RPS-BLAST 2.2.22 [Sep-27-2009]
Database: mmdb70
33,805 sequences; 4,956,049 total letters
Searching..................................................done
Query= gi|254780293|ref|YP_003064706.1| 30S ribosomal protein S9
[Candidatus Liberibacter asiaticus str. psy62]
(170 letters)
>3i1m_I 30S ribosomal protein S9; ribosome structure, protein-RNA
complex, ribonucleoprotein, ribosomal protein,
RNA-binding, rRNA-binding, antibiotic resistance; 3.19A
{Escherichia coli k-12} PDB: 1vs7_I* 3e1a_W 3e1c_W
1vs5_I 3i1o_I 3i1q_I 3i1s_I 3i1z_I 3i21_I 2qal_I* 1p6g_I
1p87_I 2aw7_I 2avy_I 2i2u_I 2i2p_I* 2qan_I* 2qb9_I*
2qbb_I* 2qbd_I ... (I:)
Length = 130
Score = 162 bits (411), Expect = 3e-41
Identities = 60/127 (47%), Positives = 84/127 (66%)
Query: 44 QRSYATGKRKTSIARVWIKSGSGKFTINYVDISKYFTQDLLVLNIKRPFNTVSQDNMYDV 103
+ Y TG+RK+S ARV+IK G+GK IN + +YF ++ + +++P V D+
Sbjct: 4 NQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDL 63
Query: 104 FATVSGGGLSGQASAICHGVAKALTYFQPDLRPQIKKGGFLTRDSRIVERKKYGKAKARR 163
+ TV GGG+SGQA AI HG+ +AL + LR +++K GF+TRD+R VERKK G KARR
Sbjct: 64 YITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARR 123
Query: 164 SFQFSKR 170
QFSKR
Sbjct: 124 RPQFSKR 130
>2vqe_I 30S ribosomal protein S9, 30S ribosomal protein S6;
tRNA-binding, rRNA-binding, metal-binding, zinc-finger,
translation; HET: TM2 PAR; 2.5A {Thermus thermophilus}
(I:)
Length = 128
Score = 159 bits (405), Expect = 1e-40
Identities = 60/127 (47%), Positives = 85/127 (66%)
Query: 44 QRSYATGKRKTSIARVWIKSGSGKFTINYVDISKYFTQDLLVLNIKRPFNTVSQDNMYDV 103
++ Y TG+RK ++ARV+++ G+GK T+N D ++YF + + P V +D
Sbjct: 2 EQYYGTGRRKEAVARVFLRPGNGKVTVNGQDFNEYFQGLVRAVAALEPLRAVDALGRFDA 61
Query: 104 FATVSGGGLSGQASAICHGVAKALTYFQPDLRPQIKKGGFLTRDSRIVERKKYGKAKARR 163
+ TV GGG SGQ AI G+A+AL + PD R ++K GFLTRD+R+VERKKYGK KARR
Sbjct: 62 YITVRGGGKSGQIDAIKLGIARALVQYNPDYRAKLKPLGFLTRDARVVERKKYGKHKARR 121
Query: 164 SFQFSKR 170
+ Q+SKR
Sbjct: 122 APQYSKR 128
>3bbn_I Ribosomal protein S9; small ribosomal subunit, spinach
chloroplast ribosome, ribonucleoprotein particle,
macromolecular complex; 9.40A {Spinacea oleracea} (I:)
Length = 197
Score = 154 bits (391), Expect = 5e-39
Identities = 64/171 (37%), Positives = 89/171 (52%), Gaps = 1/171 (0%)
Query: 1 MEDIENIRDIIEQQGGTLTEENTSQPEETSSSPAIHSRKVDQWQRSYATGKRKTSIARVW 60
+ + ++ ++ ++ + Q TG+RK +IARV
Sbjct: 27 LSNPAVVKPLVITATSATAPVEVAETADLEKFVKSRLPGGFAAQTVIGTGRRKCAIARVV 86
Query: 61 IKSGSGKFTINYVDISKYFTQDL-LVLNIKRPFNTVSQDNMYDVFATVSGGGLSGQASAI 119
++ G+GKF INY D +Y + + +K P T+ + YDVF GGGLSGQA AI
Sbjct: 87 LQEGTGKFIINYRDAKEYLQGNPLWLQYVKTPLATLGYETNYDVFVKAHGGGLSGQAQAI 146
Query: 120 CHGVAKALTYFQPDLRPQIKKGGFLTRDSRIVERKKYGKAKARRSFQFSKR 170
GVA+AL R +K+ G LTRDSRIVERKK G KAR++ QFSKR
Sbjct: 147 SLGVARALLKVSASHRAPLKQEGLLTRDSRIVERKKPGLKKARKAPQFSKR 197
>2zkq_i 40S ribosomal protein S16E; protein-RNA complex, 40S
ribosomal subunit, ribosomal protein/RNA complex; 8.70A
{Canis familiaris} (i:)
Length = 146
Score = 149 bits (378), Expect = 2e-37
Identities = 35/144 (24%), Positives = 51/144 (35%), Gaps = 12/144 (8%)
Query: 39 KVDQWQRSYATGKRKTSIARVWIKSGSGKFTINYVDISKYFTQDLLVLN-IKRPFNTVSQ 97
Q G++KT+ A K G+G +N + + L +
Sbjct: 3 SKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKER 62
Query: 98 DNMYDVFATVSGGGLSGQASAICHGVAKALTYFQPD-----LRPQIKKG------GFLTR 146
D+ V GGG Q AI ++KAL + + +IK L
Sbjct: 63 FAGVDIRVRVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVA 122
Query: 147 DSRIVERKKYGKAKARRSFQFSKR 170
D R E KK+G AR +Q S R
Sbjct: 123 DPRRCESKKFGGPGARARYQKSYR 146
>3jyv_I 40S ribosomal protein S16(A); eukaryotic ribosome, RACK1
protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG
PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus}
PDB: 1s1h_I (I:)
Length = 138
Score = 140 bits (355), Expect = 8e-35
Identities = 38/136 (27%), Positives = 57/136 (41%), Gaps = 12/136 (8%)
Query: 47 YATGKRKTSIARVWIKSGSGKFTINYVDISKYFTQDL-LVLNIKRPFNTVSQDNMYDVFA 105
GK+K++ A +K+G G +N I+ + L + + + + D+
Sbjct: 3 QTFGKKKSATAVAHVKAGKGLIKVNGSPITLVEPEILRFKVYEPLLLVGLDKFSNIDIRV 62
Query: 106 TVSGGGLSGQASAICHGVAKAL-----TYFQPDLRPQIKKG------GFLTRDSRIVERK 154
V+GGG Q AI +AK L Y + ++KK L DSR E K
Sbjct: 63 RVTGGGHVSQVYAIRQAIAKGLVAYHQKYVDEQSKNELKKAFTSYDRTLLIADSRRPEPK 122
Query: 155 KYGKAKARRSFQFSKR 170
K+G AR FQ S R
Sbjct: 123 KFGGKGARSRFQKSYR 138
>3ebk_A Allergen BLA G 4; beta barrel, cockroach, glycoprotein,
secreted; 1.90A {Blattella germanica} (A:)
Length = 176
Score = 28.9 bits (64), Expect = 0.39
Identities = 25/87 (28%), Positives = 38/87 (43%), Gaps = 12/87 (13%)
Query: 48 ATGKRKTSIARVWIKSGSGKFTINYVDISKYFTQDLLVLNIKRPFNTVSQDNMYDVFATV 107
+ GK +T+I R K KFTI+Y D K F+ P++ ++ D Y+ +A V
Sbjct: 62 SQGKNRTTI-RGRTKFEGNKFTIDYNDKGKAFSA---------PYSVLATD--YENYAIV 109
Query: 108 SGGGLSGQASAICHGVAKALTYFQPDL 134
G + I + L F P L
Sbjct: 110 EGCPAAANGHVIYVQLRMTLRRFHPKL 136
>3dzc_A UDP-N-acetylglucosamine 2-epimerase; structural genomics,
infectious diseases, isomerase; 2.35A {Vibrio cholerae}
(A:1-196,A:382-396)
Length = 211
Score = 27.2 bits (60), Expect = 1.4
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 101 YDVFATVSGGGLSGQASAICHGVAKALTYFQPDL 134
+D+ G L+G S I G+ + L+ QPD+
Sbjct: 81 FDLNIMEPGQTLNGVTSKILLGMQQVLSSEQPDV 114
>2iw3_A Elongation factor 3A; acetylation, ATP-binding, protein
biosynthesis, nucleotide-binding, phosphorylation, RNA-
binding, rRNA-binding; HET: ADP; 2.4A {Saccharomyces
cerevisiae} PDB: 2iwh_A* 2ix3_A 2ix8_A
(A:655-778,A:874-986)
Length = 237
Score = 26.1 bits (58), Expect = 2.3
Identities = 8/56 (14%), Positives = 19/56 (33%), Gaps = 4/56 (7%)
Query: 48 ATGKRKTSIARV---WIKSGSGKFTINYVDISKYFTQDLLVLNIKRPFNTVSQDNM 100
G K+++ V + SG+ + Y Q +I+ + + +
Sbjct: 53 PNGAGKSTLINVLTGELLPTSGEVYTHENCRIAYIKQHAF-AHIESHLDKTPSEYI 107
>1b6c_B TGF-B superfamily receptor type I; complex
(isomerase/protein kinase), receptor serine/threonine
kinase; 2.60A {Homo sapiens} (B:124-342)
Length = 219
Score = 25.7 bits (55), Expect = 3.1
Identities = 6/47 (12%), Positives = 15/47 (31%), Gaps = 1/47 (2%)
Query: 102 DVFATVSGGGLS-GQASAICHGVAKALTYFQPDLRPQIKKGGFLTRD 147
+F ++ ++ + A L + ++ K RD
Sbjct: 3 SLFDYLNRYTVTVEGMIKLALSTASGLAHLHMEIVGTQGKPAIAHRD 49
>1nir_A Nitrite reductase; hemoprotein, denitrification, domain
swapping; HET: HEC DHE; 2.15A {Pseudomonas aeruginosa}
(A:1-115)
Length = 115
Score = 25.4 bits (55), Expect = 4.6
Identities = 11/62 (17%), Positives = 19/62 (30%), Gaps = 4/62 (6%)
Query: 109 GGGLSGQASAICHGVAKALTYFQPDLRPQIKKGGFLTRDSRIVERKKYGKAKARRSFQFS 168
+ Q A CHGV + +P ++ G + YG ++ S
Sbjct: 39 AKQIYFQRCAGCHGVLRKGATGKPLTPDITQQRG----QQYLEALITYGTPLGMPNWGSS 94
Query: 169 KR 170
Sbjct: 95 GE 96
>1wtj_A Ureidoglycolate dehydrogenase; NADPH dependent enzyme,
oxidoreductase; 1.55A {Pseudomonas syringae PV} PDB:
2cwf_A* 2cwh_A* (A:1-71,A:310-343)
Length = 105
Score = 24.8 bits (54), Expect = 5.8
Identities = 11/44 (25%), Positives = 16/44 (36%), Gaps = 8/44 (18%)
Query: 112 LSGQASAICHGVAKALTYFQPDLRPQIKKGGFLTRDSRIVERKK 155
G S HG+ + Y + G L D R +ER +
Sbjct: 48 RDGSHS---HGIFRIPGYLS-----SLASGWVLPGDRRYLERAR 83
>1vpk_A DNA polymerase III, beta subunit; TM0262, structural
genomics, joint center for structural genomics, JCSG,
protein structure initiative; HET: DNA; 2.00A
{Thermotoga maritima MSB8} (A:1-143,A:208-255)
Length = 191
Score = 24.8 bits (54), Expect = 6.8
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 58 RVWIKSGSGKFTINYVDISKY 78
+ I SGS F I + ++
Sbjct: 107 ALVISSGSTVFRITTMPADEF 127
>3btp_A Single-strand DNA-binding protein; TIM barrel, unique
topology, novel fold, structural genomics, israel
structural proteomics center, ISPC; 2.30A {Agrobacterium
tumefaciens str} (A:1-341)
Length = 341
Score = 24.6 bits (53), Expect = 7.7
Identities = 8/47 (17%), Positives = 24/47 (51%)
Query: 122 GVAKALTYFQPDLRPQIKKGGFLTRDSRIVERKKYGKAKARRSFQFS 168
G+ ++Q D ++ + L + R ++ +KYG+ + ++ ++
Sbjct: 207 GITGTDIFYQTDKNIKLDRNYKLRPEDRYIQTEKYGRREIQKRYEHQ 253
>2nra_C PI protein; protein-DNA complex, DNA replication,
replication/DNA complex; 3.10A {Escherichia coli}
(C:1-167)
Length = 167
Score = 24.5 bits (53), Expect = 7.8
Identities = 7/45 (15%), Positives = 14/45 (31%)
Query: 125 KALTYFQPDLRPQIKKGGFLTRDSRIVERKKYGKAKARRSFQFSK 169
+ + K D I+E Y + S +F++
Sbjct: 95 DIIALAKELNLLSTAKNSSEELDLNIIEWIAYSPDEGYLSLKFTR 139
>1fn9_A Outer-capsid protein sigma 3; zinc binding motif, viral
protein; 1.80A {Reovirus SP} (A:1-22,A:73-365)
Length = 315
Score = 24.6 bits (53), Expect = 8.0
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 2 EDIENIRDIIEQQGGTLTEENTSQPEETSSSPAIHSRKVDQWQ 44
+D++ +R +GG+L E N Q + S +IHS D Q
Sbjct: 66 DDLDRVR----TEGGSLVELNWLQVDPNSMFRSIHSSWTDPLQ 104
>1v4v_A UDP-N-acetylglucosamine 2-epimerase; UDP-GLCNAC, two
domains, homodimer, riken structural genomics/proteomics
initiative, RSGI; HET: MSE; 1.80A {Thermus thermophilus}
(A:1-176,A:349-376)
Length = 204
Score = 24.1 bits (52), Expect = 9.9
Identities = 7/34 (20%), Positives = 11/34 (32%)
Query: 101 YDVFATVSGGGLSGQASAICHGVAKALTYFQPDL 134
++ L A+ I A+AL D
Sbjct: 61 RNLDVXQERQALPDLAARILPQAARALKEXGADY 94
Database: mmdb70
Posted date: Jun 20, 2010 3:12 AM
Number of letters in database: 4,956,049
Number of sequences in database: 33,805
Lambda K H
0.316 0.131 0.374
Gapped
Lambda K H
0.267 0.0604 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,237,593
Number of extensions: 50850
Number of successful extensions: 149
Number of sequences better than 10.0: 1
Number of HSP's gapped: 144
Number of HSP's successfully gapped: 20
Length of query: 170
Length of database: 4,956,049
Length adjustment: 82
Effective length of query: 88
Effective length of database: 2,184,039
Effective search space: 192195432
Effective search space used: 192195432
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: 51 (23.7 bits)