RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

Searching..................................................done

Query= gi|254780437|ref|YP_003064850.1| 30S ribosomal protein S21
[Candidatus Liberibacter asiaticus str. psy62]
         (95 letters)



>3bbn_U Ribosomal protein S21; small ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Cucumis sativus}
          Length = 190

 Score = 66.9 bits (163), Expect = 1e-12
 Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 20  VYVLVRDN-NVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMR 78
           V V+V DN   E+ L   ++++   GV++E K R  +E     R R   EA +R+R+   
Sbjct: 97  VQVVVDDNEPEERLLNRFRREVMRAGVIQECKRRRFFENTQDVRKRKTREAAKRNRRRRP 156

Query: 79  K 79
           +
Sbjct: 157 Q 157


>3i1m_U 30S ribosomal protein S21; ribosome structure, protein-RNA
          complex, ribonucleoprotein, ribosomal protein,
          RNA-binding, rRNA-binding, antibiotic resistance; 3.19A
          {Escherichia coli k-12} PDB: 1vs7_U* 2avy_U 2aw7_U
          2vho_U 2vhp_U 3df1_U* 3df3_U* 3e1a_Q 3e1c_Q 1vs5_U
          3i1o_U 3i1q_U 3i1s_U 3i1z_U 3i21_U 2qal_U* 2i2u_U
          2i2p_U* 2qan_U* 2qb9_U* ...
          Length = 71

 Score = 49.7 bits (119), Expect = 1e-07
 Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 1/64 (1%)

Query: 22 VLVRDN-NVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKI 80
          + VR+N   + ALR  K+  +  GVL E++ R  YEKP+ +R R K+ A++R  K + + 
Sbjct: 4  IKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARE 63

Query: 81 AQRE 84
            R 
Sbjct: 64 NARR 67


>3ofo_U 30S ribosomal protein S21; protein biosynthesis, ribosomes, RNA,
          tRNA, transfer, eryThr ketolide, macrolide, antibiotic,
          EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_U*
          2wwl_U 3ofp_U
          Length = 51

 Score = 44.7 bits (106), Expect = 5e-06
 Identities = 20/51 (39%), Positives = 32/51 (62%), Gaps = 1/51 (1%)

Query: 22 VLVRDN-NVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIR 71
          + VR+N   + ALR  K+  +  GVL E++ R  YEKP+ +R R K+ A++
Sbjct: 1  IKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVK 51


>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 = 30.7 bits (69), Expect = 0.085
 Identities = 21/106 (19%), Positives = 34/106 (32%), Gaps = 42/106 (39%)

Query: 1   MLVFNAFRGI----FSEGREISAVY-VLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHY 55
           + +F   +G     F E R++   Y VLV D         L K    E  L EL      
Sbjct: 157 VAIFGG-QGNTDDYFEELRDLYQTYHVLVGD---------LIKFS-AE-TLSEL------ 198

Query: 56  EKPSQKRVRLKSEAIR-RSRKL--MRKIAQRE---------GAPVS 89
                  +R   +A +  ++ L  +  +               P+S
Sbjct: 199 -------IRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPIS 237



 Score = 27.6 bits (61), Expect = 0.69
 Identities = 14/84 (16%), Positives = 27/84 (32%), Gaps = 20/84 (23%)

Query: 2   LVFNAFRGIFSEGREISAVYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYE----- 56
           L    F   + EG +I A   L      E    ++K K     +++      +       
Sbjct: 86  LCLTEFENCYLEGNDIHA---LAAKLLQENDTTLVKTK----ELIKN-----YITARIMA 133

Query: 57  -KPSQKRVR--LKSEAIRRSRKLM 77
            +P  K+    L       + +L+
Sbjct: 134 KRPFDKKSNSALFRAVGEGNAQLV 157



 Score = 25.7 bits (56), Expect = 2.8
 Identities = 27/156 (17%), Positives = 44/156 (28%), Gaps = 79/156 (50%)

Query: 7   FRGIF------SEGREISAVYVLVRD------NNVEQALRVL----------------KK 38
            R         S+G  ++AV +   D       +V +A+ VL                  
Sbjct: 263 LRSYLKGATGHSQGL-VTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPP 321

Query: 39  KM------QGEGV------LRELKMRGHYEK---------PSQKRVRLKSEAI-----RR 72
            +        EGV      +  L  +   +          P+ K+V      I      +
Sbjct: 322 SILEDSLENNEGVPSPMLSISNLT-QEQVQDYVNKTNSHLPAGKQV-----EISLVNGAK 375

Query: 73  S-------RKL------MRKIAQREGAPVSRLRQHR 95
           +       + L      +RK      AP S L Q R
Sbjct: 376 NLVVSGPPQSLYGLNLTLRKA----KAP-SGLDQSR 406


>1zhv_A Hypothetical protein ATU0741; NESG, ATR8, structural genomics, PSI,
           protein structure initiative; 1.50A {Agrobacterium
           tumefaciens str} SCOP: d.58.18.8 d.58.18.8
          Length = 134

 Score = 26.0 bits (57), Expect = 2.4
 Identities = 6/19 (31%), Positives = 12/19 (63%)

Query: 21  YVLVRDNNVEQALRVLKKK 39
           ++LVR N++E+   +L   
Sbjct: 103 HLLVRSNDLEKTADLLANA 121


>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule,
          structural genomics, sentrin2, NPPFSA; NMR {Homo
          sapiens} SCOP: d.15.1.1
          Length = 104

 Score = 25.6 bits (56), Expect = 2.8
 Identities = 10/44 (22%), Positives = 21/44 (47%), Gaps = 4/44 (9%)

Query: 49 LKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQREGAPVSRLR 92
          LK+ G      Q +++  +       KLM+   +R+G  + ++R
Sbjct: 27 LKVAGQDGSVVQFKIKRHTPL----SKLMKAYCERQGLSMRQIR 66


>3oet_A Erythronate-4-phosphate dehydrogenase; structural genomics, center
           for structural genomics of infec diseases, csgid; HET:
           NAD; 2.36A {Salmonella enterica subsp}
          Length = 381

 Score = 25.7 bits (56), Expect = 2.9
 Identities = 11/33 (33%), Positives = 16/33 (48%)

Query: 4   FNAFRGIFSEGREISAVYVLVRDNNVEQALRVL 36
           F+  R  + E RE S++YV+  D      L  L
Sbjct: 339 FDKLRKNYLERREWSSLYVMCDDETAAALLCKL 371


>3gke_A DDMC; rieske cluster, non-heme mononuclear iron, oxygenase,
           oxidoreductase; 1.75A {Stenotrophomonas maltophilia}
           PDB: 3gb4_A 3gl0_A* 3gl2_A* 3gob_A* 3gte_A 3gts_A*
          Length = 349

 Score = 24.3 bits (51), Expect = 6.7
 Identities = 8/38 (21%), Positives = 15/38 (39%), Gaps = 1/38 (2%)

Query: 50  KMRGHYEKPSQKRVRLKSEA-IRRSRKLMRKIAQREGA 86
           + R + E    +   L  +    R  + + K+ Q E A
Sbjct: 303 RRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAA 340


>1ujn_A Dehydroquinate synthase; riken structural genomics/proteomics
           initiative, RSGI, structural genomics, lyase; 1.80A
           {Thermus thermophilus HB8} SCOP: e.22.1.1
          Length = 348

 Score = 24.5 bits (52), Expect = 6.9
 Identities = 6/34 (17%), Positives = 17/34 (50%), Gaps = 1/34 (2%)

Query: 15  REISAVYVL-VRDNNVEQALRVLKKKMQGEGVLR 47
                + V  + +  + +A    +++++G G+LR
Sbjct: 315 LAPGRLVVRPLPEGLLREAFAAWREELKGLGLLR 348


>1zvp_A Hypothetical protein VC0802; structural genomics, PSI, protein
           structure initiative, midwest center for structural
           genomics, MCSG; 2.20A {Vibrio cholerae} SCOP: d.58.18.9
           d.58.18.9
          Length = 133

 Score = 24.0 bits (52), Expect = 8.0
 Identities = 5/18 (27%), Positives = 11/18 (61%)

Query: 21  YVLVRDNNVEQALRVLKK 38
           ++ V+    +QAL+ L +
Sbjct: 112 HIFVQKEKAQQALQALGE 129


>1l2n_A Ubiquitin-like protein SMT3; structure, protein binding; NMR
          {Saccharomyces cerevisiae} SCOP: d.15.1.1
          Length = 101

 Score = 24.0 bits (52), Expect = 8.6
 Identities = 10/39 (25%), Positives = 18/39 (46%), Gaps = 6/39 (15%)

Query: 57 KPSQKRVRLKSEAIRRS---RKLMRKIAQREGAPVSRLR 92
                +  K   I+++   R+LM   A+R+G  +  LR
Sbjct: 29 SDGSSEIFFK---IKKTTPLRRLMEAFAKRQGKEMDSLR 64


>2z6v_A Putative uncharacterized protein; sulfotransferase, unknown
           function; HET: PLM; 2.60A {Mycobacterium avium}
          Length = 414

 Score = 24.1 bits (51), Expect = 8.6
 Identities = 6/51 (11%), Positives = 14/51 (27%)

Query: 22  VLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRR 72
           ++V + N         ++   +     L  R       Q    +    + R
Sbjct: 57  LIVDEVNTSPVFTPFGRQRVLDDATNALGRRLQVHAYIQDHPEVLDAPVER 107


>2io1_B Small ubiquitin-related modifier 3 precursor; SUMO, SENP, ULP,
          complex, protein binding, hydrolase; 2.60A {Homo
          sapiens} SCOP: d.15.1.1
          Length = 94

 Score = 23.7 bits (51), Expect = 9.4
 Identities = 6/19 (31%), Positives = 12/19 (63%)

Query: 74 RKLMRKIAQREGAPVSRLR 92
           KLM+   +R+G  + ++R
Sbjct: 31 SKLMKAYCERQGLSMRQIR 49


>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle
          structural center for infectious disease, brucellosis,
          orchitis, epididymitis; 2.20A {Brucella melitensis}
          Length = 360

 Score = 23.7 bits (51), Expect = 9.9
 Identities = 9/26 (34%), Positives = 16/26 (61%), Gaps = 3/26 (11%)

Query: 70 IRRS---RKLMRKIAQREGAPVSRLR 92
          I+++   R+LM   A+R+G  +  LR
Sbjct: 37 IKKTTPLRRLMEAFAKRQGKEMDSLR 62


  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
   0.323    0.136    0.367 

Gapped
Lambda     K      H
   0.267   0.0706    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 780,553
Number of extensions: 33026
Number of successful extensions: 239
Number of sequences better than 10.0: 1
Number of HSP's gapped: 239
Number of HSP's successfully gapped: 45
Length of query: 95
Length of database: 5,693,230
Length adjustment: 61
Effective length of query: 34
Effective length of database: 4,214,346
Effective search space: 143287764
Effective search space used: 143287764
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 50 (23.1 bits)