 MT---YYNPIYRAGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEI-AREEGIKTVFLAA 141 query 122 PQRLGE-WDVPKVERVMDR-INGFMIHNNCENKD------FGLFDRMLGEIEERFGALIA 173 : :::::::::::: :::::: :::::::::::::: d1geqa_ 142 P-----NTPDERLKVIDDMTTGFVYL--------VSLYEIPKTAYDLLRRAKRI------ 182 query 174 RV--DWVSLGGGIHFTGDDYPVDA-----FSARLRAFSDRYGVQIYLEPGEASITKSTTL 226 ::::: :::::::::: ::: ::::::::: d1geqa_ 183 --CRNKVAV---------------GFGVSKREHVVSLLK-EGA-NGVVVGSAL------- 216 query 227 EVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDVFGE 286 d1geqa_ 217 ------------------------------------------------------------ 217 query 287 FRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADYEQS 346 d1geqa_ 217 ------------------------------------------------------------ 217 query 347 LS------------------------- 348 d1geqa_ 217 --VKIIGEKGREATEFLKKKVEELLGI 241 TMalign alignment (TM-score: 0.43 Raw score:149.14) query 1 --MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCF--A-T-WSVFDLMRDYMDG 54 : :::::::::::: : : ::::::::::::: d1geqa_ 1 MF-------------------------K-DGSLIPYLTAGDPDKQSTLNFLLALDEYAGA 34 query 55 TTSSS-------------------------LFEVRLGRERF---G-KETHAYSVA--YG- 82 ::::: ::::::::::: : ::::::::: :: d1geqa_ 35 IELGIPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIYR 94 query 83 --D-NEIDEVVS-HADKIIFN-S-ISQLERFADKAA--GIARGLRLNPQRLGEWDVPKVE 134 : :::::::: :::::::: : :::::::::::: ::::::::::: ::::::: d1geqa_ 95 AGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEIAREEGIKTVFLAAPN----TPDERLK 150 query 135 RVMDRIN-GFMIHNNCENKDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPV 193 ::::::: :::::::: :::::::::::::::: ::::::::::::: : d1geqa_ 151 VIDDMTTGFVYLVSLY------EIPKTAYDLLRRAKRI--CRNKVAVGFGVSK------R 196 query 194 DAFSARLRAFSDRYGVQIYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDL 253 :::::::::: ::::: :::::::: : : d1geqa_ 197 -EHVVSLLKEG----ANGVV-VGSALVKI-I-------------------------G--- 221 query 254 LIYRETAKVLPNEGSHSYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKN 313 ::: d1geqa_ 222 -------------------------------------------------EKG-------- 224 query 314 WFNGVKMPAIAIRE------------LDGSVRTVREFTYADYEQSLS 348 ::::: d1geqa_ 225 ---------REATEFLKKKVEELLGI--------------------- 241 HHsearch alignment (Probability: 0.07 E-value:0.12) query 19 ERIAHVREKSGAKALLALKCFATWSVFDLMRD---------YMDGTTSSSLFEVRLGRER 69 :::::::::::::::::::::::::::::::: ::::::::::::::::::: d1geqa_ 123 KEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYEIPKTAYDLLRRAKRI 182 query 70 FGKETHAYSVAYGDNEIDEVVS-HADKIIFNS 100 :::::::::::::::::::::: ::::::::: d1geqa_ 183 CRNKVAVGFGVSKREHVVSLLKEGANGVVVGS 214
Intermediate <-- 0.636 --> HitDALI alignment (Z-score: 2.8 Raw score:383.40) d1geqa_ 1 mfkdgslipyltagdpdkqstlnfllaldeyagaielgipfsdpiadgktiQESHYralk 60 ::::: d1svia_ 1 -------------------------------------------------mkVTKSE---- 7 d1geqa_ 61 nGFKLreafwivKEFRrhsstpIVLMT--------------------------------Y 88 :::: :::: ::::: : d1svia_ 8 iVISAvkpeqypEGGL-----pEIALAgrsnvgkssfinslinrqtlnfyiindelhfvD 62 d1geqa_ 89 YNP------------iYRAGVRNFLAEakASGVDGILVV----dlpVFHAKEFTEIAREE 132 ::: ::::::::::: :::::::::: :::::::::::::: d1svia_ 63 VPGygfakvsksereaWGRMIETYITT--REELKAVVQIvdlrhapSNDDVQMYEFLKYY 120 d1geqa_ 133 GIKTVFLAAPN------tPDERLKVID--DMTT--GFVYLVSLYeipktaydllrrakri 182 ::::::::::: ::::::::: :::: ::::::::: d1svia_ 121 GIPVIVIATKAdkipkgkWDKHAKVVRqtLNIDpeDELILFSSE---------------- 164 d1geqa_ 183 crnkvaVGFGvskrehvvsllkegangVVVGsalvkiigekgreateflkkkveellgi 241 :::: :::: d1svia_ 165 ----tkKGKD-----------------EAWG--------------------aikkminr 182 FAST alignment (Normalized score: 2.70 Raw score:565.50) d1geqa_ 1 MFK---------------------DGSLIPY----------------------------- 10 ::::::: d1svia_ 1 ---MKVTKSEIVISAVKPEQYPEGGLPEIALAGRSNVGKSSFINSLINRQTLNFYIINDE 57 d1geqa_ 11 ------LTAGDP-------DKQSTLNFLLAL---DEYAGAIELGIPFSDPIADGKTIQES 54 :::: :::::::::::: :::::::::: d1svia_ 58 LHFVDVPGYG--FAKVSKSEREAWGRMIETYITTREELKAVVQI---------------- 99 d1geqa_ 55 HYRALKNGFK-------LREAFWIVKEFRRHSSTPIVLMTYYNPIYRAGVRNFLAEAKAS 107 ::::::::::::: :::::::: d1svia_ 100 ----------VDLRHAPSNDDVQMYEFLKY-YGIPVIVI--------------------- 127 d1geqa_ 108 GVDGILV----VDLPVFHAKEFTEIARE-----EGIKTVFLAAPNTPDERLKVIDDMTTG 158 ::::::::::::::::: ::::::::::: d1svia_ 128 -------ATKADKIPKGKWDKHAKVVRQTLNIDPEDELILFSSE---------------- 164 d1geqa_ 159 FVYLVSLYEIPKTAYDLLRRAKRICRNKVAVGFGVSKREHVVSLLKEGANGVVVGSALVK 218 d1svia_ 165 ------------------------------------------------------------ 165 d1geqa_ 219 IIGEKGREATEFLKKKVEELLGI------------------ 241 d1svia_ 165 -----------------------TKKGKDEAWGAIKKMINR 182 TMalign alignment (TM-score: 0.37 Raw score:89.00) d1geqa_ 1 MFKDGSL-IPYL-TAGDPDKQSTLNFLLALDEYAGAIELGIPFSDPIAD--G----KT-- 50 :::: ::: :: :::::: ::::::: :::::::::::::: : : d1svia_ 1 ---MKVTK-SEIV---IS--AVKPEQ-YPEGGLP-EIALAGRSNVGKSSFINSLIN-RQT 48 d1geqa_ 51 -I------------QESHY--RAL-KNG--FKLREAFWIVKEF-RRHSSTPIVLMTYY-N 90 : ::: : ::: :::::: :::::: :::::::::::::: : d1svia_ 49 LNFYIINDELHFVD--VPGYG--FAKVSKSEREAWG-RMIETYITTREELKAVVQIVDLR 103 d1geqa_ 91 PIYRAGVRNFLAEAKASGVDG-ILVVDL--P----V-FHAKEFTE--IAREEGIKTVF-L 139 ::::::::::::::::::::: :::::: : : :::::::: :::: : :::: : d1svia_ 104 HAPSNDDVQMYEFLKYYGIPVIVIATKADKIPKGKWDKHAKVVRQTLNIDP-E-DELILF 161 d1geqa_ 140 AAPNTPDERLKVIDDMTTGFVYLVSLYEIPKTAYDLLRRAKRICRNKVAVGFGVSKREHV 199 :::::: : : :::: ::: d1svia_ 162 SSETKK---G--K------DEAW-----------------------GAI----------- 176 d1geqa_ 200 VSLLKEGANG----VVVGSALVKIIGEKGREATEFLKKKVEELLGI 241 :: d1svia_ 177 --------KKMINR-------------------------------- 182 HHsearch alignment (Probability: 0.08 E-value:0.20) d1geqa_ 83 IVLMTYYNP 91 ::::::::: d1svia_ 26 IALAGRSNV 34