RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780249|ref|YP_003064662.1| 50S ribosomal protein L5
[Candidatus Liberibacter asiaticus str. psy62]
         (185 letters)



>gnl|CDD|30443 COG0094, RplE, Ribosomal protein L5 [Translation, ribosomal
           structure and biogenesis].
          Length = 180

 Score =  265 bits (680), Expect = 4e-72
 Identities = 111/178 (62%), Positives = 141/178 (79%)

Query: 8   PRLKKEYCLRIREAMQQEFSYKNVMQIPKIEKVVVNMGVGESIADSKKAESAAADLALIT 67
            RLK++Y   I  A+ ++F Y N MQ+P+IEKVVVNMGVGE+ AD K+ E AA DL LIT
Sbjct: 2   NRLKEKYKDEIVPALIKKFGYSNPMQVPRIEKVVVNMGVGEAAADGKRLEKAAKDLELIT 61

Query: 68  GQKPVITRARRSIAGFKLRTGMPIGTKVTLRGTNMYDFLDRLINMGMPRIRDFHGLNSRS 127
           GQKPVIT+A++SIAGFK+R GMPIG KVTLRG  MY+FLDRL+N+ +PR+RDF GL+ +S
Sbjct: 62  GQKPVITKAKKSIAGFKIREGMPIGVKVTLRGERMYEFLDRLLNIALPRVRDFRGLSPKS 121

Query: 128 FDGSGNFSFGIREHIVFPEINYDKVDCVLGMDISICTTTRSDREAKYLLTLFGFPFPK 185
           FDG GN+SFGI+E I+FPEI+YD +  + GMDI+I TT + D EA+ LL+ FG PF K
Sbjct: 122 FDGRGNYSFGIKEQIIFPEIDYDPIIGIRGMDITIVTTAKGDVEARALLSAFGIPFRK 179


>gnl|CDD|177017 CHL00078, rpl5, ribosomal protein L5.
          Length = 181

 Score =  262 bits (671), Expect = 6e-71
 Identities = 95/176 (53%), Positives = 133/176 (75%)

Query: 8   PRLKKEYCLRIREAMQQEFSYKNVMQIPKIEKVVVNMGVGESIADSKKAESAAADLALIT 67
            RLK  Y  +I   + ++F YKN+ Q+PK++K+V+N G+GE+  +SK  ES+  +L +IT
Sbjct: 3   QRLKSLYKEKIVPKLIEKFLYKNIHQVPKLKKIVINRGLGEASQNSKILESSIKELTIIT 62

Query: 68  GQKPVITRARRSIAGFKLRTGMPIGTKVTLRGTNMYDFLDRLINMGMPRIRDFHGLNSRS 127
           GQKP+ITRA+++IAGFK+R  MP+G  VTLRG  MY FLDRLIN+ +PRIRDF GL+ +S
Sbjct: 63  GQKPIITRAKKAIAGFKIREKMPVGVSVTLRGDKMYAFLDRLINLALPRIRDFQGLSPKS 122

Query: 128 FDGSGNFSFGIREHIVFPEINYDKVDCVLGMDISICTTTRSDREAKYLLTLFGFPF 183
           FDG GN++ G++E ++FPEI+YDK+D + GMDISI TT ++D+E   LL   G PF
Sbjct: 123 FDGHGNYNLGLKEQLMFPEIDYDKIDQIRGMDISIVTTAKTDQEGLALLKELGMPF 178


>gnl|CDD|35619 KOG0398, KOG0398, KOG0398, Mitochondrial/chloroplast ribosomal
           protein L5/L7 [Translation, ribosomal structure and
           biogenesis].
          Length = 278

 Score =  190 bits (484), Expect = 2e-49
 Identities = 92/179 (51%), Positives = 122/179 (68%), Gaps = 4/179 (2%)

Query: 9   RLKKEYCLRIREAMQQEFSYKNVMQIPKIEKVVVNMGVGESIADSKKAESAAADLALITG 68
           R +  Y  R  +A+  EF Y N+  +PK++KVVVN G+GE+  + K  E+A  D+ALITG
Sbjct: 95  RNRPPYLERGIKALLPEFKYVNIHNVPKVQKVVVNCGIGEAAQNDKGLEAAMKDIALITG 154

Query: 69  QKPVITRARRSIAGFKLRTGMPIGTKVTLRGTNMYDFLDRLINMGMPRIRDFHGLNSRSF 128
           QKP+ TRAR  +A +KLR G P+G KVTLRG  MY FL RLI + +PR RDF G++  S 
Sbjct: 155 QKPIKTRARADVATWKLREGQPLGIKVTLRGDVMYSFLSRLIELVLPRTRDFKGVSPSSG 214

Query: 129 DGSGNFSFGIREHI--VFPEI--NYDKVDCVLGMDISICTTTRSDREAKYLLTLFGFPF 183
           DG+GN SFG++     VFPEI  N+D V    GMD++I TT +SD+EA+ LL+L G PF
Sbjct: 215 DGNGNISFGLKAEDQGVFPEIRANFDAVPKTRGMDVNISTTAKSDQEARKLLSLMGMPF 273


>gnl|CDD|144317 pfam00673, Ribosomal_L5_C, ribosomal L5P family C-terminus.  This
           region is found associated with pfam00281.
          Length = 95

 Score =  163 bits (414), Expect = 4e-41
 Identities = 60/94 (63%), Positives = 75/94 (79%)

Query: 90  PIGTKVTLRGTNMYDFLDRLINMGMPRIRDFHGLNSRSFDGSGNFSFGIREHIVFPEINY 149
           PIG KVTLRG  MY+FLDRLIN+ +PRIRDF GL+ +SFDG GN+SFGI+EHI+FPEI Y
Sbjct: 1   PIGCKVTLRGEKMYEFLDRLINIVLPRIRDFRGLSPKSFDGRGNYSFGIKEHIIFPEIKY 60

Query: 150 DKVDCVLGMDISICTTTRSDREAKYLLTLFGFPF 183
           D +  + GMDI+I TT ++D+EA+ LL   G PF
Sbjct: 61  DPIIGIFGMDITIVTTAKTDKEARALLKELGMPF 94


>gnl|CDD|109342 pfam00281, Ribosomal_L5, Ribosomal protein L5. 
          Length = 56

 Score = 83.1 bits (206), Expect = 4e-17
 Identities = 35/57 (61%), Positives = 48/57 (84%), Gaps = 1/57 (1%)

Query: 30 NVMQIPKIEKVVVNMGVGESIADSKKAESAAADLALITGQKPVITRARRSIAGFKLR 86
          NVM++PK+EK+VVNMGVGE+  D+K  E AA +L  I+GQKP+IT+A++SIA FK+R
Sbjct: 1  NVMEVPKLEKIVVNMGVGEA-GDNKILEKAALELEEISGQKPIITKAKKSIASFKIR 56


>gnl|CDD|35618 KOG0397, KOG0397, KOG0397, 60S ribosomal protein L11 [Translation,
           ribosomal structure and biogenesis].
          Length = 176

 Score = 77.7 bits (191), Expect = 2e-15
 Identities = 50/145 (34%), Positives = 78/145 (53%), Gaps = 10/145 (6%)

Query: 29  KNVMQIPKIEKVVVNMGVGESIADSKKAESAAADLALITGQKPVITRARRSIAGFKLRTG 88
           +N M+  KI+K+V+N+ VGES     +   AA  L  +TGQ PV ++AR ++  F +R  
Sbjct: 7   QNPMRELKIQKLVLNICVGES---GDRLTRAAKVLEQLTGQTPVFSKARYTVRSFGIRRN 63

Query: 89  MPIGTKVTLRGTNMYDFLDRLINMGMPRIRDFHGLNSRSFDGSGNFSFGIREHIVFPEIN 148
             I   VT+RG    + L+R +     +++++  L  R+F  +GNF FGI+EHI    I 
Sbjct: 64  EKIAVHVTVRGPKAEEILERGL-----KVKEYE-LRKRNFSDTGNFGFGIQEHIDL-GIK 116

Query: 149 YDKVDCVLGMDISICTTTRSDREAK 173
           YD    + GMD  +       R A+
Sbjct: 117 YDPSIGIYGMDFYVVLGRPGYRVAR 141


>gnl|CDD|143824 pfam00035, dsrm, Double-stranded RNA binding motif.  Putative
          motif shared by proteins that bind to dsRNA. At least
          some DSRM proteins seem to bind to specific RNA
          targets. Exemplified by Staufen, which is involved in
          localisation of at least five different mRNAs in the
          early Drosophila embryo. Also by interferon-induced
          protein kinase in humans, which is part of the cellular
          response to dsRNA.
          Length = 66

 Score = 31.1 bits (71), Expect = 0.20
 Identities = 15/57 (26%), Positives = 22/57 (38%), Gaps = 4/57 (7%)

Query: 13 EYCLRIREAMQQEFSYKNVMQIPKIEKVVVNMG---VGESIADSKK-AESAAADLAL 65
          E C +  +    E+  +          V V +G    G     SKK A+  AA+ AL
Sbjct: 7  ELCQKKGKKPPYEYVEEEGPSHSPTFTVTVTVGGKKYGTGTGSSKKEAKQLAAEKAL 63


>gnl|CDD|29328 cd01343, PL1_Passenger_AT, Pertactin-like passenger domains
           (virulence factors), C-terminal, subgroup 1, of
           autotransporter proteins of the type V secretion system
           of Gram-negative bacteria. This subgroup includes the
           passenger domains of Neisseria and Haemophilus IgA1
           proteases, SPATEs (serine protease autotransporters
           secreted by Enterobacteriaceae), Bordetella pertacins,
           and nonprotease autotransporters, TibA and similar
           AIDA-like proteins..
          Length = 233

 Score = 29.9 bits (67), Expect = 0.42
 Identities = 17/94 (18%), Positives = 32/94 (34%), Gaps = 8/94 (8%)

Query: 47  GESIADSKKAESAAADLALITGQKPVITRARRSIAGFKLRTGMPIGTKVTLRGTNMYDFL 106
           G  +  + +   A A+L L             +I G      + + +  TL G +  + L
Sbjct: 61  GTVVLGAGQPLQALAELLLGGN-----AAWTGAIQGLNATVSLNLNSVWTLTGDSNVNNL 115

Query: 107 ---DRLINMGMPRIRDFHGLNSRSFDGSGNFSFG 137
                 ++   P    F+ L   +  G+G F   
Sbjct: 116 TLNGGTVDFNGPSAGKFNTLTVNTLSGNGTFVMR 149


>gnl|CDD|30612 COG0263, ProB, Glutamate 5-kinase [Amino acid transport and
           metabolism].
          Length = 369

 Score = 27.1 bits (60), Expect = 2.6
 Identities = 8/36 (22%), Positives = 12/36 (33%)

Query: 59  AAADLALITGQKPVITRARRSIAGFKLRTGMPIGTK 94
            AA +A   G   +I    +         G  +GT 
Sbjct: 221 EAAKIATRAGVPVIIASGSKPDVILDALEGEAVGTL 256


>gnl|CDD|144336 pfam00696, AA_kinase, Amino acid kinase family.  This family
           includes kinases that phosphorylate a variety of amino
           acid substrates, as well as uridylate kinase and
           carbamate kinase. This family includes: Aspartokinase
           EC:2.7.2.4. Acetylglutamate kinase EC:2.7.2.8. Glutamate
           5-kinase EC:2.7.2.11. Uridylate kinase EC:2.7.4.-.
           Carbamate kinase EC:2.7.2.2.
          Length = 230

 Score = 25.4 bits (56), Expect = 8.7
 Identities = 18/69 (26%), Positives = 31/69 (44%), Gaps = 4/69 (5%)

Query: 38  EKVVVNMGVGESIADSKKAESAAADLALIT--GQKPVITRARRSIAGFKLRTGMPIGTKV 95
           +++V+ +G G S+ D    +  A ++AL++  G K V+          KL     I  K+
Sbjct: 1   KRIVIKLG-GSSLTDEDAIKRIAEEIALLSELGIKVVVVSGGGGFTD-KLLAAYGIAEKI 58

Query: 96  TLRGTNMYD 104
            LR T    
Sbjct: 59  GLRVTAGAT 67


>gnl|CDD|36517 KOG1303, KOG1303, KOG1303, Amino acid transporters [Amino acid
           transport and metabolism].
          Length = 437

 Score = 25.3 bits (55), Expect = 9.6
 Identities = 8/20 (40%), Positives = 9/20 (45%)

Query: 128 FDGSGNFSFGIREHIVFPEI 147
           F   G  +F    H V PEI
Sbjct: 231 FTALGIIAFAYGGHAVLPEI 250


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.324    0.140    0.410 

Gapped
Lambda     K      H
   0.267   0.0682    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,249,512
Number of extensions: 114682
Number of successful extensions: 250
Number of sequences better than 10.0: 1
Number of HSP's gapped: 246
Number of HSP's successfully gapped: 12
Length of query: 185
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 97
Effective length of database: 4,362,145
Effective search space: 423128065
Effective search space used: 423128065
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (24.7 bits)