RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780584|ref|YP_003064997.1| 50S ribosomal protein L28
[Candidatus Liberibacter asiaticus str. psy62]
(97 letters)
>3bbo_Y Ribosomal protein L28; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Nicotiana tabacum}
Length = 151
Score = 80.3 bits (198), Expect = 9e-17
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 2/80 (2%)
Query: 1 MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVE 60
R+C T K NKVSH+N+KT++ NL + + ++ +LR+S A++++E
Sbjct: 74 ARRICPFTGKKSNRANKVSHSNHKTKKLQFVNLQYKRIWWEAGKRYVKLRLSTKAIKTIE 133
Query: 61 RQGGLDRFLSNSKKENLSAR 80
+ GLD +LS +
Sbjct: 134 K-NGLDAVA-KKAGIDLSKK 151
>3ofq_X 50S ribosomal protein L28; protein biosynthesis, ribosomes, RNA,
tRNA, transfer, antibi EXIT, peptidyl, ribosomal
subunit, large; 3.10A {Escherichia coli} PDB: 2i2v_X
2wwq_0* 3fik_X 2i2t_X 3ofr_X* 3i1n_X 1vt2_X* 2qao_Z*
2qba_Z* 2qbc_Z* 2qbe_Z 2qbg_Z 2qbi_Z* 2qbk_Z* 2qov_Z
2qox_Z 2qoz_Z* 2qp1_Z* 2z4l_Z* 2z4n_Z* ...
Length = 77
Score = 77.3 bits (191), Expect = 7e-16
Identities = 27/72 (37%), Positives = 43/72 (59%), Gaps = 1/72 (1%)
Query: 2 SRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVER 61
SRVC++T K ++GN SHA N T+RRFLPNL + ++ LR+S +R +++
Sbjct: 1 SRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDK 60
Query: 62 QGGLDRFLSNSK 73
G+D L+ +
Sbjct: 61 -KGIDTVLAELR 71
>3i1n_X 50S ribosomal protein L28; ribosome structure, protein-RNA
complex, acetylation, ribonucleoprotein, ribosomal
protein, RNA-binding, rRNA- binding, methylation; 3.19A
{Escherichia coli k-12} PDB: 2qao_Z* 2qba_Z* 2qbc_Z*
2qbe_Z 2qbg_Z 2qbi_Z* 2qbk_Z* 2qov_Z 2qox_Z 2qoz_Z*
2qp1_Z* 2z4l_Z* 2z4n_Z* 3df2_Z 3df4_Z 2qam_Z 3i1p_X
3i1r_X 3i1t_X 3i20_X ...
Length = 78
Score = 77.0 bits (190), Expect = 8e-16
Identities = 28/76 (36%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 1 MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVE 60
MSRVC++T K ++GN SHA N T+RRFLPNL + ++ LR+S +R ++
Sbjct: 1 MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVID 60
Query: 61 RQGGLDRFLSNSKKEN 76
+ G+D L+ +
Sbjct: 61 K-KGIDTVLAELRARG 75
>2jz6_A 50S ribosomal protein L28; structure, NESG, ribonucleoprotein,
structural genomics, PSI-2, protein structure
initiative; NMR {Thermotoga maritima MSB8} SCOP:
d.325.1.1
Length = 77
Score = 70.4 bits (173), Expect = 8e-14
Identities = 20/74 (27%), Positives = 39/74 (52%), Gaps = 5/74 (6%)
Query: 1 MSRVCELTKKTVMSGNKVSHANNKTRRRFLPNLCRITLISDIMEQKYQLRISKCALRSVE 60
M++ CE+ K SGN VSH++ K+ R F PNL ++ ++ ++R+ L+S
Sbjct: 6 MAKRCEVCGKAPRSGNTVSHSDKKSERWFRPNLQKVRVVLPD-GTIKRMRVCTSCLKS-- 62
Query: 61 RQGGLDRFLSNSKK 74
G + +++ +
Sbjct: 63 --GKVKKYVGQVSE 74
>2jl6_1 50S ribosomal protein L28, 50S ribosomal protein L25;
methylation, translation, paromomycin, tRNA-binding,
tRNA, zinc, mRNA, ribosome, repressor, RNA-binding;
3.45A {Thermus thermophilus} PDB: 2jl8_1
Length = 89
Score = 59.5 bits (144), Expect = 2e-10
Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 15/74 (20%)
Query: 1 MSRVCELTKKTVMSGNKVSH-------------ANNKTRRRFLPNLCRITLISDIMEQKY 47
MS+VCE++ K + N + ++RR PNL ++ + Q+
Sbjct: 1 MSKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVA--GQEI 58
Query: 48 QLRISKCALRSVER 61
R++ + V
Sbjct: 59 TFRVAASHIPKVYE 72
>2j01_1 50S ribosomal protein L28; ribosome, tRNA, paromomycin, mRNA,
translation; 2.8A {Thermus thermophilus} SCOP:
d.325.1.1 PDB: 2j03_1 2v47_1 2v49_1 2wdi_1 2wdj_1
2wdl_1 2wdn_1 2wh2_1 2wh4_1 3hux_1 3huz_1 3f1f_1 1vsp_V
1vsa_V 3d5d_1 3d5b_1 3f1h_1 3fin_1
Length = 98
Score = 57.5 bits (139), Expect = 6e-10
Identities = 19/104 (18%), Positives = 40/104 (38%), Gaps = 22/104 (21%)
Query: 1 MSRVCELTKKTVMSGNKVSH-------------ANNKTRRRFLPNLCRITLISDIMEQKY 47
MS+VCE++ K + N + ++RR PNL ++ + Q+
Sbjct: 1 MSKVCEISGKRPIVANSIQRRGKAKREGGVGKKTTGISKRRQYPNLQKVRVRVA--GQEI 58
Query: 48 QLRISKCALRSVERQGGLDRFLSNSKKENLSA-RMRTLRSQILK 90
R++ + V + +K L + ++ ++LK
Sbjct: 59 TFRVAASHIPKV------YELVERAKGLKLEGLSPKEIKKELLK 96
>2zjr_U 50S ribosomal protein L28; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: d.325.1.1 PDB: 2zjp_U 2zjq_U 3cf5_U*
3dll_U*
Length = 81
Score = 54.8 bits (132), Expect = 4e-09
Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 15/76 (19%)
Query: 1 MSRVCELTKKTVMSGNKV-------------SHANNKTRRRFLPNLCRITLISDIMEQKY 47
MSR C LT K + N V T+R NL + + + Q
Sbjct: 1 MSRECYLTGKKNLVVNSVIRRGKARADGGVGRKTTGITKRVQRANLHKKAIREN--GQVK 58
Query: 48 QLRISKCALRSVERQG 63
+ +S ALR++ +
Sbjct: 59 TVWLSANALRTLSKGP 74
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 27.6 bits (61), Expect = 0.80
Identities = 19/101 (18%), Positives = 35/101 (34%), Gaps = 29/101 (28%)
Query: 7 LTKKTVMSG---NKVSHANNKTR--RRFLPNLCRIT------LISD----IMEQ--KYQL 49
L K SG +++ + K + RFLP + L+ I + K +
Sbjct: 393 LRKAKAPSGLDQSRIPFSERKLKFSNRFLP----VASPFHSHLLVPASDLINKDLVKNNV 448
Query: 50 RISKCALR-SV-ERQGGLDRFLSNSKKENLSARMRTLRSQI 88
+ ++ V + G D L ++S R + I
Sbjct: 449 SFNAKDIQIPVYDTFDGSD--LRVL-SGSISER---IVDCI 483
>1u04_A Argonaute, hypothetical protein PF0537; RNAI, silencing, PIWI, PAZ,
RISC, slicer, RNAse H, hydrolase/gene regulation
complex; 2.25A {Pyrococcus furiosus dsm 3638} SCOP:
b.34.14.1 c.55.3.10 PDB: 1z25_A 1z26_A
Length = 771
Score = 26.2 bits (57), Expect = 1.8
Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 2/75 (2%)
Query: 12 VMSGNKVSHANNKTRRRFL-PNLCRITLISDIMEQKYQLRISKCA-LRSVERQGGLDRFL 69
+++ NK + +L P L T ++ +E I + L ER+ L+ L
Sbjct: 246 ILAKFASKIKKNKNYKIYLLPQLVVPTYNAEQLESDVAKEILEYTKLMPEERKELLENIL 305
Query: 70 SNSKKENLSARMRTL 84
+ + + + +
Sbjct: 306 AEVDSDIIDKSLSEI 320
>1vh4_A SUFD protein; structural genomics, protein binding protein; 1.75A
{Escherichia coli} SCOP: b.80.6.1 PDB: 2zu0_A*
Length = 435
Score = 24.6 bits (52), Expect = 5.2
Identities = 8/30 (26%), Positives = 16/30 (53%)
Query: 40 SDIMEQKYQLRISKCALRSVERQGGLDRFL 69
S+ ++Q + L ++ RS + Q L + L
Sbjct: 10 SNALQQWHHLFEAEGTKRSPQAQQHLQQLL 39
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.319 0.128 0.342
Gapped
Lambda K H
0.267 0.0730 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 699,669
Number of extensions: 26007
Number of successful extensions: 78
Number of sequences better than 10.0: 1
Number of HSP's gapped: 71
Number of HSP's successfully gapped: 13
Length of query: 97
Length of database: 5,693,230
Length adjustment: 63
Effective length of query: 34
Effective length of database: 4,165,858
Effective search space: 141639172
Effective search space used: 141639172
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.0 bits)