RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780357|ref|YP_003064770.1| hypothetical protein
CLIBASIA_01210 [Candidatus Liberibacter asiaticus str. psy62]
         (394 letters)



>gnl|CDD|146422 pfam03772, Competence, Competence protein.  Members of this family
           are integral membrane proteins with 6 predicted
           transmembrane helices. Some members of this family have
           been shown to be essential for bacterial competence in
           uptake of extracellular DNA. These proteins may
           transport DNA across the cell membrane. These proteins
           contain a highly conserved motif in the amino terminal
           transmembrane region that has two histidines that may
           form a metal binding site.
          Length = 270

 Score = 55.7 bits (135), Expect = 2e-08
 Identities = 23/94 (24%), Positives = 47/94 (50%), Gaps = 2/94 (2%)

Query: 103 HFHCIPVYGLIANILAIPILSFVVIPAGLIAILLMILSLDNIPFG-VMAWGLDIIIHIAH 161
           HF    +  L+AN+LA+P++SFVV+P  L+A+LL +          +  W L++++ +  
Sbjct: 174 HFGQFSLVSLLANLLAVPLVSFVVLPLALLALLLSLFPPLAALLLWLADWLLELLLALLE 233

Query: 162 RIS-VAHNEFCIGRIPETSFVTIVVEFLLMVFCK 194
            ++ +      +GR      +   +  LL++   
Sbjct: 234 WLASLPGASLWVGRPSLWLLLLYYLLLLLLLLLL 267


>gnl|CDD|31236 COG1033, COG1033, Predicted exporters of the RND superfamily
           [General function prediction only].
          Length = 727

 Score = 34.8 bits (80), Expect = 0.045
 Identities = 31/132 (23%), Positives = 49/132 (37%), Gaps = 13/132 (9%)

Query: 112 LIANILAIPILSFVVIPAGLIAILLMILSLDNIPFG--VMAWGLDIIIHIAHRISVAHNE 169
           L A I  IPI   V    GL+ +L + L+      G  ++  G+D  IHI  R      +
Sbjct: 593 LKAIIPLIPIAIVVGWNFGLMGLLGIPLTPATATLGAIILGIGVDYSIHITERYREERKK 652

Query: 170 FC-----------IGRIPETSFVTIVVEFLLMVFCKTNIRHIGSIMIGITIIILFTFPYS 218
                         G+    S +T  + FL ++F    I     ++  I I++       
Sbjct: 653 GGPKEAIETTVERTGKAILASALTTAIGFLALIFSPFPIISNFGLLTVIGILLSLLASLV 712

Query: 219 FSPDLLISEKGN 230
             P LL+   G 
Sbjct: 713 LLPALLVLLDGR 724


>gnl|CDD|48241 cd03345, eu_TyrOH, Eukaryotic tyrosine hydroxylase (TyrOH); a
          member of the biopterin-dependent aromatic amino acid
          hydroxylase family of non-heme, iron(II)-dependent
          enzymes that also includes prokaryotic and eukaryotic
          phenylalanine-4-hydroxylase (PheOH) and eukaryotic
          tryptophan hydroxylase (TrpOH). TyrOH catalyzes the
          conversion of tyrosine to L-dihydroxyphenylalanine
          (L-DOPA), the rate-limiting step in the biosynthesis of
          the catecholamines dopamine, noradrenaline, and
          adrenaline..
          Length = 298

 Score = 28.4 bits (63), Expect = 3.4
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 4/53 (7%)

Query: 20 IARLSPPSGPAFPGLFDFNFSSYYKGISAIGYFYS----IPKMIYSSESHNTW 68
          + +  P      PG  D  +    K I+ I + Y     IP++ Y++E   TW
Sbjct: 16 VTKYEPDLDLDHPGFSDKVYRERRKLIAEIAFQYKHGDPIPRVEYTAEEIATW 68


>gnl|CDD|132746 cd06948, NR_LBD_COUP-TF, Ligand binding domain of chicken ovalbumin
           upstream promoter transcription factors, a member of the
           nuclear receptor family.  The ligand binding domain of
           chicken ovalbumin upstream promoter transcription
           factors (COUP-TFs): COUP-TFs are orphan members of the
           steroid/thyroid hormone receptor superfamily. They are
           expressed in many tissues and are involved in the
           regulation of several important biological processes,
           such as neurogenesis, organogenesis, cell fate
           determination, and metabolic homeostasis. In mammals two
           isoforms named COUP-TFI and COUP-TFII have been
           identified. Both genes show an exceptional homology and
           overlapping expression patterns, suggesting that they
           may serve redundant functions. Although COUP-TF was
           originally characterized as a transcriptional activator
           of the chicken ovalbumin gene, COUP-TFs are generally
           considered to be repressors of transcription for other
           nuclear hormone receptors, such as retinoic acid
           receptor (RAR), thyroid hormone receptor (TR), vitamin D
           receptor (VDR), peroxisome proliferator activated
           receptor (PPAR), and hepatocyte nuclear factor 4 (HNF4).
           Like other members of the nuclear receptor (NR)
           superfamily of ligand-activated transcription factors,
           COUP-TFs  have  a central well cons erved DNA binding
           domain (DBD), a variable N-terminal domain, a flexible
           hinge and a C-terminal ligand binding domain (LBD).
          Length = 236

 Score = 28.6 bits (64), Expect = 3.5
 Identities = 12/26 (46%), Positives = 18/26 (69%), Gaps = 3/26 (11%)

Query: 272 EDLQEKNQSSLKEILRSM---QPRKF 294
           E LQEK+Q +L+E +R+    QP +F
Sbjct: 158 ESLQEKSQCALEEYVRTQYPNQPTRF 183


>gnl|CDD|38206 KOG2996, KOG2996, KOG2996, Rho guanine nucleotide exchange factor
           VAV3 [Signal transduction mechanisms].
          Length = 865

 Score = 28.1 bits (62), Expect = 4.5
 Identities = 11/27 (40%), Positives = 16/27 (59%), Gaps = 2/27 (7%)

Query: 282 LKEILRSMQPRKFLCIK--KSFCVGCH 306
           LKEI    Q  +FLC+K  ++F + C 
Sbjct: 57  LKEINLRPQMSQFLCLKNIRTFLMFCC 83


>gnl|CDD|32610 COG2717, COG2717, Predicted membrane protein [Function unknown].
          Length = 209

 Score = 27.9 bits (62), Expect = 5.2
 Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 6/65 (9%)

Query: 77  KQSFLNEIRANIGTYGSASASIFLIKHFHCIPVYGLIANI--LAIPILSFVVIPAGLIAI 134
           KQ  L  IR  +G +    A  + + HF    V  L  ++  L + +L    I  G+IA 
Sbjct: 69  KQPKLIRIRRALGLW----AFFYALLHFTAYLVLDLGLDLALLGLDLLKRPYITIGMIAF 124

Query: 135 LLMIL 139
           LL+I 
Sbjct: 125 LLLIP 129


>gnl|CDD|133465 cd06855, GT_GPT_euk, UDP-GlcNAc:dolichol-P GlcNAc-1-P transferase
           (GPT) catalyzes the transfer of GlcNAc-1-P from
           UDP-GlcNAc to dolichol-P to form GlcNAc-P-P-dolichol.
           The reaction is the first step in the assembly of
           dolichol-linked oligosaccharide intermediates and is
           essential for eukaryotic N-glycosylation. GPT activity
           has been identified in all eukaryotic cells examined to
           date. A series of six conserved motifs designated A
           through F, ranging in length from 5 to 13 amino acid
           residues, has been identified in this family. They have
           been determined to be important for stable expression,
           substrate binding, or catalytic activities.
          Length = 283

 Score = 27.6 bits (62), Expect = 6.5
 Identities = 26/166 (15%), Positives = 55/166 (33%), Gaps = 39/166 (23%)

Query: 92  GSASASIFLIKHFHCIPVYGLIANILAIPILSFVVIPAGLIAILLMIL------------ 139
           G     +FLI     + ++     +   P    V   + L++I  M              
Sbjct: 31  GLVPGIVFLI----VLFLFIPFPFLKDFPHDKLVEYLSALLSICCMTFLGFADDVLDLRW 86

Query: 140 -------SLDNIPFGVMAWGLDIIIHIAHRISVAHNEFCIGRIPETSFVTIVVEFLLMVF 192
                  +  ++P  ++ +G   I        +      +G + +   +  V   LL VF
Sbjct: 87  RHKLILPTFASLPLLMVYYGNTGITLP-----IVPLRPLLGTLIDLGILYYVYMILLAVF 141

Query: 193 CKTNIRHI----------GSIMIGITIIILFTFPYSFSPDLLISEK 228
           C TN  +I           S++I ++I++      + S   +  + 
Sbjct: 142 C-TNSINIYAGINGLEVGQSLVIALSILLYNLLELNGSSGSMTLDA 186


>gnl|CDD|99971 cd03798, GT1_wlbH_like, This family is most closely related to the
           GT1 family of glycosyltransferases. wlbH in Bordetella
           parapertussis has been shown to be required for the
           biosynthesis of a trisaccharide that, when attached to
           the B. pertussis lipopolysaccharide (LPS) core (band B),
           generates band A LPS..
          Length = 377

 Score = 27.3 bits (61), Expect = 6.8
 Identities = 11/35 (31%), Positives = 13/35 (37%), Gaps = 2/35 (5%)

Query: 121 ILSFVVIPAGLIAILLMILSLDNIPFGVMAWGLDI 155
           I +    P G  A LL       IP  V   G D+
Sbjct: 97  IHAHFAYPDGFAAALLK--RKLGIPLVVTLHGSDV 129


>gnl|CDD|34310 COG4694, COG4694, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 758

 Score = 27.3 bits (60), Expect = 7.8
 Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 270 QKEDLQEKNQSSLKEILRSMQPRKFL-CIKKSFCVGCHRSDVIVGVLKRKDMIRL 323
              +L +KN+   KE L + + +KF   I K F      +  IVG+ K K+ I +
Sbjct: 159 CWRNLYKKNEERFKEYLENFKRKKFKRKILKEFENAKINASEIVGLEKVKEKIEI 213


>gnl|CDD|146838 pfam04401, DUF540, Protein of unknown function (DUF540).
           Uncharacterized bacterial integral membrane protein,
           possibly involved in cysteine biosynthesis. Speculated
           to be involved in sulphate transport.
          Length = 183

 Score = 26.8 bits (60), Expect = 9.7
 Identities = 8/27 (29%), Positives = 17/27 (62%)

Query: 111 GLIANILAIPILSFVVIPAGLIAILLM 137
            L+A +L+IP+++ +V P  +    L+
Sbjct: 156 LLVALLLSIPLVNLLVPPLAVAGATLL 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
   0.325    0.141    0.425 

Gapped
Lambda     K      H
   0.267   0.0748    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,974,780
Number of extensions: 276368
Number of successful extensions: 1028
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1022
Number of HSP's successfully gapped: 49
Length of query: 394
Length of database: 6,263,737
Length adjustment: 96
Effective length of query: 298
Effective length of database: 4,189,273
Effective search space: 1248403354
Effective search space used: 1248403354
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: 40 (21.6 bits)
S2: 58 (26.1 bits)