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: T0542_Ad2+3.pdb
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1t57a_ | Hypothetical protein MTH1675 | PK C-terminal domain-like | Pyruvate kinase C-terminal domain-like | α/β |
| Hit | d1ogca_ | Ribose transport protein RbsD | Ribose transport protein RbsD | Ribose transport protein RbsD | α/β |
Query <-- 0.668 --> IntermediateDALI alignment (Z-score: 4.8 Raw score:501.90) query 1 ---------dadeeVYSALVVGLRAYVAKNGFRSVLIGLSGgidsALVAAIACDALGaQN 51 ::::::::::::::::::::::::::: :::::::::::: :: d1t57a_ 1 mekkicyfeepgkeNTERVLELVGERADQLGIRNFVVASVS----GETALRLSEMVE-GN 55 query 52 VYGVSMPSK---YSSDhSKGD-AAELARRTGLNFRTVSI--ePMFDAYMASLGLtglaEE 105 ::::::::: :::: :::: ::::::::::::::::: :::::::::::: :: d1t57a_ 56 IVSVTHHAGfreKGQL-ELEDeARDALLERGVNVYAGSHalsGVGRGISNRFGG---vTP 111 query 106 NL----------qsrlrgTTLMAISNQ-------eGHIVLAPGnkselavgystlygdsV 148 :: ::::::::: :::::::: : d1t57a_ 112 VEimaetlrmvsqgfkvcVEIAIMAADaglipvdeEVIAIGGT-----------awgadT 160 query 149 GAYgpikdvyktsifrlaewrnraaaergqtppipeasitkpdypvldailelyvdrdtg 208 ::: d1t57a_ 161 ALV--------------------------------------------------------- 163 query 209 adaivaagydrelvvktlrmvdtaeykrrqyPPGTkisakgfgkdrrlpitnrwregh 266 :::: d1t57a_ 164 ----------------ltpahmnsvfdlrihEVIA-------------------mprp 186 FAST alignment (Normalized score: 3.32 Raw score:738.10) query 1 DAD------------EEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDS--ALVAAIACDA 46 ::::::::::::::::::::::::::: :::::::::: d1t57a_ 1 ---MEKKICYFEEPGKENTERVLELVGERADQLGIRNFVVAS------VSGETALRLSEM 51 query 47 LGAQ--NVYGVSMPSKYSSDH-------------SKGDAAELARRTGLNFRTVSI----- 86 : :::::: ::::::::: ::::::::: d1t57a_ 52 V---EGNIVSVT---------HHAGFREKGQLELEDEARDALL-ERGVNVYAG--SHALS 96 query 87 EPMFDAYMASLGLTGLAEENLQ-----------------------SRLRGTTLMAI---- 119 ::::::::: :::::::::: d1t57a_ 97 GVGRGISNR-------------FGGVTPVEIMAETLRMVSQGFKVCVEIAIMAAD-AGLI 142 query 120 SNQEGHIVLAPGNKSELAVGYSTLYGDSVGAYGPIKDVYKTSIFRLAEWRNRAAAERGQT 179 :::::::::: d1t57a_ 143 PVDEEVIAIG-------------------------------------------------- 152 query 180 PPIPEASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQY 239 d1t57a_ 153 ------------------------------------------------------------ 153 query 240 PPGTKISAKGFGKDRRLPITNRWREGH--------------------------------- 266 d1t57a_ 153 ---------------------------GTAWGADTALVLTPAHMNSVFDLRIHEVIAMPR 185 query 267 - 267 d1t57a_ 186 P 186 TMalign alignment (TM-score: 0.36 Raw score:96.37) query 1 ---------------DADEEVYSALVVGLRAYVAKNGFRSVLIGLSGGIDSALVAAIACD 45 :::::::::::::::::::::::::: :: ::::::: d1t57a_ 1 MEKKICYFEEPGKEN------TERVLELVGERADQLGIRNFVVASVS---GE-TALRLSE 50 query 46 ALGAQNVYGVSMPSKYSS--DHSKGD-AAELARRTGLNFRTVSIEPMFDAYMASL-GLTG 101 ::: :::::::::::::: :::::: :::::::::::::::::::::::::::: ::: d1t57a_ 51 MVE-GNIVSVTHHAGFREKGQLELEDEARDALLERGVNVYAGSHALSGVGRGISNRFGG- 108 query 102 LAE--ENL--QSRL---------RG-TTLMA--I----SNQE-GHIVLAPGNKSELAVGY 140 :: : :: :: ::::: : :::: :::::::: d1t57a_ 109 -VTPV--EIM--AETLRMVSQGFKVCVEIAIMAADAGLIPVDEEVIAIGGT--------- 154 query 141 STLYGDSVGAY----------------GPIKDVYKTSIFRLAEWRNRAAAERGQTPPIPE 184 ::: :::::: d1t57a_ 155 -AWG-ADTALVLTPAHMNSVFDLRIHE--------------------------------- 179 query 185 ASITKPDYPVLDAILELYVDRDTGADAIVAAGYDRELVVKTLRMVDTAEYKRRQYPPGTK 244 :::: d1t57a_ 180 ------------------------------------------------------VIAM-- 183 query 245 ISAKGFGKDRRLPITNRWREGH 266 : : : d1t57a_ 184 -----P-R-----P-------- 186 HHsearch alignment (Probability: 0.08 E-value:0.04) query 16 AYVAKNGFRSVLIGLSGGIDSALVAAIACDALGAQNVYGVSMPSKYSSDHSKGDAAELAR 75 :::::::::::::::::: :::::::::: ::::::::::::::::::::::::::: d1t57a_ 25 ERADQLGIRNFVVASVSG----ETALRLSEMV-EGNIVSVTHHAGFREKGQLELEDEARD 79 query 76 RT 77 :: d1t57a_ 80 AL 81
Intermediate <-- 0.622 --> HitDALI alignment (Z-score: 1.9 Raw score:216.10) d1t57a_ 1 -----------------------------------mekkICYFEEPGkeNTERVLELVGE 25 :::::::: ::::::::::: d1ogca_ 1 mkkhgilnshlakiladlghtdkiviadaglpvpdgvlkIDLSLKPGlpAFQDTAAVLAE 60 d1t57a_ 26 RAdqlGIRNFVVASVSG----ETALRLSEMVE-GNIVSVTHhagfrekgqleledearda 80 :: :::::::::::: ::::::::::: :::::::: d1ogca_ 61 EM---AVEKVIAAAEIKasnqENAKFLENLFSeQEIEYLSH------------------- 98 d1t57a_ 81 llergvnvyagshalsgvgrgisnrfggvtpveimaetlrmvsqgfkvcveIAIMaadag 140 :::: d1ogca_ 99 -------------------------------------------------eeFKLL----- 104 d1t57a_ 141 lipvdeeviaiggtawgadtalvltpahmnsvfdLRIHEVIAMP--------------rp 186 :::::::::: d1ogca_ 105 ---------------------------------tKDAKAVIRTGeftpyancilqagvlf 131 FAST alignment (Normalized score: 2.62 Raw score:408.50) d1t57a_ 1 MEKKICYFEEPGKENT-------ERVLELVGERADQLGI----RNFVVASVS-------- 41 :::::::::: :::: d1ogca_ 1 ----------------MKKHGILNSHLAKILAD------LGHTDKIV-----IADAGLPV 33 d1t57a_ 42 ------------------GETALRLSEMVEGN--IVSVTHHAGFREKGQLEL------ED 75 ::::::::::: :::::: :: d1ogca_ 34 PDGVLKIDLSLKPGLPAFQDTAAVLAEEM---AVEKVIAA------------AEIKASNQ 78 d1t57a_ 76 EARDALLE--RGVNVYAGSHALSGVGRGISNRFGGVTPVEIMAETLRMVSQGFKVCVEIA 133 :::::::: ::::::::: d1ogca_ 79 ENAKFLENLFSEQEIEYLS----------------------------------------- 97 d1t57a_ 134 IMAADAGLIPVDEE-----------VIAIGGTAWGADTALVLTPAHMNSVFDLRIHEVIA 182 :::::: d1ogca_ 98 --------------HEEFKLLTKDAKAVIRT----------------------------- 114 d1t57a_ 183 MPRP----------------- 186 d1ogca_ 115 ----GEFTPYANCILQAGVLF 131 TMalign alignment (TM-score: 0.31 Raw score:57.05) d1t57a_ 1 -----------MEKK------------------------ICYFEEPGKENTERVLELVGE 25 :::: ::::::::::::::::::::: d1ogca_ 1 MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPAFQDTAAVLAE 60 d1t57a_ 26 RADQLGIRNFVV-AS--VSGETALRLSEMV-EGNIVSVTHHAGFREKGQLELEDEARDAL 81 ::: ::::::: :: ::::::::::::: ::::::: d1ogca_ 61 EMA--VEKVIAAAEIKASNQENAKFLENLFSEQEIEYL---------------------- 96 d1t57a_ 82 LERGVNVYAGSHALSGVGRGISNRFGGVTPVEIMAETLRMVSQGFKVCVEIAIMAADAGL 141 : :: :::: d1ogca_ 97 ---------S-HE------------------------------------EFKL------- 103 d1t57a_ 142 IPVDEEVIAIGGTAWGADTALVLTPAHMNSVFDLRIHEVIAMPR---------------- 185 :: :::::: :::: d1ogca_ 104 ------------------------LT-------KDAKAV-IRTGEFTPYANCILQAGVLF 131 d1t57a_ 186 P 186 d1ogca_ 132 - 132 HHsearch alignment (Probability: 0.01 E-value:0.09) d1t57a_ 34 N 34 : d1ogca_ 66 K 66