RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780329|ref|YP_003064742.1| 30S ribosomal protein S6
[Candidatus Liberibacter asiaticus str. psy62]
(135 letters)
>1cqm_A Ribosomal protein S6; alzheimer disease, oligomerization; 1.65A
{Thermus thermophilus} SCOP: d.58.14.1 PDB: 1cqn_A
1qjh_A 1ris_A 1fka_F 1gix_I* 1hnw_F* 1hnx_F* 1hnz_F*
1hr0_F 1i94_F* 1i95_F* 1i96_F* 1i97_F* 1ibk_F* 1ibl_F*
1ibm_F 1j5e_F 1jgo_I* 1jgp_I* 1jgq_I* ...
Length = 101
Score = 110 bits (276), Expect = 1e-25
Identities = 24/100 (24%), Positives = 49/100 (49%)
Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60
M+ YE +L ++ Q+ Q ++ G V V LG+R +AY I K+ + Y+
Sbjct: 1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVAILGLRRLAYPIAKDPQGYF 60
Query: 61 VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSP 100
++ + P ++++ R++RI +NV R + + +
Sbjct: 61 LWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLAN 100
>3ofo_F 30S ribosomal protein S6; protein biosynthesis, ribosomes, RNA,
tRNA, transfer, eryThr ketolide, macrolide, antibiotic,
EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_F*
3iy8_F 2wwl_F 3ofp_F 2gy9_F 2gyb_F
Length = 100
Score = 107 bits (269), Expect = 8e-25
Identities = 31/100 (31%), Positives = 53/100 (53%), Gaps = 1/100 (1%)
Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60
M+ YE VF++ D S +Q+ I +Y + I G++ + + G R +AY I K KA+Y
Sbjct: 1 MRHYEIVFMVHPDQS-EQVPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHY 59
Query: 61 VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSP 100
V MN+ +P I E++ R ++ V+RS+ +
Sbjct: 60 VLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEA 99
>3i1m_F 30S ribosomal protein S6; ribosome structure, protein-RNA complex,
ribonucleoprotein, ribosomal protein, RNA-binding,
rRNA-binding, antibiotic resistance; 3.19A {Escherichia
coli k-12} PDB: 1p6g_F 1p87_F* 1vs7_F* 2avy_F 2aw7_F
1vs5_F 2i2u_F 2i2p_F* 2qan_F* 2qb9_F* 2qbb_F* 2qbd_F
2qbf_F 2qbh_F* 2qbj_F* 2qou_F* 2qow_F* 2qoy_F* 2qp0_F*
2vho_F ...
Length = 135
Score = 99.6 bits (248), Expect = 2e-22
Identities = 33/126 (26%), Positives = 59/126 (46%), Gaps = 1/126 (0%)
Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60
M+ YE VF++ D S Q + I +Y + I G++ + + G R +AY I K KA+Y
Sbjct: 1 MRHYEIVFMVHPDQSEQ-VPGMIERYTAAITGAEGKIHRLEDWGRRQLAYPINKLHKAHY 59
Query: 61 VFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDRDDRNDRFPRDR 120
V MN+ +P I E++ R ++ V+RS+ + + ++ D +
Sbjct: 60 VLMNVEAPQEVIDELETTFRFNDAVIRSMVMRTKHAVTEASPMVKAKDERRERRDDFANE 119
Query: 121 NVDRKQ 126
D +
Sbjct: 120 TADDAE 125
>3bbn_F Ribosomal protein S6; small ribosomal subunit, spinach chloroplast
ribosome, ribonucleoprotein particle, macromolecular
complex; 9.40A {Spinacea oleracea}
Length = 168
Score = 98.5 bits (245), Expect = 4e-22
Identities = 22/106 (20%), Positives = 48/106 (45%), Gaps = 9/106 (8%)
Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKA-- 58
++ YE + +LR D++ + +Y+ L+ G V G+ +AY I++ KA
Sbjct: 62 LRQYETMAVLRPDMTEDERLTLTQKYEELLVAGGAMYVEVFNRGVIPLAYSIKRKNKAGE 121
Query: 59 -------YYVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHE 97
Y+ + P +I ++ + D++V+RS + + +
Sbjct: 122 TNNYLDGIYLLFTYFTKPESISPLEAALVTDDDVIRSSSFKIRKRK 167
>1vmb_A 30S ribosomal protein S6; TM0603, structural genomics, JCSG,
protein structure initiative, PSI, joint center for
structural genomics; 1.70A {Thermotoga maritima} SCOP:
d.58.14.1
Length = 140
Score = 94.6 bits (235), Expect = 7e-21
Identities = 20/116 (17%), Positives = 52/116 (44%), Gaps = 1/116 (0%)
Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQEN-GGEVRLVNELGMRTIAYRIRKNRKAY 59
++YE +F++ ++ ++ ++ + + + +I+E G++ V +GMR AY I+K +
Sbjct: 18 ERIYESMFIIAPNVPEEERENLVERVKKIIEERVKGKIDKVERMGMRKFAYEIKKFNEGD 77
Query: 60 YVFMNIASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSPTLTIQRHDRDDRNDR 115
Y + + E++ R+ ++R T E+ + + +
Sbjct: 78 YTVIYFRCDGQNLQELENFYRVTPEIIRWQTFRRFDLEKKERKAQREKAAAEATES 133
>2j5a_A 30S ribosomal protein S6; ribonucleoprotein, RNA-binding,
rRNA-binding, protein folding; 2.3A {Aquifex aeolicus}
SCOP: d.58.14.1
Length = 110
Score = 91.5 bits (227), Expect = 6e-20
Identities = 29/101 (28%), Positives = 54/101 (53%), Gaps = 1/101 (0%)
Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYY 60
++ YE VF ++ +S +++K Q + I++ GGE+ + GMR +AY I+K A Y
Sbjct: 7 LRYYETVFAVKPTLSEEEMKKKFEQVKEFIKQKGGEILYEEDWGMRQLAYPIQKFNNARY 66
Query: 61 VFMNI-ASPPAAIHEMKRKMRIDENVLRSLTLLVDSHEQSP 100
+ P +E+ +++IDE+V+R L + + E
Sbjct: 67 FLVQFKTENPQLPNELDFQLKIDEDVIRWLNIQIKESEVKK 107
>2kjw_A TS9, 30S ribosomal protein S6; S6 permutant, solution structure,
backbone dynamics, folding, ribonucleoprotein,
RNA-binding, rRNA-binding; NMR {Thermus thermophilus}
Length = 96
Score = 57.5 bits (139), Expect = 9e-10
Identities = 16/54 (29%), Positives = 24/54 (44%)
Query: 1 MKLYEHVFLLRQDISSQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRK 54
YE +L ++ Q+ Q ++ G V V ELG+R +AY I K
Sbjct: 43 PGRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAK 96
>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 = 35.7 bits (82), Expect = 0.003
Identities = 13/75 (17%), Positives = 28/75 (37%), Gaps = 21/75 (28%)
Query: 82 DENVLRSLTLL----VDSHEQSPTLTIQ---RHDRDDRNDRFP----RDRNVDRKQ---- 126
+V +++T+L V +E P ++ D + N+ P N+ ++Q
Sbjct: 293 FVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDY 352
Query: 127 ------HVSEEKPLS 135
H+ K +
Sbjct: 353 VNKTNSHLPAGKQVE 367
Score = 30.7 bits (69), Expect = 0.13
Identities = 14/69 (20%), Positives = 30/69 (43%), Gaps = 18/69 (26%)
Query: 13 DISSQQIKDTIGQY-QSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAA 71
+++ +Q++D + + L E+ LVN G KN V ++ PP +
Sbjct: 343 NLTQEQVQDYVNKTNSHLPAGKQVEISLVN--G--------AKN----LV---VSGPPQS 385
Query: 72 IHEMKRKMR 80
++ + +R
Sbjct: 386 LYGLNLTLR 394
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 31.9 bits (71), Expect = 0.049
Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 82 DENVLR----SLTLLVDSHEQSPTLTIQ 105
++ L+ SL L D + +P L I+
Sbjct: 18 EKQALKKLQASLKLYAD--DSAPALAIK 43
>2bkk_A Aminoglycoside 3'-phosphotransferase; transferase/peptide,
transferase/designed protein complex,
CO-crystallization, inhibitor design; HET: ADP; 2.15A
{Enterococcus faecalis} PDB: 1j7l_A* 1j7i_A* 1j7u_A*
3h8p_A* 1l8t_A* 2b0q_A*
Length = 264
Score = 25.4 bits (54), Expect = 4.1
Identities = 11/66 (16%), Positives = 27/66 (40%), Gaps = 9/66 (13%)
Query: 16 SQQIKDTIGQYQSLIQENGGEVRLVNELGMRTIAYRIRKNRKAYYVFMNIASPPAAIHEM 75
S ++K I +Y+S+ G V Y++ + Y+ M + +++
Sbjct: 7 SPELKKLIEKYRSVKDTEGMSPAKV---------YKLVGENENLYLKMTDSRYKGTTYDV 57
Query: 76 KRKMRI 81
+R+ +
Sbjct: 58 EREKDM 63
>2h84_A Steely1; thiolase-fold, type III polyketide synthase, PKS,
chalcone- stilbene synthase superfamily, type I PKS;
HET: P6G; 2.90A {Dictyostelium discoideum AX4}
Length = 374
Score = 24.5 bits (52), Expect = 8.6
Identities = 2/21 (9%), Positives = 7/21 (33%)
Query: 66 ASPPAAIHEMKRKMRIDENVL 86
AS + ++ + +
Sbjct: 335 ASVIFVMDHARKSKSLPTYSI 355
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
0.320 0.135 0.375
Gapped
Lambda K H
0.267 0.0690 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,080,340
Number of extensions: 45278
Number of successful extensions: 121
Number of sequences better than 10.0: 1
Number of HSP's gapped: 116
Number of HSP's successfully gapped: 14
Length of query: 135
Length of database: 5,693,230
Length adjustment: 82
Effective length of query: 53
Effective length of database: 3,705,222
Effective search space: 196376766
Effective search space used: 196376766
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: 51 (23.5 bits)