RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780876|ref|YP_003065289.1| hypothetical protein
CLIBASIA_03865 [Candidatus Liberibacter asiaticus str. psy62]
         (210 letters)



>gnl|CDD|100032 cd02196, PurM, PurM (Aminoimidazole Ribonucleotide [AIR]
           synthetase), one of eleven enzymes required for purine
           biosynthesis, catalyzes the conversion of
           formylglycinamide ribonucleotide (FGAM) and ATP to AIR,
           ADP, and Pi, the fifth step in de novo purine
           biosynthesis. The N-terminal domain of PurM is related
           to the ATP-binding domains of hydrogen
           expression/formation protein HypE, the AIR synthases,
           selenophosphate synthetase (SelD), and FGAM synthase and
           is thought to bind ATP..
          Length = 297

 Score = 30.5 bits (70), Expect = 0.34
 Identities = 8/37 (21%), Positives = 16/37 (43%), Gaps = 2/37 (5%)

Query: 34  YDSNGYDVKVRGTAQHIAERYSVLARDAMSAGDYVVA 70
           Y    YD+   G A  + E+  ++    +  GD ++ 
Sbjct: 111 YAEGEYDLA--GFAVGVVEKDKIIDGSKIKPGDVLIG 145


>gnl|CDD|36212 KOG0994, KOG0994, KOG0994, Extracellular matrix glycoprotein Laminin
            subunit beta [Extracellular structures].
          Length = 1758

 Score = 27.4 bits (60), Expect = 3.0
 Identities = 13/54 (24%), Positives = 22/54 (40%)

Query: 69   VAENHLQHAEHYNRIVSMAQAQIQEKLQRDEQDDLLVKEQKERAQNALSEFEAS 122
             A   L  A   +  +    A+ ++ L    +  L   E ++ AQ AL +  AS
Sbjct: 1409 RAGGALLMAGDADTQLRSKLAEAEQTLSMVREAKLSASEAQQSAQRALEQANAS 1462


>gnl|CDD|132735 cd06937, NR_LBD_RAR, The ligand binding domain (LBD) of retinoic
           acid receptor (RAR), a members of the nuclear receptor
           superfamily.  The ligand binding domain (LBD) of
           retinoic acid receptor (RAR): Retinoic acid receptors
           are members of the nuclear receptor (NR) superfamily of
           ligand-regulated transcription factors. RARs mediate the
           biological effect of retinoids, including both naturally
           dietary vitamin A (retinol) metabolites and active
           synthetic analogs. Retinoids play key roles in a wide
           variety of essential biological processes, such as
           vertebrate embryonic morphogenesis and organogenesis,
           differentiation and apoptosis, and homeostasis. RARs
           function as heterodimers with retinoic X receptors by
           binding to specific RAR response elements (RAREs) found
           in the promoter regions of retinoid target genes. In the
           absence of ligand, the RAR-RXR heterodimer recruits the
           corepressor proteins NCoR or AMRT, and associated
           factors such as histone deacetylases or
           DNA-methyltransferases, leading to an inactive condensed
           chromatin structure, preventing transcription. Upon
           ligand binding, the corepressors are released, and
           coactivator complexes such as histone acetyltransferase
           or histone arginine methyltransferases are recruited to
           activate transcription. There are three RAR subtypes
           (alpha, beta, gamma), originating from three distinct
           genes. For each subtype, several isoforms exist that
           differ in their N-terminal region, allowing retinoids to
           exert their pleiotropic effects. Like other members of
           the nuclear receptor (NR) superfamily of
           ligand-activated transcription factors, retinoic acid
           receptors have a central well conserved DNA binding
           domain (DBD), a variable N-terminal domain, a
           non-conserved hinge and a C-terminal ligand binding
           domain (LBD).
          Length = 231

 Score = 26.7 bits (59), Expect = 4.7
 Identities = 7/13 (53%), Positives = 10/13 (76%)

Query: 164 VRRRRPLRPRVFP 176
            R+RRP +P +FP
Sbjct: 178 ARKRRPDKPHMFP 190


>gnl|CDD|113294 pfam04518, DUF582, Protein of unknown function, DUF582.  This
           family contains several uncharacterized chlamydial
           proteins.
          Length = 380

 Score = 26.5 bits (59), Expect = 5.7
 Identities = 10/36 (27%), Positives = 18/36 (50%)

Query: 87  AQAQIQEKLQRDEQDDLLVKEQKERAQNALSEFEAS 122
           A+A + + L R + D  L  EQK    + L+ +  +
Sbjct: 223 AKAVLNKLLARIKADAKLTSEQKSELLDTLNNYTDN 258


>gnl|CDD|146600 pfam04053, Coatomer_WDAD, Coatomer WD associated region.  This
           region is composed of WD40 repeats.
          Length = 435

 Score = 26.4 bits (59), Expect = 6.6
 Identities = 8/26 (30%), Positives = 15/26 (57%)

Query: 57  LARDAMSAGDYVVAENHLQHAEHYNR 82
           L   A+S G+  +AE   Q A+ +++
Sbjct: 345 LGDAALSQGNIKLAEEAYQKAKDFDK 370


>gnl|CDD|147657 pfam05605, Di19, Drought induced 19 protein (Di19).  This family
           consists of several drought induced 19 (Di19) like
           proteins. Di19 has been found to be strongly expressed
           in both the roots and leaves of Arabidopsis thaliana
           during progressive drought. The precise function of Di19
           is unknown.
          Length = 210

 Score = 26.3 bits (58), Expect = 7.4
 Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 3/30 (10%)

Query: 91  IQEKLQRDEQ-DDLLVKEQKERAQNALSEF 119
            Q+  +R+ Q   L  +EQ+E+A+   SEF
Sbjct: 174 DQKLSERNSQDSSLSKEEQEEKAKR--SEF 201


>gnl|CDD|147546 pfam05416, Peptidase_C37, Southampton virus-type processing
           peptidase.  Corresponds to Merops family C37.
           Norwalk-like viruses (NLVs), including the Southampton
           virus, cause acute non-bacterial gastroenteritis in
           humans. The NLV genome encodes three open reading frames
           (ORFs). ORF1 encodes a polyprotein, which is processed
           by the viral protease into six proteins.
          Length = 535

 Score = 26.0 bits (57), Expect = 8.2
 Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 110 ERAQNALSEFEASPCPLIEEGKEPIFENSIQ--PKVEDVAFKTPDISREKDVSYKKVRRR 167
           E  ++AL +++ +PC +I  G      +  +    VE V   TP +  E   + +++R  
Sbjct: 98  EELKHALKDYKIAPCQIIYRGATYSVSSDGKGNVSVEKVLVTTPQLVNELSNALRRLRAA 157

Query: 168 R 168
           R
Sbjct: 158 R 158


>gnl|CDD|34155 COG4477, EzrA, Negative regulator of septation ring formation [Cell
           division and chromosome partitioning].
          Length = 570

 Score = 25.6 bits (56), Expect = 9.1
 Identities = 19/82 (23%), Positives = 34/82 (41%), Gaps = 4/82 (4%)

Query: 41  VKVRGTAQHIAERYS----VLARDAMSAGDYVVAENHLQHAEHYNRIVSMAQAQIQEKLQ 96
             VR   + + E  S    +L         Y   +++L+  E     +   Q ++QE L 
Sbjct: 347 GSVRKFEKELKELESVLDEILENIEAQEVAYSELQDNLEEIEKALTDIEDEQEKVQEHLT 406

Query: 97  RDEQDDLLVKEQKERAQNALSE 118
              +D+L  +E  ER ++ L E
Sbjct: 407 SLRKDELEARENLERLKSKLHE 428


  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    0.356 

Gapped
Lambda     K      H
   0.267   0.0522    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,353,413
Number of extensions: 115241
Number of successful extensions: 252
Number of sequences better than 10.0: 1
Number of HSP's gapped: 252
Number of HSP's successfully gapped: 28
Length of query: 210
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 120
Effective length of database: 4,318,927
Effective search space: 518271240
Effective search space used: 518271240
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 (21.8 bits)
S2: 55 (25.4 bits)