RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780250|ref|YP_003064663.1| 50S ribosomal protein L24
[Candidatus Liberibacter asiaticus str. psy62]
(102 letters)
>3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 191
Score = 104 bits (260), Expect = 6e-24
Identities = 32/102 (31%), Positives = 56/102 (54%), Gaps = 3/102 (2%)
Query: 3 KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTPNKEAG-IISKEA 61
++ GD V V++G +KGK G++ + + + ++ +N +H + E G II EA
Sbjct: 68 HVKVGDTVKVISGGEKGKIGEISKIHKHNSTVIIKDLNFKTKHVKSKEEGEQGQIIKIEA 127
Query: 62 SIHLSNLSLID-KDGKQVRVGFSFV-DGKKIRIAKRSGEPID 101
+IH SN+ LI + RVG + D +K+R ++GE +D
Sbjct: 128 AIHSSNVMLILKEQEVADRVGHKILEDVRKVRYLIKTGEIVD 169
>3ofq_U 50S ribosomal protein L24; protein biosynthesis, ribosomes, RNA,
tRNA, transfer, antibi EXIT, peptidyl, ribosomal
subunit, large; 3.10A {Escherichia coli} PDB: 2j28_U*
3fik_U 2wwq_U 3ofr_U* 3i1n_U 1vs8_U 1vs6_U 1vt2_U 3i1p_U
3i1r_U 3i1t_U 3i20_U 3i22_U 3kcr_U 3orb_U* 3e1b_O 3e1d_O
2qam_U* 1p85_S 1p86_S ...
Length = 102
Score = 100 bits (251), Expect = 8e-23
Identities = 49/101 (48%), Positives = 68/101 (67%), Gaps = 4/101 (3%)
Query: 3 KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTP--NKEAGIISKE 60
KIR D V+VL GKDKGK G+V V+ G+ V+G+N+VK+HQ+ P N+ GI+ KE
Sbjct: 3 KIRRDDEVIVLTGKDKGKRGKVKNVLSS-GKVIVEGINLVKKHQKPVPALNQPGGIVEKE 61
Query: 61 ASIHLSNLSLID-KDGKQVRVGFSFVDGKKIRIAKRSGEPI 100
A+I +SN+++ + GK RVGF F DGKK+R K + E I
Sbjct: 62 AAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETI 102
>2j01_Y 50S ribosomal protein L24; ribosome, tRNA, paromomycin, mRNA,
translation; 2.8A {Thermus thermophilus} SCOP: b.34.5.1
PDB: 1vsp_S 2hgj_X 2hgq_X 2hgu_X 1vsa_S 2j03_Y 2jl6_Y
2jl8_Y 2v47_Y 2v49_Y 2wdi_Y 2wdj_Y 2wdl_Y 2wdn_Y 2wh2_Y
2wh4_Y 3d5b_Y 3d5d_Y 3f1f_Y 3f1h_Y ...
Length = 110
Score = 97.5 bits (243), Expect = 6e-22
Identities = 42/102 (41%), Positives = 59/102 (57%), Gaps = 3/102 (2%)
Query: 3 KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTPN-KEAGIISKEA 61
++ GD VLV +GK KG+ G+V V+ K V+GVNIVK+ R +P + G I KEA
Sbjct: 6 HVKKGDTVLVASGKYKGRVGKVKEVLPKKYAVIVEGVNIVKKAVRVSPKYPQGGFIEKEA 65
Query: 62 SIHLSNLSLID-KDGKQVRVGFSFV-DGKKIRIAKRSGEPID 101
+H S + I GK RV F+ +GKKIR+ + G +D
Sbjct: 66 PLHASKVRPICPACGKPTRVRKKFLENGKKIRVCAKCGGALD 107
>3i1n_U 50S ribosomal protein L24; ribosome structure, protein-RNA complex,
acetylation, ribonucleoprotein, ribosomal protein,
RNA-binding, rRNA- binding, methylation; 3.19A
{Escherichia coli k-12} PDB: 1vs8_U 1vs6_U 3i1p_U 3i1r_U
3i1t_U 3i20_U 3i22_U 3e1b_O 3e1d_O 2qam_U* 1p85_S 1p86_S
2awb_U 2aw4_U 2i2v_U 2i2t_U* 2qao_U* 2qba_U* 2qbc_U*
2qbe_U ...
Length = 104
Score = 95.9 bits (239), Expect = 2e-21
Identities = 49/101 (48%), Positives = 68/101 (67%), Gaps = 4/101 (3%)
Query: 3 KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTP--NKEAGIISKE 60
KIR D V+VL GKDKGK G+V V+ G+ V+G+N+VK+HQ+ P N+ GI+ KE
Sbjct: 4 KIRRDDEVIVLTGKDKGKRGKVKNVLSS-GKVIVEGINLVKKHQKPVPALNQPGGIVEKE 62
Query: 61 ASIHLSNLSLID-KDGKQVRVGFSFVDGKKIRIAKRSGEPI 100
A+I +SN+++ + GK RVGF F DGKK+R K + E I
Sbjct: 63 AAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETI 103
>2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal subunit,
ribonucleoprotein, RNA-binding, rRNA-binding,
tRNA-binding, methylation; 2.91A {Deinococcus
radiodurans} SCOP: b.34.5.1 PDB: 1nwx_S* 1nwy_S* 1sm1_S*
1xbp_S* 2d3o_S 2zjp_R* 2zjq_R 1nkw_S 3cf5_R* 3dll_R*
1pnu_S 1pny_S 1vor_V 1vou_V 1vow_V 1voy_V 1vp0_V
Length = 115
Score = 95.6 bits (238), Expect = 2e-21
Identities = 37/101 (36%), Positives = 64/101 (63%), Gaps = 2/101 (1%)
Query: 3 KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTP-NKEAGIISKEA 61
+ GD V+VL+GK KG+ G+V+ + + + V+GVN++ ++ + + N + G +E
Sbjct: 15 HFKKGDTVIVLSGKHKGQTGKVLLALPRDQKVVVEGVNVITKNVKPSMTNPQGGQEQREL 74
Query: 62 SIHLSNLSLID-KDGKQVRVGFSFVDGKKIRIAKRSGEPID 101
++H S ++L+D + GK RV VDGKK+R+A SG+ ID
Sbjct: 75 ALHASKVALVDPETGKATRVRKQIVDGKKVRVAVASGKTID 115
>2ftc_N Mitochondrial ribosomal protein L24; mitochondrial ribosome, large
ribosomal subunit, ribosomal RNA; 12.10A {Bos taurus}
PDB: 3iy9_N
Length = 96
Score = 86.7 bits (215), Expect = 1e-18
Identities = 32/96 (33%), Positives = 52/96 (54%), Gaps = 2/96 (2%)
Query: 7 GDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTPNKEAGIISKEASIHLS 66
GD V +L GKD GK G+V+ V+R+ V G+N R+ +T + +I EA +
Sbjct: 1 GDTVEILEGKDAGKQGKVVQVIRQRNWVVVGGLNTHYRYIGKTMDYRGTMIPSEAPLLHR 60
Query: 67 NLSLID-KDGKQVRVGFSFV-DGKKIRIAKRSGEPI 100
+ L+D D K + + F G+++R++ RSG I
Sbjct: 61 QVKLVDPMDRKPTEIEWRFTEAGERVRVSTRSGRII 96
>2wwb_L 60S ribosomal protein L26-A; ribosome, protein EXIT tunnel,
cotranslational protein translocation, protein
conducting channel; 6.48A {Triticum aestivum} PDB:
2wwa_L 2ww9_L 1s1i_U
Length = 127
Score = 62.4 bits (152), Expect = 2e-11
Identities = 21/96 (21%), Positives = 33/96 (34%), Gaps = 19/96 (19%)
Query: 3 KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTPNKEAGIISKEAS 62
IR D VLV+ G KG+ G++ V R V V K + +
Sbjct: 49 PIRRDDEVLVVRGSKKGQEGKISSVYRLKFAVQVDKVTKEKVNGAS----------VPIN 98
Query: 63 IHLSNLSLIDKDGKQVRVGFSFVDGKKIRIAKRSGE 98
+H S L + +K I ++ G+
Sbjct: 99 LHPSKLVITKLHLD---------KDRKALIQRKGGK 125
>1vq8_T 50S ribosomal protein L24P; ribosome 50S, protein-protein complex,
RNA-RNA complex, protein-RNA complex, peptidyl
transferase reaction; HET: 1MA OMU OMG UR3 PSU SPS;
2.20A {Haloarcula marismortui} SCOP: b.34.5.1 PDB:
1vq4_T* 1vq5_T* 1vq6_T* 1vq7_T* 1s72_T* 1vq9_T* 1vqk_T*
1vql_T* 1vqm_T* 1vqn_T* 1vqo_T* 1vqp_T* 1yhq_T* 1yi2_T*
1yij_T* 1yit_T* 1yj9_T* 1yjn_T* 1yjw_T* 2otj_T* ...
Length = 120
Score = 62.0 bits (151), Expect = 3e-11
Identities = 17/81 (20%), Positives = 29/81 (35%), Gaps = 11/81 (13%)
Query: 3 KIRTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRHQRQTPNKEAGIISKEAS 62
++ GD V VL G G+ G+V+ V V+ V + K +
Sbjct: 42 RVNAGDTVEVLRGDFAGEEGEVINVDLDKAVIHVEDVTLEKTDGEE----------VPRP 91
Query: 63 IHLSNLSLID-KDGKQVRVGF 82
+ SN+ + D + R
Sbjct: 92 LDTSNVRVTDLDLEDEKREAR 112
>2zkr_t 60S ribosomal protein L26; protein-RNA complex, 60S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 145
Score = 34.0 bits (78), Expect = 0.008
Identities = 22/80 (27%), Positives = 34/80 (42%), Gaps = 15/80 (18%)
Query: 4 IRTGDRVLVLAGKDKGK-AGQVMGVVRKSGRAFVQGVNIVKRHQRQTPNKEAGIISKEAS 62
IR D V V+ G KG+ G+V+ V RK +++ V K +
Sbjct: 49 IRKDDEVQVVRGHYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVH----------VG 98
Query: 63 IHLSNLSLI----DKDGKQV 78
IH S + + DKD K++
Sbjct: 99 IHPSKVVITRLKLDKDRKKI 118
>3gqh_A Preneck appendage protein; beta barrel, viral protein; 1.80A
{Bacillus phage PHI29} PDB: 3gqk_A*
Length = 163
Score = 28.6 bits (64), Expect = 0.38
Identities = 7/29 (24%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 73 KDGKQVRVGFSFV-DGKKIRIAKRSGEPI 100
G+ + G+ + KIR A++ + I
Sbjct: 9 LGGQVIETGYLVTLEKGKIRKAEKGEKII 37
>1b34_A Protein (small nuclear ribonucleoprotein SM D1); snRNP, splicing,
spliceosome, core snRNP domain, systemic lupus
erythematosus, SLE; 2.50A {Homo sapiens} SCOP: b.38.1.1
PDB: 3cw1_B
Length = 119
Score = 28.6 bits (64), Expect = 0.39
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 62 SIHLSNLSLIDKDGKQVRVGFSFVDGKKIR 91
+ HL + + K+ + V++ + G IR
Sbjct: 37 NTHLKAVKMTLKNREPVQLETLSIRGNNIR 66
>2ckk_A KIN17; beta barrel, ribosomal protein, ribonucleoprotein, nuclear
protein; 1.45A {Homo sapiens}
Length = 127
Score = 27.5 bits (61), Expect = 0.76
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 5 RTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQ 37
G R+LVL G +G G + + K+ A +
Sbjct: 72 APGKRILVLNGGYRGNEGTLESINEKTFSATIV 104
>3gqn_A Preneck appendage protein; coiled coil, beta helix, beta barrel,
ATP binding, viral protein; HET: ATP; 2.15A {Bacillus
phage PHI29}
Length = 772
Score = 26.3 bits (57), Expect = 1.6
Identities = 7/28 (25%), Positives = 14/28 (50%), Gaps = 1/28 (3%)
Query: 74 DGKQVRVG-FSFVDGKKIRIAKRSGEPI 100
G+ + G ++ KIR A++ + I
Sbjct: 619 GGQVIETGYLVTLEKGKIRKAEKGEKII 646
>1e7u_A Phosphatidylinositol 3-kinase catalytic subunit; phosphoinositide
3-kinase gamma, secondary messenger generation, PI3K, PI
3K, wortmannin; HET: KWT; 2.0A {Sus scrofa} SCOP:
a.118.1.6 b.7.1.1 d.15.1.5 d.144.1.4 PDB: 1e8x_A*
1e8w_A* 1e7v_A* 1e90_A* 3dbs_A* 3l13_A* 3csf_A* 3cst_A*
3l16_A* 3l17_A* 3ene_A* 1e8y_A 1e8z_A* 2a4z_A* 2a5u_A*
2chw_A* 2chx_A* 2chz_A* 2v4l_A* 3dpd_A* ...
Length = 961
Score = 26.1 bits (57), Expect = 1.9
Identities = 5/22 (22%), Positives = 10/22 (45%), Gaps = 1/22 (4%)
Query: 64 HLSNLSLIDKDGKQVRVGFSFV 85
H N+ +I + G + F +
Sbjct: 807 HNDNI-MISETGNLFHIDFGHI 827
>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 = 26.1 bits (57), Expect = 2.0
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 65 LSNLSLIDKDGKQVRV 80
L L+ +KDG VRV
Sbjct: 512 LGVLTHRNKDGTGVRV 527
>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay,
RNR family, hydrolase; 2.35A {Escherichia coli K12}
SCOP: b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A*
2ix1_A
Length = 644
Score = 26.1 bits (56), Expect = 2.1
Identities = 6/31 (19%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 7 GDRVLV-LAGKDKGKAGQVMGVVRKSGRAFV 36
GDR++ + + + ++ + +V FV
Sbjct: 57 GDRIIAVIHSEKERESAEPEELVEPFLTRFV 87
>1qd6_C Protein (outer membrane phospholipase (ompla)); anti-parallel beta
barrel dimer, membrane protein; HET: HDS; 2.10A
{Escherichia coli} SCOP: f.4.2.1
Length = 240
Score = 25.9 bits (57), Expect = 2.4
Identities = 9/20 (45%), Positives = 10/20 (50%), Gaps = 2/20 (10%)
Query: 69 SLIDKDGKQ--VRVGFSFVD 86
SLID + Q V VG D
Sbjct: 219 SLIDYNFNQTRVGVGVMLND 238
>1qd5_A Outer membrane phospholipase A; anti-parallel beta barrel, membrane
protein; HET: BOG; 2.17A {Escherichia coli} SCOP:
f.4.2.1 PDB: 1fw2_A* 1fw3_A* 1ilz_A* 1ild_A* 1im0_A*
Length = 275
Score = 25.5 bits (56), Expect = 2.9
Identities = 9/20 (45%), Positives = 10/20 (50%), Gaps = 2/20 (10%)
Query: 69 SLIDKDGKQ--VRVGFSFVD 86
SLID + Q V VG D
Sbjct: 254 SLIDYNFNQTRVGVGVMLND 273
>2p31_A CL683, glutathione peroxidase 7; thioredoxin fold, NPGPX,
phospholipid hydroperoxidase, structural genomics,
structural genomics consortium, SGC; 2.00A {Homo
sapiens}
Length = 181
Score = 24.9 bits (53), Expect = 4.5
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 70 LIDKDGKQVRVGFSFVDGKKIR 91
L+ DGK V V +++R
Sbjct: 152 LVAPDGKVVGAWDPTVSVEEVR 173
>2d7e_A Primosomal protein N'; inter-twined, hydrolase; 2.50A
{Escherichia coli} PDB: 2d7g_A* 2d7h_A* 2dwl_A 2dwm_A
2dwn_A*
Length = 105
Score = 24.2 bits (52), Expect = 6.8
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 2 EKIRTGDRVLVLAGKDKGKAGQVMGVVRKS 31
++ G RV V GK + + G V+ V S
Sbjct: 24 MTVKAGCRVRVPFGKQQERIGIVVSVSDAS 53
>1d3b_A Protein (small nuclear ribonucleoprotein SM D3); snRNP, splicing,
core snRNP domain, systemic lupus erythematosus, SLE;
HET: CIT; 2.00A {Homo sapiens} SCOP: b.38.1.1
Length = 75
Score = 24.3 bits (53), Expect = 6.8
Identities = 8/30 (26%), Positives = 19/30 (63%)
Query: 62 SIHLSNLSLIDKDGKQVRVGFSFVDGKKIR 91
+ +SN+++ +DG+ ++ ++ G KIR
Sbjct: 40 NCQMSNITVTYRDGRVAQLEQVYIRGCKIR 69
>1ry2_A Acetyl-coenzyme A synthetase 1, acyl-activating enzyme 1; AMP
forming, related to firefly luciferase, ligase; HET:
AMP; 2.30A {Saccharomyces cerevisiae} SCOP: e.23.1.1
Length = 663
Score = 24.0 bits (51), Expect = 7.6
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 40 NIVKRHQRQTPNKEA 54
N V RH +TPNK+A
Sbjct: 86 NCVDRHALKTPNKKA 100
>3dwv_A Glutathione peroxidase-like protein; alpha beta, 3-layer(ABA)
sandwich, glutaredoxin fold, oxidoreductase; 1.41A
{Trypanosoma brucei} PDB: 2rm5_A 2rm6_A 3e0u_A
Length = 187
Score = 24.2 bits (51), Expect = 7.9
Identities = 8/22 (36%), Positives = 9/22 (40%)
Query: 70 LIDKDGKQVRVGFSFVDGKKIR 91
LID+DG V K I
Sbjct: 154 LIDRDGVPVERFSPGASVKDIE 175
>2gp4_A 6-phosphogluconate dehydratase; N-terminal domain largely
alpha-helical, C-terminal domain mainly beta-sheet
(trefoil-like); 2.49A {Shewanella oneidensis mr-1} SCOP:
c.8.2.2 d.334.1.1
Length = 628
Score = 23.9 bits (51), Expect = 8.2
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 8 DRVLVLAGKDKGKAGQVMGVVR 29
D L+L DK G ++G +
Sbjct: 166 DGALLLGICDKIVPGLLIGALS 187
>1djx_A PLC-D1, phosphoinositide-specific phospholipase C, isozyme delta1;
phosphoric diester hydrolase, hydrolase, lipid
degradation, transducer; HET: I3P; 2.30A {Rattus
norvegicus} SCOP: a.39.1.7 b.7.1.1 c.1.18.1 PDB: 1djg_A
1dji_A 1djh_A* 1djw_A* 1djy_A* 1djz_A* 2isd_A 1qas_A
1qat_A
Length = 624
Score = 24.2 bits (52), Expect = 8.3
Identities = 10/45 (22%), Positives = 18/45 (40%)
Query: 56 IISKEASIHLSNLSLIDKDGKQVRVGFSFVDGKKIRIAKRSGEPI 100
+I S+H S G+ SF + + +R+ + SG
Sbjct: 363 MIIYCKSVHFGGFSSPGTSGQAFYEMASFSESRALRLLQESGNGF 407
>2zkq_e 40S ribosomal protein S2E; protein-RNA complex, 40S ribosomal
subunit, ribosomal protein/RNA complex; 8.70A {Canis
familiaris}
Length = 179
Score = 23.8 bits (51), Expect = 9.4
Identities = 8/41 (19%), Positives = 14/41 (34%)
Query: 5 RTGDRVLVLAGKDKGKAGQVMGVVRKSGRAFVQGVNIVKRH 45
RT + V G G G + ++ A + + K
Sbjct: 29 RTRFKAFVAIGDHNGHVGLGVKCSKEVATAIRGAIILAKLS 69
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
0.317 0.137 0.373
Gapped
Lambda K H
0.267 0.0697 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 848,776
Number of extensions: 35358
Number of successful extensions: 213
Number of sequences better than 10.0: 1
Number of HSP's gapped: 192
Number of HSP's successfully gapped: 47
Length of query: 102
Length of database: 5,693,230
Length adjustment: 67
Effective length of query: 35
Effective length of database: 4,068,882
Effective search space: 142410870
Effective search space used: 142410870
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.1 bits)