RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781010|ref|YP_003065423.1| hypothetical protein
CLIBASIA_04560 [Candidatus Liberibacter asiaticus str. psy62]
         (195 letters)



>gnl|CDD|38740 KOG3532, KOG3532, KOG3532, Predicted protein kinase [General
           function prediction only].
          Length = 1051

 Score = 29.3 bits (65), Expect = 0.72
 Identities = 21/113 (18%), Positives = 48/113 (42%), Gaps = 15/113 (13%)

Query: 57  TIFKTEVKRDIRRASRLSLEEKSKN---------ADKPTVIENQADNINIEVEVATNLNP 107
           T  K E   ++       L++K+KN           +P V   + D+ ++   + T    
Sbjct: 323 THIKMEGGIEVTVLECSRLKDKNKNYEVYCTVTIESRPIVQNEEQDSQHVVNVLDTFSRY 382

Query: 108 NHQASEIDIAIENLPDLKSNHQASEIDIAIENLPDLKSNHQASEIDIAIENLP 160
           +  +S I +  +     K+ ++A ++    +N    K+  +  ++ +AI N+P
Sbjct: 383 D-VSSPIGLVFD-----KNTNRAVKVCTVEDNSLADKAAFKPGDVLVAINNVP 429


>gnl|CDD|176148 cd08459, PBP2_DntR_NahR_LinR_like, The C-terminal substrate binding
           domain of LysR-type transcriptional regulators that are
           involved in the catabolism of dinitrotoluene,
           naphthalene and gamma-hexachlorohexane; contains the
           type 2 periplasmic binding fold.  This CD includes
           LysR-like bacterial transcriptional regulators, DntR,
           NahR, and LinR, which are involved in the degradation of
           aromatic compounds. The transcription of the genes
           encoding enzymes involved in such degradation is
           regulated and expression of these enzymes is enhanced by
           inducers, which are either an intermediate in the
           metabolic pathway or compounds to be degraded.  DntR
           from Burkholderia species controls genes encoding
           enzymes for oxidative degradation of the nitro-aromatic
           compound 2,4-dinitrotoluene. The active form of DntR is
           homotetrameric, consisting of a dimer of dimers. NahR is
           a salicylate-dependent transcription activator of the
           nah and sal operons for naphthalene degradation.
           Salicylic acid is an intermediate of the oxidative
           degradation of the aromatic ring in soil bacteria.  LinR
           positively regulates expression of the genes (linD and
           linE) encoding enzymes for gamma-hexachlorocyclohexane
           (a haloorganic insecticide) degradation. Expression of
           linD and linE are induced by their substrates,
           2,5-dichlorohydroquinone (2,5-DCHQ) and
           chlorohydroquinone (CHQ). The structural topology of
           this substrate-binding domain 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.
          Length = 201

 Score = 27.5 bits (62), Expect = 2.1
 Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 2/37 (5%)

Query: 110 QASEIDIAIENLP--DLKSNHQASEIDIAIENLPDLK 144
            A  + I    LP  +L+   ++ EID+AI  LPDL 
Sbjct: 25  VAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLG 61


>gnl|CDD|143851 pfam00069, Pkinase, Protein kinase domain. 
          Length = 260

 Score = 27.6 bits (62), Expect = 2.2
 Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 7/34 (20%)

Query: 1   MKSKNILIVSTLVICVLSISSCDLGDSIAKKRNT 34
           +K +NIL+    V+ +      D G  +AKK   
Sbjct: 124 LKPENILLDENGVVKI-----ADFG--LAKKLEK 150


>gnl|CDD|35157 COG5598, COG5598, Trimethylamine:corrinoid methyltransferase
           [Coenzyme metabolism].
          Length = 526

 Score = 27.2 bits (60), Expect = 3.3
 Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 5/47 (10%)

Query: 150 SEIDIAIENLPDHQVDRN-----HTLSNLRGACYQPSLVSNSSLKLW 191
           SE  +A + + +     +     HTL+  + A Y P L    S + W
Sbjct: 428 SEEALAFDAIREVGPGGHFLGCPHTLALYQTAFYDPMLADRRSFEQW 474


>gnl|CDD|39006 KOG3802, KOG3802, KOG3802, Transcription factor OCT-1, contains POU
           and HOX domains [Transcription].
          Length = 398

 Score = 26.2 bits (57), Expect = 5.3
 Identities = 7/24 (29%), Positives = 14/24 (58%)

Query: 30  KKRNTIGNTIKKSINRVIQENNKP 53
           KKR +I   ++ ++ +   +N KP
Sbjct: 296 KKRTSIEVNVRGALEKHFLKNPKP 319


>gnl|CDD|34887 COG5296, COG5296, Transcription factor involved in TATA site
           selection and in elongation by RNA polymerase II
           [Transcription].
          Length = 521

 Score = 25.5 bits (55), Expect = 8.9
 Identities = 10/47 (21%), Positives = 22/47 (46%)

Query: 38  TIKKSINRVIQENNKPRNMTIFKTEVKRDIRRASRLSLEEKSKNADK 84
            I K +    + + K  N+   KTE+++  +RA  L  ++ +    +
Sbjct: 345 EISKMVACKDEVHPKRSNVIHEKTELRQKRQRAIELKNKKAAMEYQR 391


  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
   0.312    0.128    0.347 

Gapped
Lambda     K      H
   0.267   0.0706    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,031,269
Number of extensions: 95380
Number of successful extensions: 182
Number of sequences better than 10.0: 1
Number of HSP's gapped: 180
Number of HSP's successfully gapped: 16
Length of query: 195
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 106
Effective length of database: 4,340,536
Effective search space: 460096816
Effective search space used: 460096816
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (25.0 bits)