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)