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 | d1vkfa_ | Glycerol uptake operon antiterminator-related protein TM1436 | GlpP-like | TIM beta/alpha-barrel | α/β |
| Hit | d1jlra_ | Uracil PRTase, Upp | PRTase-like | PRTase-like | α/β |
Query <-- 0.926 --> IntermediateDALI alignment (Z-score: 8.5 Raw score:752.00) query 1 mietpyylidkakltrnmeriahvreksgAKALLALKcfATWSvFDLMrdYMDGTTSSSL 60 :::::::: :::: :::: :::::::::: d1vkfa_ 1 ---------------------------mfKGIIAALW--DMDS-IGEI--EPDVVFLLKS 28 query 61 F--evrlgRERFG---KETHAYSV-----aYGDNEIDEVVS-HADKIIFNSISQLERFAD 109 : ::::: :::::::: ::::::::::: :::::::::::::::::: d1vkfa_ 29 DilnlkfhLKILKdrgKTVFVDMDfvnglgEGEEAILFVKKaGADGIITIKPKNYVVAKK 88 query 110 KAagIARGLRLNPQ--rlgeWDVPKVERVMdrINGFMIHNNcenkdfglfdrMLGEIEER 167 :: :::::::::: :::::::::: ::::::::: :::::::: d1vkfa_ 89 NG--IPAVLRFFALdskaveRGIEQIETLG--VDVVEVLPG----------aVAPKVARK 134 query 168 fgalIARVdWVSLGGGIHFTgddypvdafSARLRafsdrygvqIYLEPGeASITksttle 227 :::: ::::::::::: ::::: :::::: :::: d1vkfa_ 135 ----IPGR-TVIAAGLVETE------eeaREILK-------hvSAISTS-SRIL------ 169 query 228 vtvldtlynknlaivdssieahmldlliyretakvlpnegshsymicgksclagdvfgef 287 d1vkfa_ 170 ------------------------------------------------------------ 170 query 288 rfaeelkvgdrisfqdaagytmvkknwfngvkmpaiaireldgsvrtvreftyadyeqsl 347 d1vkfa_ 170 ----------------------------------------------------------wk 171 query 348 s 348 d1vkfa_ 172 m 172 FAST alignment (Normalized score: 5.89 Raw score:1441.00) query 1 MIETPYYLIDKAKLTRNMERIAHVREKSGA---KALLALKCFATWSVFDLMRDYMDGTTS 57 ::::: ::: :::::: :::::::: d1vkfa_ 1 ------------------------------MFKGIIAA-LWD--MDSIGE--IEPDVVFL 25 query 58 S------SLFEVRLGRERFGKETHAYSVAY---------GDNEIDEVVS-HADKIIFNSI 101 : ::::::::: ::::::::: :::::::::: :::::::::: d1vkfa_ 26 LKSDILNLKFHLKILK-DRGKTVFVD----MDFVNGLGEGEEAILFVKKAGADGIITIKP 80 query 102 SQLERFADKAAGIARGLRLNPQRLGEW---------DVPKVERVMD-RINGFMIHNNCEN 151 :::::::: :::::::::: ::::::: :::::::: d1vkfa_ 81 KNYVVAKK--NGIPAVLRFF-------ALDSKAVERGIEQIET---LGVDVVEVL----- 123 query 152 KDFGLFDRMLGEIEERFGALIARVDWVSLGGGIHFTGDDYPVDA-FSARLRAFSDRYGVQ 210 ::::::::::: ::: ::::::::: ::::::::::: d1vkfa_ 124 --------PGAVAPKVARK-IPG-RTVIAAGLV-----------ETEEEAREILKH---- 158 query 211 -IYLEPGEASITKSTTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSH 269 :::::: d1vkfa_ 159 VSAISTS----------------------------------------------------- 165 query 270 SYMICGKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELD 329 d1vkfa_ 166 ------------------------------------------------------------ 166 query 330 GSVRTVREFTYADYEQSLS------- 348 d1vkfa_ 166 -------------------SRILWKM 172 TMalign alignment (TM-score: 0.33 Raw score:114.32) query 1 -MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSS 59 :: :::::::: d1vkfa_ 1 M-----------------------------FK--------------------GIIAALWD 11 query 60 LFEVRLGRERFGKETHAYSVAY-G-DNEIDEVVSH-ADKII-FN------SI-SQLERFA 108 ::: :: :::::::::::::: : :::::::::: ::::: :: :: ::::::: d1vkfa_ 12 MDS-IG--EIEPDVVFLLKSDILNLKFHLKILKDRGKTVFVDMDFVNGLGEGEEAILFVK 68 query 109 DKAAGIARGLRLNPQRLGEWDVPKVERVM-DRINGFMIHNNCENKDFGLFDRMLGEIEER 167 :::: : ::::: :: : :::::: ::::::::::: : : :::::::::: d1vkfa_ 69 KAGA-D-GIITI------KP-K-NYVVAKKNGIPAVLRFFA--L----D-SKAVERGIEQ 111 query 168 FGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEASITKS---- 223 :::: : :::::: ::::: :::::::::: ::::::: ::::::: d1vkfa_ 112 IETL-G-VDVVEV-LPGAV---------APKVARKIPG---RTVIAAG-LVETEEEAREI 155 query 224 ---------TTLEVTVLDTLYNKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMIC 274 d1vkfa_ 156 LKHVSAIST--------------------------------------------------- 164 query 275 GKSCLAGDVFGEFRFAEELKVGDRISFQDAAGYTMV-----KKNWFNGVKMPAIAIRELD 329 : :: d1vkfa_ 165 --------------------------------S-SRILWKM------------------- 172 query 330 GSVRTVREFTYADYEQSLS 348 d1vkfa_ 173 ------------------- 173 HHsearch alignment (Probability: 0.01 E-value:0.17) query 6 YYLIDKAKLTRNMERIAHVREK 27 :::::::::::::::::::::: d1vkfa_ 97 FFALDSKAVERGIEQIETLGVD 118
Intermediate <-- 0.833 --> HitDALI alignment (Z-score: 2.6 Raw score:270.50) d1vkfa_ 1 ------------------------------------------------------------ 1 d1jlra_ 1 llvdprystndqeesilqdiitrfpnvvlmkqtaqlrammtiirdketpkeefvfyadrl 60 d1vkfa_ 1 ------------------------------mfkGIIAALWD------------------- 11 :::::::: d1jlra_ 61 irllieealnelpfqkkevttpldvsyhgvsfySKICGVSIvragesmesglravcrgvr 120 d1vkfa_ 12 ------------------mdSIGE-IEPDVVFLLK---sdILNLKFHLKILKDRGK---T 46 :::: :::::::::: :::::::::::::::: : d1jlra_ 121 igkiliqrdettaepkliyeKLPAdIRERWVMLLDpmcatAGSVCKAIEVLLRLGVkeeR 180 d1vkfa_ 47 VFVDMDfvnglgEGEEAILFVKKAG-aDGIITIKPKnyvvakkngipavlrffaldskav 105 :::::: ::::::::::::: ::::::::: d1jlra_ 181 IIFVNI-----lAAPQGIERVFKEYpkVRMVTAAVD------------------------ 211 d1vkfa_ 106 ergieqietlgvdvvevlpgavapkvarkipgrtviaaglveteeeareilkhvsaists 165 d1jlra_ 212 -------------------------------------------iclnsryyivpgigdfg 228 d1vkfa_ 166 srilwkm 172 d1jlra_ 229 dryfgtm 235 FAST alignment (Normalized score: 1.51 Raw score:304.40) d1vkfa_ 1 MFKGIIAALWDMDSIGEIEPDVVFLLKSDILNLKFHLKILKDRGKTVFVDMDFVNGLGEG 60 d1jlra_ 1 ------------------------------------------------------------ 1 d1vkfa_ 61 EEAILFVKKAGA------------------------------------------------ 72 d1jlra_ 1 ------------LLVDPRYSTNDQEESILQDIITRFPNVVLMKQTAQLRAMMTIIRDKET 48 d1vkfa_ 73 -----------------------------------------------DGIITI----KPK 81 ::::: ::: d1jlra_ 49 PKEEFVFYADRLIRLLIEEALNELPFQKKEVTTPLDVSYHGVSFYSKICGVS-IVRAGES 107 d1vkfa_ 82 NYVVAKK--NGIPAVLRFFALDSKAVERGIEQIETLGVDVVEVLP--------------- 124 ::::::: :::::: :::: d1jlra_ 108 MESGLRAVCRGVRIG-KILI-------------------------QRDETTAEPKLIYEK 141 d1vkfa_ 125 -------------------GAVAPKVARKIPGR---------TVIAAGLV---ETEEEAR 153 :::::::::: ::::: ::::::: d1jlra_ 142 LPADIRERWVMLLDPMCATAGSVCKAIEV----LLRLGVKEERIIFV---NILAAPQGIE 194 d1vkfa_ 154 EILKHV---SAISTSSRILWKM---------------------------- 172 ::::: ::::: d1jlra_ 195 RVFKE-YPKVRMVT--------AAVDICLNSRYYIVPGIGDFGDRYFGTM 235 TMalign alignment (TM-score: 0.40 Raw score:69.21) d1vkfa_ 1 ------------------------MFKGIIAALWDMDSI-----------------GEIE 19 :::::::::::::: d1jlra_ 1 LLVDPRYSTNDQEESILQDIITRF-PNVVLMKQTAQLRAMMTIIRDKETPKEEFVF---- 55 d1vkfa_ 20 PDVVFLLKSD-ILNLKFHLKIL-KDRGKTVFV----------------------DMDFVN 55 ::::: : : : :::: d1jlra_ 56 -----YADRLI---R---L--LI-----EEALNELPFQKKEVTTPLDVSYHGVS------ 91 d1vkfa_ 56 GLGEGEEAILFVKKAGAD---GII---------TIK-PKN--YVVAKKNGIPAVLRFFAL 100 : ::: ::: :: ::::: :::::: d1jlra_ 92 -----------------FYSKICGVSIVRAGESMESG-LRAVCRGVR-------IGKILI 126 d1vkfa_ 101 D---------SKAVERGIEQIETLG--VDVVEVL-PG--A-VAPKVARKIP----G--RT 139 : ::: : :: :::: ::::::: :: : :::::::::: : :: d1jlra_ 127 QRDETTAEPKLIY--E--KL-PADIRERWVMLLDPMCATAGSVCKAIEVLLRLGVKEERI 181 d1vkfa_ 140 VIAAGLVETEEEAREILK-HV-SAISTSSRIL-----------------------WKM 172 :::::::: ::::::::: :: :::::::::: d1jlra_ 182 IFVNILAA-PQGIERVFKEYPKVRMVTAAVDICLNSRYYIVPGIGDFGDRYFGTM--- 235 HHsearch alignment (Probability: 0.01 E-value:0.11) d1vkfa_ 53 FVNGLGEGEEAILFVKKAGADGIITIKP-----KNYVVAKKNGIPAVLRFFALDS----- 102 :::::::::::::::::::::::::::: :::::::::::::::::::::: d1jlra_ 102 VRAGESMESGLRAVCRGVRIGKILIQRDETTAEPKLIYEKLPADIRERWVMLLDPMCATA 161 d1vkfa_ 103 KAVERGIEQIETLGVD--------VVEVLPGAVAPKVARKIPGRTVIAAGLVE 147 :::::::::::::::: ::::::: :::::::::::::::::::: d1jlra_ 162 GSVCKAIEVLLRLGVKEERIIFVNILAAPQG--IERVFKEYPKVRMVTAAVDI 212