RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780244|ref|YP_003064657.1| 30S ribosomal protein S5
[Candidatus Liberibacter asiaticus str. psy62]
         (199 letters)



>3bbn_E Ribosomal protein S5; small ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Spinacea oleracea}
          Length = 308

 Score =  172 bits (437), Expect = 4e-44
 Identities = 62/170 (36%), Positives = 96/170 (56%)

Query: 3   QKERSQRDNWQNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHS 62
            K+ +   +   +E+  +   + +V + RV+  + GG+   F  +VVVGD K +VG    
Sbjct: 133 IKKATGFGSKSKKEKIRDGFEENVVQVRRVTKVVKGGKHMRFRAIVVVGDKKGQVGVGVG 192

Query: 63  TAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGA 122
            A+EV  AV+KA   A+RN+I+V +    T  H     +GA +V++R A  GTGVIAGGA
Sbjct: 193 KAKEVVSAVQKAAVDARRNIITVPMTKYLTFPHRNEADYGAARVMLRPAAPGTGVIAGGA 252

Query: 123 IRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172
           +R V E+ G+ + + K +GS+N  N  RAT   +++     DVA  RGI 
Sbjct: 253 VRTVLEMAGVENALGKQLGSNNALNNARATIVAVQTMRQFSDVARDRGIP 302


>3ofo_E 30S ribosomal protein S5; protein biosynthesis, ribosomes, RNA,
           tRNA, transfer, eryThr ketolide, macrolide, antibiotic,
           EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_E*
           3iy8_E 2wwl_E 3ofp_E 2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E
           2i2u_E 2i2p_E* 2qan_E* 2qb9_E* 2qbb_E* 2qbd_E 2qbf_E
           2qbh_E* 2qbj_E* 2qou_E* 2qow_E* ...
          Length = 150

 Score =  152 bits (384), Expect = 7e-38
 Identities = 75/147 (51%), Positives = 105/147 (71%), Gaps = 1/147 (0%)

Query: 24  DRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMI 83
           ++++A+NRVS  + GGR F+F+ L VVGD   +VGF +  AREVP A++KA E A+RNMI
Sbjct: 4   EKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMI 63

Query: 84  SVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSS 143
           +V+L +  TL H   G H   +V M+ A  GTG+IAGGA+RAV EV G+H+V+AK+ GS+
Sbjct: 64  NVAL-NNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGST 122

Query: 144 NPHNVIRATFEVLRSQSHPRDVANRRG 170
           NP NV+RAT + L + + P  VA +RG
Sbjct: 123 NPINVVRATIDGLENMNSPEMVAAKRG 149


>3i1m_E 30S ribosomal protein S5; ribosome structure, protein-RNA complex,
           ribonucleoprotein, ribosomal protein, RNA-binding,
           rRNA-binding, antibiotic resistance; 3.19A {Escherichia
           coli k-12} PDB: 1vs7_E* 1vs5_E 3i1o_E 3i1q_E 3i1s_E
           3i1z_E 3i21_E 2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E
           2i2p_E* 2qan_E* 2qb9_E* 2qbb_E* 2qbd_E 2qbf_E 2qbh_E*
           ...
          Length = 167

 Score =  148 bits (376), Expect = 7e-37
 Identities = 76/159 (47%), Positives = 110/159 (69%), Gaps = 1/159 (0%)

Query: 14  NREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRK 73
           + E++   + ++++A+NRVS  + GGR F+F+ L VVGD   +VGF +  AREVP A++K
Sbjct: 3   HIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQK 62

Query: 74  ATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMH 133
           A E A+RNMI+V+L +  TL H   G H   +V M+ A  GTG+IAGGA+RAV EV G+H
Sbjct: 63  AMEKARRNMINVAL-NNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVH 121

Query: 134 DVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172
           +V+AK+ GS+NP NV+RAT + L + + P  VA +RG  
Sbjct: 122 NVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKS 160


>1pkp_A Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus} SCOP:
           d.14.1.1 d.50.1.2 PDB: 1eg0_B 1dv4_E* 1qd7_D
          Length = 150

 Score =  142 bits (359), Expect = 6e-35
 Identities = 71/136 (52%), Positives = 98/136 (72%), Gaps = 1/136 (0%)

Query: 24  DRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMI 83
           +R+VA+NRV+  + GGRR  FS LVVVGD    VGF    A+EVPEA+RKA E AK+N+I
Sbjct: 13  ERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIRKAIEDAKKNLI 72

Query: 84  SVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSS 143
            V +  G T+ H+ +G  GAG++I++ A  GTGVIAGG  RAV E+ G+ D+++KSIGS+
Sbjct: 73  EVPI-VGTTIPHEVIGHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSKSIGSN 131

Query: 144 NPHNVIRATFEVLRSQ 159
            P N++RATF+ L+  
Sbjct: 132 TPINMVRATFDGLKQL 147


>3jyv_E 40S ribosomal protein S2; eukaryotic ribosome, RACK1 protein,
           flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC
           7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} PDB: 1s1h_E
          Length = 162

 Score =  137 bits (347), Expect = 1e-33
 Identities = 42/157 (26%), Positives = 72/157 (45%), Gaps = 11/157 (7%)

Query: 24  DRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMI 83
           D ++ I  V      G+R  F  +VVVGD+   VG    TA+EV  A+R     AK ++I
Sbjct: 4   DEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVI 63

Query: 84  SV-------SLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVV 136
            +       +L    +L     G+ G+  V +  A  G+G++A  A++ + ++ G+ DV 
Sbjct: 64  PIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVY 123

Query: 137 AKSIGSSN-PHNVIRATFEVL---RSQSHPRDVANRR 169
            +S G +    N ++A F  +        P   A + 
Sbjct: 124 TQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQP 160


>2vqe_E 30S ribosomal protein S5; tRNA-binding, rRNA-binding,
           metal-binding, zinc-finger, translation; HET: TM2 PAR;
           2.5A {Thermus thermophilus} SCOP: i.1.1.3 PDB: 1fka_E
           1gix_H* 1hnw_E* 1hnx_E* 1hnz_E* 1hr0_E 1ibk_E* 1ibl_E*
           1ibm_E 1jgo_H* 1jgp_H* 1jgq_H* 1ml5_H* 1xmo_E* 1xmq_E*
           1xnq_E* 1xnr_E* 1yl4_H 2b64_E* 2b9m_E* ...
          Length = 162

 Score =  136 bits (343), Expect = 4e-33
 Identities = 62/154 (40%), Positives = 87/154 (56%), Gaps = 1/154 (0%)

Query: 19  DNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAA 78
           +    ++++ I R +    GGRRF F  LVVVGD + +VG     A EVP AV+KA   A
Sbjct: 3   ETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYA 62

Query: 79  KRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAK 138
           +RNM+ V L    T+ H+     GA K++++ A  GTGVIAG   RA+ E+ G+ D++ K
Sbjct: 63  RRNMVEVPL-QNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTK 121

Query: 139 SIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172
            +GS NP N+  AT E LR      DV   R  +
Sbjct: 122 ELGSRNPINIAYATMEALRQLRTKADVERLRKGE 155


>2zkq_e 40S ribosomal protein S2E; protein-RNA complex, 40S ribosomal
           subunit, ribosomal protein/RNA complex; 8.70A {Canis
           familiaris}
          Length = 179

 Score =  124 bits (313), Expect = 1e-29
 Identities = 36/147 (24%), Positives = 63/147 (42%), Gaps = 8/147 (5%)

Query: 21  SIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKR 80
           S+ D ++ I  V      G+R  F   V +GD    VG     ++EV  A+R A   AK 
Sbjct: 9   SLKDEVLKIVPVQKQTRAGQRTRFKAFVAIGDHNGHVGLGVKCSKEVATAIRGAIILAKL 68

Query: 81  NMISV-------SLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMH 133
           +++ V        +    T+     GR G+  V +  A  GTG+++    + +  + G+ 
Sbjct: 69  SIVPVRRGYWGNKIGKPHTVPCKVTGRSGSVPVRLIPAPRGTGIVSAPVPKKLLMMAGID 128

Query: 134 DVVAKSIGSSNP-HNVIRATFEVLRSQ 159
           D    + G +    N  +ATF+ +   
Sbjct: 129 DCYTSARGCTATLGNFAKATFDAISKT 155


>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 = 39.2 bits (91), Expect = 6e-04
 Identities = 38/229 (16%), Positives = 63/229 (27%), Gaps = 115/229 (50%)

Query: 6   RSQR-------------DNWQNREE--------RDNSI--VDRIVAINRVSTALPGGRRF 42
           R                D+ +N E          + +   V     +N+ ++ LP G++ 
Sbjct: 309 RCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDY--VNKTNSHLPAGKQV 366

Query: 43  AFSV------LVVVGDTKSKVGFAHSTARE-----------VPEAVRK------------ 73
             S+      LVV G  +S  G    T R+           +P + RK            
Sbjct: 367 EISLVNGAKNLVVSGPPQSLYGLN-LTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVAS 425

Query: 74  ---------ATEAAKRNM------ISVSLL--------DGRTL----------------- 93
                    A++   +++       +   +        DG  L                 
Sbjct: 426 PFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIR 485

Query: 94  ---H----------H--D-GVGR-HGAGKVIMRSAMAGTG--VIAGGAI 123
                         H  D G G   G G +  R+   GTG  VI  G +
Sbjct: 486 LPVKWETTTQFKATHILDFGPGGASGLGVLTHRN-KDGTGVRVIVAGTL 533



 Score = 31.8 bits (72), Expect = 0.099
 Identities = 15/93 (16%), Positives = 27/93 (29%), Gaps = 38/93 (40%)

Query: 125 AV-CEVLGM--------------HD---VVAKSIGSS--------NPHNVIRATFEV-LR 157
            V  ++LG               H    V A +I  +        +    I   F + +R
Sbjct: 250 VVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVR 309

Query: 158 SQ-SHPR---------D-VANRRGIKHSLLQAR 179
              ++P          D + N  G+   +L   
Sbjct: 310 CYEAYPNTSLPPSILEDSLENNEGVPSPMLSIS 342


>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 = 30.0 bits (66), Expect = 0.40
 Identities = 10/24 (41%), Positives = 12/24 (50%), Gaps = 8/24 (33%)

Query: 172 KHSL--LQARRVVSSKSSSYSRDS 193
           K +L  LQA    S K   Y+ DS
Sbjct: 19  KQALKKLQA----SLKL--YADDS 36



 Score = 29.6 bits (65), Expect = 0.45
 Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 8/34 (23%)

Query: 122 AIRAVCEVLGMH-DVVAKSIGSSNPHNVIRATFE 154
           A++ +   L ++ D        S P   I+AT E
Sbjct: 21  ALKKLQASLKLYAD-------DSAPALAIKATME 47


>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
           vesicle, membrane, Ca structural protein; 7.94A {Bos
           taurus}
          Length = 190

 Score = 29.1 bits (64), Expect = 0.62
 Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 7/33 (21%)

Query: 1   MAQ--KERSQRD--NWQNREERD---NSIVDRI 26
           M Q  +E++++D   W  R+      N I +RI
Sbjct: 108 MEQEWREKAKKDLEEWNQRQSEQVEKNKINNRI 140


>1v77_A PH1877P, hypothetical protein PH1877; RNAse P protein, TIM-barrel,
           RNA binding protein; 1.80A {Pyrococcus horikoshii} SCOP:
           c.6.3.2 PDB: 2czv_A*
          Length = 212

 Score = 26.0 bits (57), Expect = 6.0
 Identities = 17/134 (12%), Positives = 38/134 (28%), Gaps = 31/134 (23%)

Query: 37  PGGRRFAFSVLVVV----GDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRT 92
               R++    V         +   G  H  A+              +  +++       
Sbjct: 86  LRVIRYSIEKGVDAIISPWVNRKDPGIDHVLAK-----------LMVKKNVALGFSLRPL 134

Query: 93  LHHDGVGR----------------HGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVV 136
           L+ +   R                +   + +  SA     V     + ++  V+GM    
Sbjct: 135 LYSNPYERANLLRFMMKAWKLVEKYKVRRFLTSSAQEKWDVRYPRDLISLGVVIGMEIPQ 194

Query: 137 AKSIGSSNPHNVIR 150
           AK+  S  P  +++
Sbjct: 195 AKASISMYPEIILK 208


>1mgt_A MGMT, protein (O6-methylguanine-DNA methyltransferase); DNA repair
           protein, suicidal enzyme, hyperthermostability; 1.80A
           {Thermococcus kodakarensis KOD1} SCOP: a.4.2.1 c.55.7.1
          Length = 174

 Score = 25.7 bits (56), Expect = 7.4
 Identities = 14/54 (25%), Positives = 25/54 (46%)

Query: 64  AREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGV 117
           A+ +  + R    A KRN   + +   R + HDG+G + +G    +  +   GV
Sbjct: 116 AKALNTSPRAVGGAMKRNPYPIVVPCHRVVAHDGIGYYSSGIEEKKFLLEIEGV 169


  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
   0.316    0.129    0.359 

Gapped
Lambda     K      H
   0.267   0.0589    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,593,177
Number of extensions: 70578
Number of successful extensions: 221
Number of sequences better than 10.0: 1
Number of HSP's gapped: 212
Number of HSP's successfully gapped: 25
Length of query: 199
Length of database: 5,693,230
Length adjustment: 88
Effective length of query: 111
Effective length of database: 3,559,758
Effective search space: 395133138
Effective search space used: 395133138
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 (21.7 bits)
S2: 54 (24.9 bits)