RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780712|ref|YP_003065125.1| 30S ribosomal protein S16
[Candidatus Liberibacter asiaticus str. psy62]
         (116 letters)



>gnl|CDD|30577 COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal
          structure and biogenesis].
          Length = 87

 Score =  106 bits (265), Expect = 2e-24
 Identities = 51/83 (61%), Positives = 64/83 (77%), Gaps = 2/83 (2%)

Query: 3  LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHW 62
          +KIRLA GGSK R  YRIVVA+SRSPRDG+FIE+LGT+NP L KE   R  ++ ERI +W
Sbjct: 2  VKIRLARGGSKKRPFYRIVVADSRSPRDGRFIERLGTYNPLLGKEE--RVKLDEERILYW 59

Query: 63 MSKGAQPTDRILFFLDKAGLIKR 85
          +S+GAQP+D +   L KAGL K+
Sbjct: 60 LSQGAQPSDTVRRLLKKAGLAKK 82


>gnl|CDD|144471 pfam00886, Ribosomal_S16, Ribosomal protein S16. 
          Length = 58

 Score = 92.9 bits (232), Expect = 2e-20
 Identities = 36/61 (59%), Positives = 45/61 (73%), Gaps = 4/61 (6%)

Query: 10 GGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQP 69
          GG K R  YRIVVA+SRSPRDG+FIE+LGT+NP    E      ++ ERI++W+ KGAQP
Sbjct: 2  GGRKKRPFYRIVVADSRSPRDGRFIEELGTYNPIANGE----VKLDVERIKYWLGKGAQP 57

Query: 70 T 70
          T
Sbjct: 58 T 58


>gnl|CDD|38629 KOG3419, KOG3419, KOG3419, Mitochondrial/chloroplast ribosomal
           protein S16 [Translation, ribosomal structure and
           biogenesis].
          Length = 112

 Score = 90.0 bits (223), Expect = 1e-19
 Identities = 45/106 (42%), Positives = 65/106 (61%)

Query: 1   MTLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQ 60
           M +KIRLA  G K+R  YRIVVA+SR  RDGK IE+LGT++P   ++N     +NF+RI+
Sbjct: 1   MVVKIRLARFGCKNRPFYRIVVADSRKRRDGKPIEQLGTYDPLPNQDNEKLVALNFDRIK 60

Query: 61  HWMSKGAQPTDRILFFLDKAGLIKRSPQNNPKKSQPKKKALERLAS 106
           +W+  GAQP+D +   L KAGL    P       + ++   E++  
Sbjct: 61  YWLGVGAQPSDTVEELLGKAGLFPIHPMTFMNAKRNRRLTAEQVLP 106


>gnl|CDD|176950 CHL00005, rps16, ribosomal protein S16.
          Length = 82

 Score = 68.5 bits (168), Expect = 4e-13
 Identities = 29/82 (35%), Positives = 47/82 (57%), Gaps = 5/82 (6%)

Query: 3  LKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHW 62
          +K+RL   G K +  YRIV  + RS R+G+ +EK+G ++P   +       +N   I ++
Sbjct: 2  VKLRLKRCGRKQQAVYRIVAIDVRSRREGRDLEKVGFYDPIKNQ-----TYLNVPAILYF 56

Query: 63 MSKGAQPTDRILFFLDKAGLIK 84
          + KGAQPT+ +   L KA + K
Sbjct: 57 LEKGAQPTETVYDILKKAEVFK 78


>gnl|CDD|36240 KOG1022, KOG1022, KOG1022, Acetylglucosaminyltransferase
          EXT2/exostosin 2 [Carbohydrate transport and
          metabolism, Cell wall/membrane/envelope biogenesis,
          Extracellular structures].
          Length = 691

 Score = 28.1 bits (62), Expect = 0.55
 Identities = 13/39 (33%), Positives = 13/39 (33%), Gaps = 3/39 (7%)

Query: 20 IVVANSRSPRDGKFIEK---LGTWNPTLPKENPLRFTMN 55
          I    S SP   K IEK      W  T P   P   T  
Sbjct: 42 IGWFYSDSPFSLKPIEKRNISDAWPVTNPAITPASETGL 80


>gnl|CDD|107386 cd06391, PBP1_iGluR_delta_2, N-terminal
           leucine/isoleucine/valine-binding protein (LIVBP)-like
           domain of the delta2 receptor of an orphan glutamate
           receptor family.  N-terminal
           leucine/isoleucine/valine-binding protein (LIVBP)-like
           domain of the delta2 receptor of an orphan glutamate
           receptor family. While this N-terminal domain belongs to
           the periplasmic-binding fold type I superfamily, the
           glutamate-binding domain of the iGluR is structurally
           homologous to the periplasmic-binding fold type II. The
           LIVBP-like domain of iGluRs is thought to play a role in
           the initial assembly of iGluR subunits, but it is not
           well understood how this domain is arranged and
           functions in intact iGluR. Although the delta receptors
           are a member of the ionotropic glutamate receptor
           family, they cannot be activated by AMPA, kainate, NMDA,
           glutamate, or any other ligands. Phylogenetic analysis
           shows that both GluRdelta1 and GluRalpha2 are closer
           related to non-NMDA receptors. GluRdelta2 was shown to
           function as an AMPA-like receptor by mutation analysis.
           Moreover, targeted disruption of GluRdelta2 gene caused
           motor coordination impairment, Purkinje cell maturation,
           and long-term depression of synaptic transmission. It
           has been suggested that GluRdelta2 is the receptor for
           cerebellin 1, a glycoprotein of the Clq and tumor
           necrosis factor family that is secreted from cerebellar
           granule cells.
          Length = 400

 Score = 26.9 bits (59), Expect = 1.3
 Identities = 12/42 (28%), Positives = 19/42 (45%), Gaps = 1/42 (2%)

Query: 1   MTLKIRLACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNP 42
           +T ++     G     H+ I+  N      G+ + KLG WNP
Sbjct: 354 LTGELEFNENGGNPNVHFEILGTNYGEDL-GRGVRKLGCWNP 394


>gnl|CDD|34757 COG5156, DOC1, Anaphase-promoting complex (APC), subunit 10 [Cell
          division and chromosome partitioning /
          Posttranslational modification, protein turnover,
          chaperones].
          Length = 189

 Score = 25.8 bits (56), Expect = 2.8
 Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 1/37 (2%)

Query: 34 IEKLGTWNPTLPK-ENPLRFTMNFERIQHWMSKGAQP 69
          +  L  W  +  K  +PLR  ++     +W S G QP
Sbjct: 26 VTHLAEWRLSSFKRGHPLRELLDDNMDTYWQSDGVQP 62


>gnl|CDD|146017 pfam03180, Lipoprotein_9, NLPA lipoprotein.  This family of
           bacterial lipoproteins contains several antigenic
           members, that may be involved in bacterial virulence.
           Their precise function is unknown. However they are
           probably distantly related to pfam00497 which are solute
           binding proteins.
          Length = 236

 Score = 24.9 bits (55), Expect = 5.1
 Identities = 9/13 (69%), Positives = 10/13 (76%)

Query: 72  RILFFLDKAGLIK 84
           R L  L+KAGLIK
Sbjct: 111 RALLLLEKAGLIK 123


>gnl|CDD|31574 COG1384, LysS, Lysyl-tRNA synthetase (class I) [Translation,
           ribosomal structure and biogenesis].
          Length = 521

 Score = 24.4 bits (53), Expect = 7.1
 Identities = 9/22 (40%), Positives = 13/22 (59%)

Query: 18  YRIVVANSRSPRDGKFIEKLGT 39
           YR+++   R PR G F+  LG 
Sbjct: 489 YRVLIGKERGPRLGSFLALLGV 510


>gnl|CDD|37740 KOG2529, KOG2529, KOG2529, Pseudouridine synthase [Translation,
           ribosomal structure and biogenesis].
          Length = 395

 Score = 24.2 bits (52), Expect = 7.6
 Identities = 21/113 (18%), Positives = 37/113 (32%), Gaps = 13/113 (11%)

Query: 17  HYRIVVANS--RSPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRIL 74
           + R+VV +S   +P  G  +   G    +   + P        + +   SK A+ + R +
Sbjct: 275 YKRVVVKDSTVNAPCYGAKLLVPGLLRYSDDIDGPFEVVDMTTKGEAIASKIAEMSLRQV 334

Query: 75  FFLDKAGLIKRSPQNNPK-----------KSQPKKKALERLASKKNADEHATT 116
              D   + K                   K+ P K+A       K    + TT
Sbjct: 335 ASCDHGVVAKTKRVIMEADVYERCWGLGPKASPGKEAKAEGKLDKFGKGNETT 387


>gnl|CDD|99782 cd06185, PDR_like, Phthalate dioxygenase reductase (PDR) is an
          FMN-dependent reductase that mediates electron transfer
          from NADH to FMN to an iron sulfur cluster. PDR has an
          an N-terminal  ferrredoxin reductase (FNR)-like NAD(H)
          binding domain and a C-terminal iron-sulfur [2Fe-2S]
          cluster domain. Although structurally homologous to
          FNR, PDR binds FMN rather than FAD in it's FNR-like
          domain. Electron transfer between pyrimidines and
          iron-sulfur clusters (Rieske center [2Fe-2S]) or heme
          groups is mediated by flavins in respiration,
          photosynthesis, and oxygenase systems. Type I
          dioxygenase systems, including the hydroxylate
          phthalate system, have 2 components, a monomeric
          reductase consisting of a flavin and a 2Fe-2S center
          and a multimeric oxygenase. In contrast to other Rieske
          dioxygenases the ferredoxin like domain is C-, not
          N-terminal..
          Length = 211

 Score = 24.4 bits (54), Expect = 7.8
 Identities = 9/21 (42%), Positives = 9/21 (42%), Gaps = 3/21 (14%)

Query: 9  CGGSKSRHHYRIVV---ANSR 26
          CG    R  YRI V     SR
Sbjct: 47 CGDPADRDRYRIAVLREPASR 67


>gnl|CDD|173885 cd08520, PBP2_NikA_DppA_OppA_like_21, The substrate-binding
           component of an uncharacterized ABC-type
           nickel/dipeptide/oligopeptide-like import system
           contains the type 2 periplasmic binding fold.  This CD
           represents the substrate-binding domain of an
           uncharacterized ATP-binding cassette (ABC) type
           nickel/dipeptide/oligopeptide-like transporter. The
           oligopeptide-binding protein OppA and the
           dipeptide-binding protein DppA show significant sequence
           similarity to NikA, the initial nickel receptor. The
           DppA binds dipeptides and some tripeptides and is
           involved in chemotaxis toward dipeptides, whereas the
           OppA binds peptides of a wide range of lengths (2-35
           amino acid residues) and plays a role in recycling of
           cell wall peptides, which precludes any involvement in
           chemotaxis. Most of other periplasmic binding proteins
           are comprised of only two globular subdomains
           corresponding to domains I and III of the
           dipeptide/oligopeptide binding proteins. The structural
           topology of these domains is most similar to that of the
           type 2 periplasmic binding proteins (PBP2), which are
           responsible for the uptake of a variety of substrates
           such as phosphate, sulfate, polysaccharides,
           lysine/arginine/ornithine, and histidine.  The PBP2 bind
           their ligand in the cleft between these domains in a
           manner resembling a Venus flytrap. After binding their
           specific ligand with high affinity, they can interact
           with a cognate membrane transport complex comprised of
           two integral membrane domains and two cytoplasmically
           located ATPase domains. This interaction triggers the
           ligand translocation across the cytoplasmic membrane
           energized by ATP hydrolysis.  Besides transport
           proteins, the PBP2 superfamily includes the
           ligand-binding domains from ionotropic glutamate
           receptors, LysR-type transcriptional regulators,  and
           unorthodox sensor proteins involved in signal
           transduction.
          Length = 468

 Score = 24.2 bits (53), Expect = 7.9
 Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 10/44 (22%)

Query: 16  HHYRIVVANSRSPRDGKFIEKLGTWNPTLPK------ENPLRFT 53
           +  +I +    +P    F+EK+ T  P LPK      E+P +FT
Sbjct: 113 YTVKITLKRPYAP----FLEKIATTVPILPKHIWEKVEDPEKFT 152


>gnl|CDD|34137 COG4458, SrfC, Uncharacterized protein conserved in bacteria,
           putative virulence factor [Function unknown].
          Length = 821

 Score = 24.2 bits (52), Expect = 8.2
 Identities = 19/90 (21%), Positives = 32/90 (35%), Gaps = 3/90 (3%)

Query: 27  SPRDGKFIEKLGTWNPTLPKENPLRFTMNFERIQHWMSKGAQPTDRILFFLDKAGLIKRS 86
           +P D +F EKLG + P   ++   +       +Q       +    +L  LD  G + R 
Sbjct: 438 TPFDMRFSEKLGLFKPFDLQDKVAKIKKQDSEVQQHFGDPGKAWGTLL-ALDDGG-VSRL 495

Query: 87  PQNNPKKSQPKKKALERLASKKNADEHATT 116
            +       P+ K   RL  +     H   
Sbjct: 496 AEYLSAICLPEIKY-GRLQEQLGELAHEIR 524


>gnl|CDD|38681 KOG3471, KOG3471, KOG3471, RNA polymerase II transcription
           initiation/nucleotide excision repair factor TFIIH,
           subunit TFB2 [Transcription, Replication, recombination
           and repair].
          Length = 465

 Score = 24.1 bits (52), Expect = 8.4
 Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 19/82 (23%)

Query: 8   ACGGSKSRHHYRIVVANSRSPRDGKFIEKLGTWNPTLPKENPLRFTMN-FERIQHWM--- 63
             GG K      +V+   +  RD  F++K               +    +E I H+M   
Sbjct: 118 LTGGGKQNSFGSLVLGEDKHNRDVDFLDK---------------YASERWECILHFMVGT 162

Query: 64  SKGAQPTDRILFFLDKAGLIKR 85
            +    ++ +L  L  AGL+ R
Sbjct: 163 PEAKAVSEGVLNLLKHAGLMSR 184


>gnl|CDD|36447 KOG1233, KOG1233, KOG1233, Alkyl-dihydroxyacetonephosphate synthase
           [General function prediction only].
          Length = 613

 Score = 24.2 bits (52), Expect = 8.9
 Identities = 9/11 (81%), Positives = 9/11 (81%)

Query: 7   LACGGSKSRHH 17
           LACGGS S HH
Sbjct: 562 LACGGSLSHHH 572


>gnl|CDD|31653 COG1464, NlpA, ABC-type metal ion transport system, periplasmic
           component/surface antigen [Inorganic ion transport and
           metabolism].
          Length = 268

 Score = 24.0 bits (52), Expect = 9.0
 Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 2/28 (7%)

Query: 69  PTD--RILFFLDKAGLIKRSPQNNPKKS 94
           PT+  R L  L KAGLIK     N   +
Sbjct: 137 PTNEGRALLLLQKAGLIKLKDGVNLLAT 164


  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
   0.317    0.131    0.396 

Gapped
Lambda     K      H
   0.267   0.0767    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,428,883
Number of extensions: 68040
Number of successful extensions: 161
Number of sequences better than 10.0: 1
Number of HSP's gapped: 158
Number of HSP's successfully gapped: 20
Length of query: 116
Length of database: 6,263,737
Length adjustment: 81
Effective length of query: 35
Effective length of database: 4,513,408
Effective search space: 157969280
Effective search space used: 157969280
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: 51 (23.4 bits)