RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780417|ref|YP_003064830.1| transcriptional regulator CarD
family protein [Candidatus Liberibacter asiaticus str. psy62]
         (188 letters)



>gnl|CDD|31520 COG1329, COG1329, Transcriptional regulators, similar to M. xanthus
           CarD [Transcription].
          Length = 166

 Score =  192 bits (489), Expect = 6e-50
 Identities = 80/165 (48%), Positives = 112/165 (67%)

Query: 11  RQGFRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAFDKDKMCLKVPVGKAIDIGMR 70
           +  F+ G+H+VYPAHGVG I  I+E+E+AG  LE++VI F +  M + VPV KA  +G+R
Sbjct: 2   QMAFKIGDHVVYPAHGVGIIQAIEEKEIAGETLEYYVIDFPQSDMTVMVPVAKADSVGLR 61

Query: 71  KLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPE 130
            + +   ++RAL++++G  R K TMWSRR +E + K+ SGD+I IAEVVRDL+R D Q E
Sbjct: 62  PVVDQEELDRALQVLQGGEREKPTMWSRRYKENEEKLKSGDIIDIAEVVRDLYRRDKQRE 121

Query: 131 KSYSERQLYESALNRMVREIAAVNSISEPEAINLIEVNLSSKSSK 175
            SYSER+L E AL  +  E+A    ISE EA   ++  L+SKS  
Sbjct: 122 LSYSERRLLEKALQILAGELALAEGISEEEAKTFLDEVLASKSEA 166


>gnl|CDD|145606 pfam02559, CarD_TRCF, CarD-like/TRCF domain.  CarD is a Myxococcus
           xanthus protein required for the activation of light-
           and starvation-inducible genes. This family includes the
           presumed N-terminal domain. CarD interacts with the
           zinc-binding protein CarG, to form a complex that
           regulates multiple processes in Myxococcus xanthus. This
           family also includes a domain to the N-terminal side of
           the DEAD helicase of TRCF proteins. TRCF displaces RNA
           polymerase stalled at a lesion, binds to the damage
           recognition protein UvrA, and increases the template
           strand repair rate during transcription. This domain is
           involved in binding to the stalled RNA polymerase.
          Length = 98

 Score = 77.9 bits (193), Expect = 1e-15
 Identities = 37/111 (33%), Positives = 55/111 (49%), Gaps = 15/111 (13%)

Query: 14  FRTGEHIVYPAHGVGTITEIKEQEVAGMKLEFFVIAF-DKDKMCLKVPVGKAIDIGMRKL 72
            + G+++V+P HGVG    I+  EV G K E++V+ + D DK  L VPV +   IG    
Sbjct: 2   LKVGDYVVHPDHGVGRFEGIETIEVGGEKREYYVLEYADGDK--LYVPVDQLDLIGRYIG 59

Query: 73  SEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLH 123
           SE          V    ++    W +R +    KI SGD+   AE++R L 
Sbjct: 60  SEDE--------VPVLDKLGGGTWKKRKR----KIKSGDIDIAAELLRLLA 98


>gnl|CDD|146817 pfam04373, DUF511, Protein of unknown function (DUF511).  Bacterial
           protein of unknown function.
          Length = 310

 Score = 28.8 bits (65), Expect = 0.93
 Identities = 12/73 (16%), Positives = 27/73 (36%), Gaps = 3/73 (4%)

Query: 67  IGMRKLSEAHFVERALKLVRGKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTD 126
           IG  +   A   +++  +   +   +R     R  E + K          E   +  + +
Sbjct: 47  IGSDRKELA---KKSPFIKTQEKPPRRYYLKSREDELELKALDEIKSEEDEEQSEAPKAN 103

Query: 127 SQPEKSYSERQLY 139
            + + S+ ER L+
Sbjct: 104 KKQKNSFHERDLH 116


>gnl|CDD|133181 cd05050, PTKc_Musk, Catalytic domain of the Protein Tyrosine
           Kinase, Muscle-specific kinase.  Protein Tyrosine Kinase
           (PTK) family; Muscle-specific kinase (Musk); catalytic
           (c) domain. The PTKc family is part of a larger
           superfamily that includes the catalytic domains of other
           kinases such as protein serine/threonine kinases, RIO
           kinases, and phosphoinositide 3-kinase (PI3K). PTKs
           catalyze the transfer of the gamma-phosphoryl group from
           ATP to tyrosine (tyr) residues in protein substrates.
           Musk is a receptor tyr kinase (RTK) containing an
           extracellular region with four immunoglobulin-like
           domains and a cysteine-rich cluster, a transmembrane
           segment, and an intracellular catalytic domain. Musk is
           expressed and concentrated in the postsynaptic membrane
           in skeletal muscle. It is essential for the
           establishment of the neuromuscular junction (NMJ), a
           peripheral synapse that conveys signals from motor
           neurons to muscle cells. Agrin, a large proteoglycan
           released from motor neurons, stimulates Musk
           autophosphorylation and activation, leading to the
           clustering of acetylcholine receptors (AChRs). To date,
           there is no evidence to suggest that agrin binds
           directly to Musk. Mutations in AChR, Musk and other
           partners are responsible for diseases of the NMJ, such
           as the autoimmune syndrome myasthenia gravis.
          Length = 288

 Score = 28.3 bits (63), Expect = 1.4
 Identities = 21/69 (30%), Positives = 29/69 (42%), Gaps = 15/69 (21%)

Query: 58  KVPVGKAIDIGMRKLSEAHFVERALK----LVRGKARVK-------RTMWSRRAQEYDAK 106
           ++ + K +  GM  LSE  FV R L     LV     VK       R ++S    +Y  K
Sbjct: 132 QLCIAKQVAAGMAYLSERKFVHRDLATRNCLVGENMVVKIADFGLSRNIYS---ADY-YK 187

Query: 107 INSGDLIAI 115
            +  D I I
Sbjct: 188 ASENDAIPI 196


>gnl|CDD|37497 KOG2286, KOG2286, KOG2286, Exocyst complex subunit SEC6
           [Intracellular trafficking, secretion, and vesicular
           transport].
          Length = 667

 Score = 26.4 bits (58), Expect = 4.8
 Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 2/65 (3%)

Query: 87  GKARVKRTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRM 146
           GK R     W  R  E    +   DL     V+            +Y E  LY  AL+ +
Sbjct: 225 GKMRALNKEWQVRLLEVLRFVIREDLRVAKRVLVPCFPPHYNIFSAYLE--LYHQALSDL 282

Query: 147 VREIA 151
           +R++A
Sbjct: 283 LRDLA 287


>gnl|CDD|34458 COG4849, COG4849, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 269

 Score = 26.2 bits (57), Expect = 5.5
 Identities = 10/56 (17%), Positives = 22/56 (39%)

Query: 93  RTMWSRRAQEYDAKINSGDLIAIAEVVRDLHRTDSQPEKSYSERQLYESALNRMVR 148
           +  W+ R  +YD +  +  L+ +       H +  Q     +     E+A+   +R
Sbjct: 185 KPQWALRRHDYDLETAAAALLGLDVASVASHESKRQIVDMRASVSAPEAAVLATLR 240


>gnl|CDD|35272 KOG0049, KOG0049, KOG0049, Transcription factor, Myb superfamily
           [Transcription].
          Length = 939

 Score = 25.9 bits (56), Expect = 6.3
 Identities = 11/39 (28%), Positives = 19/39 (48%), Gaps = 1/39 (2%)

Query: 122 LHRTDSQPEKSYSERQLYESALNRMVREIAAVNSISEPE 160
           + R       +  +R+ +E  L  ++R+IA V   SE E
Sbjct: 174 VARDADITSSNL-DRRQWEMELEDLMRKIAYVREKSEEE 211


>gnl|CDD|30725 COG0376, KatG, Catalase (peroxidase I) [Inorganic ion transport and
           metabolism].
          Length = 730

 Score = 26.1 bits (57), Expect = 6.4
 Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 3/32 (9%)

Query: 88  KARVKRTMWSRRAQEYDAKINSGDLIAIAEVV 119
           KAR  R +W  + ++Y  KI+  DLI +A  V
Sbjct: 139 KAR--RLLWPIK-KKYGRKISWADLIILAGNV 167


>gnl|CDD|145380 pfam02194, PXA, PXA domain.  This domain is associated with PX
           domains pfam00787.
          Length = 182

 Score = 25.7 bits (57), Expect = 7.8
 Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 7/35 (20%)

Query: 146 MVREIAA-------VNSISEPEAINLIEVNLSSKS 173
           ++REI A       V+ +S+P+ IN + + L   S
Sbjct: 148 LLREILACAVLLPLVSKLSDPDFINQLIIKLIETS 182


  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
   0.315    0.129    0.348 

Gapped
Lambda     K      H
   0.267   0.0774    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,014,637
Number of extensions: 96693
Number of successful extensions: 236
Number of sequences better than 10.0: 1
Number of HSP's gapped: 235
Number of HSP's successfully gapped: 23
Length of query: 188
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 100
Effective length of database: 4,362,145
Effective search space: 436214500
Effective search space used: 436214500
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 (21.6 bits)
S2: 54 (24.5 bits)