RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780239|ref|YP_003064652.1| 30S ribosomal protein S13
[Candidatus Liberibacter asiaticus str. psy62]
         (122 letters)



>3ofp_M 30S ribosomal protein S13; protein biosynthesis, ribosomes, RNA,
           tRNA, transfer, eryThr ketolide, macrolide, antibiotic,
           EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_M*
           2wwl_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M
           2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M 2qbf_M 2qbh_M*
           2qbj_M* 2qou_M* 2qow_M* 2qoy_M* 2qp0_M* ...
          Length = 113

 Score =  146 bits (370), Expect = 1e-36
 Identities = 62/111 (55%), Positives = 79/111 (71%), Gaps = 1/111 (0%)

Query: 2   ARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIE 61
           ARIAG+NIP  K  V AL  I+G+G   S+ I     I  + ++ +L E ++  +R  + 
Sbjct: 1   ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVA 60

Query: 62  QDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKK 112
           + + VEGDLRR ++M+IKRLMDLGCYRGLRHRRGLPVRGQRT TNARTRK 
Sbjct: 61  K-FVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKG 110


>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding,
           rRNA-binding, metal-binding, zinc-finger, translation;
           HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP:
           a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M* 1hr0_M
           1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P* 1jgq_P*
           1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M 1xmo_M*
           1xmq_M* ...
          Length = 126

 Score =  138 bits (350), Expect = 2e-34
 Identities = 72/122 (59%), Positives = 89/122 (72%)

Query: 1   MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
           MARIAGV IPR KRV  AL YI+GIG   +++   K  I P  RV  L E+EV+++R+ +
Sbjct: 1   MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV 60

Query: 61  EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKGGVAR 120
           E  +++EG+LR  VA NIKRLMD+GCYRGLRHRRGLPVRGQRT TNARTRK   K    +
Sbjct: 61  ENTWKLEGELRAEVAANIKRLMDIGCYRGLRHRRGLPVRGQRTRTNARTRKGPRKTVAGK 120

Query: 121 KR 122
           K+
Sbjct: 121 KK 122


>3i1m_M 30S ribosomal protein S13; ribosome structure, protein-RNA complex,
           ribonucleoprotein, ribosomal protein, RNA-binding,
           rRNA-binding, antibiotic resistance; 3.19A {Escherichia
           coli k-12} PDB: 1vs7_M* 3e1a_F 3e1c_F 1vs5_M 3i1o_M
           3i1q_M 3i1s_M 3i1z_M 3i21_M 2qal_M* 1p6g_M 1p87_M 2aw7_M
           2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M ...
          Length = 118

 Score =  133 bits (337), Expect = 8e-33
 Identities = 64/116 (55%), Positives = 80/116 (68%), Gaps = 1/116 (0%)

Query: 1   MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
           MARIAG+NIP  K  V AL  I+G+G   S+ I     I  + ++ +L E ++  +R  +
Sbjct: 1   MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEV 60

Query: 61  EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRKKFGKG 116
            +   VEGDLRR ++M+IKRLMDLGCYRGLRHRRGLPVRGQRT TNARTRK   K 
Sbjct: 61  AKFV-VEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKP 115


>2zkq_m 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal
           subunit, ribosomal protein/RNA complex; 8.70A {Canis
           familiaris} PDB: 1s1h_M
          Length = 152

 Score =  126 bits (317), Expect = 2e-30
 Identities = 35/144 (24%), Positives = 62/144 (43%), Gaps = 25/144 (17%)

Query: 1   MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
           + R+   NI   +++  A+  I G+G + +  +  K  I   +R  +L E EV ++   +
Sbjct: 12  ILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIM 71

Query: 61  EQDYQ----------------------VEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPV 98
           +   Q                      +   L   +  +++RL  +  +RGLRH  GL V
Sbjct: 72  QNPRQYKIPDWFLNRQKDVKDGKYSQVLANGLDNKLREDLERLKKIRAHRGLRHFWGLRV 131

Query: 99  RGQRTHTNARTRKKFGKGGVARKR 122
           RGQ T T  R  +     GV++K+
Sbjct: 132 RGQHTKTTGRRGRTV---GVSKKK 152


>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Oryza sativa}
          Length = 145

 Score =  117 bits (295), Expect = 6e-28
 Identities = 43/111 (38%), Positives = 57/111 (51%), Gaps = 12/111 (10%)

Query: 1   MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60
             RI GV IP  KRV  +L YIHGIG   S+ I   L    +              +   
Sbjct: 46  CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDNKV------------TKDLS 93

Query: 61  EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRK 111
           E++  +    +R   + I+RL ++ CYRG+RH+ GLPVRGQRT  N RT K
Sbjct: 94  EEEVIILRKEKRFNRVAIERLKEIRCYRGIRHKLGLPVRGQRTKNNCRTLK 144


>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 = 31.5 bits (71), Expect = 0.051
 Identities = 29/169 (17%), Positives = 50/169 (29%), Gaps = 79/169 (46%)

Query: 4   IAGVNIPRAKRVV----RALC----YIHGIGFKSSQDICNKLAIP-PERRVHQLVESEVI 54
           I+ VN  +   VV    ++L      +      S  D  ++  IP  ER++         
Sbjct: 368 ISLVNGAKN-LVVSGPPQSLYGLNLTLRKAKAPSGLDQ-SR--IPFSERKL-------KF 416

Query: 55  QIR-----------------QAIEQDYQVEG------DLR------------RTVAMNI- 78
             R                   I +D           D++            R ++ +I 
Sbjct: 417 SNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSIS 476

Query: 79  KRLMDLGCYRGLRHRRGLPVRGQR------TH--TNARTRKKFGKGGVA 119
           +R++D            LPV+ +       TH          FG GG +
Sbjct: 477 ERIVDCIIR--------LPVKWETTTQFKATHILD-------FGPGGAS 510



 Score = 31.1 bits (70), Expect = 0.074
 Identities = 19/113 (16%), Positives = 33/113 (29%), Gaps = 42/113 (37%)

Query: 1   MARIAGVNIPRAKRVVRAL-CYIHGIGFKSSQDICNKLAIPPERRVH-QLVESEVIQIRQ 58
           M  I+   + +       +  Y+         +  N   +P  ++V   LV       + 
Sbjct: 338 MLSISN--LTQE-----QVQDYV---------NKTNS-HLPAGKQVEISLVNGA----KN 376

Query: 59  AIEQDYQVEGDLRRTVAMNIKRLMDLGCYRGL---------R----HRRGLPV 98
            +     V G  +    +N+  L       GL         R      R LPV
Sbjct: 377 LV-----VSGPPQSLYGLNL-TLRKAKAPSGLDQSRIPFSERKLKFSNRFLPV 423



 Score = 25.3 bits (55), Expect = 4.1
 Identities = 9/31 (29%), Positives = 19/31 (61%), Gaps = 1/31 (3%)

Query: 76   MNIKRLMDLGCYRGLRHRRGLPVRGQRTHTN 106
            M+I+ L+++  YRG+  +  +P R +   +N
Sbjct: 1777 MSIESLVEVVFYRGMTMQVAVP-RDELGRSN 1806


>3nt1_A Prostaglandin-endoperoxide synthase 2; prostaglandin H2 synthase,
           cyclooxygenase-2, naproxen, oxido; HET: NAG BOG NPS HEM;
           1.73A {Mus musculus} PDB: 3ntb_A* 1pxx_A* 3pgh_A*
           1cx2_A* 4cox_A* 5cox_A* 6cox_A* 3hs5_A* 3hs6_A* 3hs7_A*
           3krk_A* 1ddx_A* 1cvu_A*
          Length = 587

 Score = 28.4 bits (63), Expect = 0.39
 Identities = 15/62 (24%), Positives = 21/62 (33%), Gaps = 2/62 (3%)

Query: 38  AIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIK--RLMDLGCYRGLRHRRG 95
           +I  E  + Q VES   QI   +     V   ++     +I   R M        R R  
Sbjct: 381 SILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFS 440

Query: 96  LP 97
           L 
Sbjct: 441 LK 442


>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 = 28.4 bits (62), Expect = 0.42
 Identities = 7/32 (21%), Positives = 16/32 (50%), Gaps = 8/32 (25%)

Query: 57 RQAIEQDYQVEGDLR-----RTVAMNIKRLMD 83
          +QA+++   ++  L+        A+ IK  M+
Sbjct: 19 KQALKK---LQASLKLYADDSAPALAIKATME 47


>1q4g_A Prostaglandin G/H synthase 1; cyclooxygenase, non-steroidal
           anti-inflammatory drug, peroxidase, prostaglandin
           synthase, EGF-like domain; HET: BOG NAG NDG BMA MAN BFL
           HEM; 2.00A {Ovis aries} SCOP: a.93.1.2 g.3.11.1 PDB:
           1diy_A* 2ayl_A* 3kk6_A* 2oyu_P* 2oye_P* 1eqg_A* 1cqe_A*
           1eqh_A* 1igz_A* 1igx_A* 1fe2_A* 1pge_A* 1pgf_A* 1pgg_A*
           1pth_A* 1u67_A* 1ht8_A* 1ebv_A* 1ht5_A* 1prh_A*
          Length = 553

 Score = 28.3 bits (63), Expect = 0.52
 Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 2/71 (2%)

Query: 29  SSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIK--RLMDLGC 86
           S +      ++  +  V  LV++   Q    I     ++  +       IK  R++ L  
Sbjct: 372 SYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDVIKESRVLRLQP 431

Query: 87  YRGLRHRRGLP 97
           +   R R G+ 
Sbjct: 432 FNEYRKRFGMK 442


>3gzu_A Inner capsid protein VP2; 7RP, DLP, metal- binding, virion, zinc,
           core protein, RNA-binding, icosaderal virus; 3.80A
           {Rotavirus A}
          Length = 800

 Score = 27.7 bits (61), Expect = 0.68
 Identities = 14/36 (38%), Positives = 20/36 (55%)

Query: 40  PPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVA 75
              R   ++V+SE   I  AI QD + EG +RR +A
Sbjct: 111 KNSRDAGKVVDSETASICDAIFQDEETEGAVRRFIA 146


>1xd7_A YWNA; structural genomics, protein structure initiative, winged
          helix DNA binding, hypothetical protein, PSI; 2.30A
          {Bacillus subtilis subsp} SCOP: a.4.5.55
          Length = 145

 Score = 26.9 bits (59), Expect = 1.2
 Identities = 10/58 (17%), Positives = 21/58 (36%), Gaps = 3/58 (5%)

Query: 11 RAKRVVRALCYIHGIGFKSSQDICNKLAIPP---ERRVHQLVESEVIQIRQAIEQDYQ 65
          R    +  L  I      SS+ I + +   P    R +  L +++++  R  +     
Sbjct: 7  RLAVAIHILSLISMDEKTSSEIIADSVNTNPVVVRRMISLLKKADILTSRAGVPGASL 64


>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
           acid synthase, acyl-carrier-protein, beta-ketoacyl
           reductase, beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 1688

 Score = 26.7 bits (58), Expect = 1.3
 Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 2/28 (7%)

Query: 72  RTVAMNIKRLMDLGCYRGLRHRRGLPVR 99
           R +  NI R+M  GC +  +  RG+  R
Sbjct: 594 RIMLTNILRMM--GCVKKQKSARGIETR 619


>1cvu_A Prostaglandin H2 synthase-2; COX-2, cyclooxygenase, prostaglandin,
           arachidonate, endoperoxide, oxidoreductase; HET: NAG MAN
           BOG ACD; 2.40A {Mus musculus} SCOP: a.93.1.2 g.3.11.1
           PDB: 3pgh_A* 1cx2_A* 4cox_A* 5cox_A* 6cox_A* 1pxx_A*
           1ddx_A*
          Length = 552

 Score = 26.7 bits (59), Expect = 1.3
 Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 2/61 (3%)

Query: 39  IPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKR--LMDLGCYRGLRHRRGL 96
           I  E  + Q VES   QI   +     V   ++     +I +   M        R R  L
Sbjct: 382 ILLEHGLTQFVESFTRQIAGRVAGGRNVPIAVQAVAKASIDQSREMKYQSLNEYRKRFSL 441

Query: 97  P 97
            
Sbjct: 442 K 442


>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein,
          ATP-binding, nucleotide-binding, hydrolase; 2.20A
          {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*
          Length = 574

 Score = 26.4 bits (57), Expect = 1.8
 Identities = 7/29 (24%), Positives = 12/29 (41%), Gaps = 2/29 (6%)

Query: 19 LCYIHGIGFKSSQDICNKLAIPP--ERRV 45
          L  + GIGF ++  +           RR+
Sbjct: 46 LTEVEGIGFLTADKLWQARGGALDDPRRL 74


>2p6r_A Afuhel308 helicase; protein-DNA complex, SF2 helicase, archaeal
           helicase, DNA repair,, DNA binding protein/DNA complex;
           3.00A {Archaeoglobus fulgidus} SCOP: a.4.5.43 a.289.1.2
           c.37.1.19 c.37.1.19 PDB: 2p6u_A
          Length = 702

 Score = 26.0 bits (56), Expect = 2.1
 Identities = 10/54 (18%), Positives = 23/54 (42%), Gaps = 11/54 (20%)

Query: 1   MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNK----LAIPPERRVHQLVE 50
           + RI  +   RA+++  A       G ++++DI        ++       ++VE
Sbjct: 634 LVRIRHIGRVRARKLYNA-------GIRNAEDIVRHREKVASLIGRGIAERVVE 680


>2cfm_A Thermostable DNA ligase; protein-nucleotide complex, cell cycle,
           cell division, DNA damage, DNA recombination, DNA
           repair, DNA replication; HET: AMP; 1.8A {Pyrococcus
           furiosus}
          Length = 561

 Score = 26.0 bits (56), Expect = 2.3
 Identities = 11/56 (19%), Positives = 25/56 (44%), Gaps = 8/56 (14%)

Query: 33  ICNKLAIPPERRVHQLVESEVIQI--------RQAIEQDYQVEGDLRRTVAMNIKR 80
           I  ++    + R   + E  +I+          + IE+  +  GDL  ++A+ +K+
Sbjct: 45  ILGEVFPEWDERELGVGEKLLIKAVAMATGIDAKEIEESVKDTGDLGESIALAVKK 100


>1m3q_A 8-oxoguanine DNA glycosylase; DNA repair, END product, HOGG,
           8-aminoguanine, RE-ligation, hydrolase/DNA complex; HET:
           DRZ ANG; 1.90A {Homo sapiens} SCOP: a.96.1.3 d.129.1.2
           PDB: 1m3h_A* 1n39_A* 1lwy_A* 1hu0_A* 1lwv_A* 1lww_A*
           1fn7_A* 1n3a_A* 1n3c_A* 1ebm_A* 1ko9_A 2noe_A* 2noh_A*
           2nol_A* 1yqk_A 2noz_A* 2nof_A* 1yqr_A* 1yql_A* 1yqm_A*
           ...
          Length = 317

 Score = 25.5 bits (55), Expect = 3.7
 Identities = 20/118 (16%), Positives = 32/118 (27%), Gaps = 26/118 (22%)

Query: 7   VNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESE------------VI 54
            NI R   +V  LC   G       D+        +      VE+             V 
Sbjct: 142 NNIARITGMVERLCQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVS 201

Query: 55  QIRQAIEQDYQVEGDLRRTVAMN----IKRLMDLGCY----------RGLRHRRGLPV 98
              +AI ++      L++    +     K L  L               L   + +PV
Sbjct: 202 ASARAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKPQAVPV 259


>1k3x_A Endonuclease VIII; hydrolase/DNA; HET: BRU PED; 1.25A {Escherichia
           coli} SCOP: a.156.1.2 b.113.1.1 g.39.1.8 PDB: 1k3w_A*
           1q39_A 2ea0_A* 2oq4_A* 1q3c_A 2opf_A* 1q3b_A*
          Length = 262

 Score = 24.4 bits (52), Expect = 6.0
 Identities = 7/62 (11%), Positives = 24/62 (38%)

Query: 13  KRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQDYQVEGDLRR 72
             ++    ++ G+G     +I  ++ +    +   L  +++  +  A+ +  +     R 
Sbjct: 154 AGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRG 213

Query: 73  TV 74
            V
Sbjct: 214 QV 215


>2qsb_A UPF0147 protein TA0600; structural genomics, four-helix bundle,
          PSI-2, protein structure initiative; HET: MSE; 1.30A
          {Thermoplasma acidophilum dsm 1728} SCOP: a.29.14.1
          Length = 89

 Score = 24.0 bits (52), Expect = 9.3
 Identities = 10/42 (23%), Positives = 20/42 (47%)

Query: 42 ERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMD 83
            RV Q + +EV+ +   + QD  V  ++R+    +  +L  
Sbjct: 4  MVRVDQNLFNEVMYLLDELSQDITVPKNVRKVAQDSKAKLSQ 45


  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
   0.326    0.141    0.416 

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: 1,062,662
Number of extensions: 45151
Number of successful extensions: 238
Number of sequences better than 10.0: 1
Number of HSP's gapped: 234
Number of HSP's successfully gapped: 32
Length of query: 122
Length of database: 5,693,230
Length adjustment: 81
Effective length of query: 41
Effective length of database: 3,729,466
Effective search space: 152908106
Effective search space used: 152908106
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.1 bits)