RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781219|ref|YP_003065632.1| hypothetical protein
CLIBASIA_05630 [Candidatus Liberibacter asiaticus str. psy62]
         (200 letters)



>gnl|CDD|31918 COG1732, OpuBC, Periplasmic glycine betaine/choline-binding
           (lipo)protein of an ABC-type transport system
           (osmoprotectant binding protein) [Cell envelope
           biogenesis, outer membrane].
          Length = 300

 Score = 27.9 bits (62), Expect = 2.2
 Identities = 8/51 (15%), Positives = 21/51 (41%), Gaps = 8/51 (15%)

Query: 29  YSPESYSNTYREQKLRDKIIELRRKFAKENGLKTVTEVCPKPKDITYSLSH 79
             P  ++NTY         + +R+  A++  L+T++++      +      
Sbjct: 129 LKPAGFNNTY--------ALAVRKDVAEKYNLETISDLAKHSNQLKLGADS 171


>gnl|CDD|145760 pfam02776, TPP_enzyme_N, Thiamine pyrophosphate enzyme, N-terminal
           TPP binding domain. 
          Length = 172

 Score = 27.2 bits (61), Expect = 3.3
 Identities = 12/50 (24%), Positives = 21/50 (42%), Gaps = 7/50 (14%)

Query: 143 ALIRYLEDFYKEIKHTFGNPADALSPHISELADEIHTTCFTLQFVVNPSE 192
           AL   L+     + H FG P  ++ P +  LA         +++V+   E
Sbjct: 6   ALAEALKAL--GVDHVFGVPGGSILPLLDALAKS-----PGIRYVLVRHE 48


>gnl|CDD|36613 KOG1399, KOG1399, KOG1399, Flavin-containing monooxygenase
           [Secondary metabolites biosynthesis, transport and
           catabolism].
          Length = 448

 Score = 26.9 bits (59), Expect = 4.2
 Identities = 11/47 (23%), Positives = 17/47 (36%)

Query: 110 LHDKLNKILKKSVRNYSRDSGHLNRDVIFHSRYALIRYLEDFYKEIK 156
           ++  L   L K +  YS           F S   ++ YL D+ K   
Sbjct: 58  VYKSLRTNLPKEMMGYSDFPFPERDPRYFPSHREVLEYLRDYAKHFD 104


>gnl|CDD|31075 COG0731, COG0731, Fe-S oxidoreductases [Energy production and
           conversion].
          Length = 296

 Score = 26.8 bits (59), Expect = 4.3
 Identities = 21/70 (30%), Positives = 30/70 (42%), Gaps = 7/70 (10%)

Query: 135 DVIFHSRYALIRYLEDFYKEIKH-TF---GNPADALSPHISELADEIH-TTCFTLQFVVN 189
           + I      L+ Y  D   E  H T    G P   L P++ EL +EI      T   V N
Sbjct: 60  ESILEELKLLLGYKGDEATEPDHVTISLSGEPT--LYPNLGELIEEIKKRGKKTTFLVTN 117

Query: 190 PSEAELLEKV 199
            S  ++LE++
Sbjct: 118 GSLPDVLEEL 127


>gnl|CDD|153437 cd07968, OBF_DNA_ligase_IV, The Oligonucleotide/oligosaccharide
           binding (OB)-fold domain of ATP-dependent DNA ligase IV
           is a DNA-binding module that is part of the catalytic
           core unit.  ATP-dependent polynucleotide ligases
           catalyze phosphodiester bond formation using nicked
           nucleic acid substrates with the high energy nucleotide
           of ATP as a cofactor in a three step reaction mechanism.
           DNA ligases play a vital role in the diverse processes
           of DNA replication, recombination and repair.
           ATP-dependent ligases are present in many organisms such
           as viruses, bacteriohages, eukarya, archaea and
           bacteria. There are three classes of ATP-dependent DNA
           ligases in eukaryotic cells (I, III and IV). DNA ligase
           IV is required for DNA non-homologous end joining
           pathways, including recombination of the V(D)J
           immunoglobulin gene segments in cells of the mammalian
           immune system. DNA ligase IV is stabilized by forming a
           complex with XRCC4, a nuclear phosphoprotein, which is
           phosphorylated by DNA-dependent protein kinase. DNA
           ligases have a highly modular architecture consisting of
           a unique arrangement of two or more discrete domains.
           The adenylation and C-terminal
           oligouncleotide/oligosaccharide binding (OB)-fold
           domains comprise a catalytic core unit that is common to
           most members of the ATP-dependent DNA ligase family. The
           catalytic core unit contains six conserved sequence
           motifs (I, III, IIIa, IV, V and VI) that define this
           family of related nucleotidyltransferases. The OB-fold
           domain contacts the nicked DNA substrate and is required
           for the ATP-dependent DNA ligase nucleotidylation step.
           The RxDK motif (motif VI), which is essential for ATP
           hydrolysis, is located in the OB-fold domain.
          Length = 140

 Score = 26.4 bits (59), Expect = 5.5
 Identities = 12/56 (21%), Positives = 26/56 (46%), Gaps = 6/56 (10%)

Query: 77  LSHFIEGLIESERSKITEKFKPLAVAKVVS----DELLHDKLNKILKKSVRNYSRD 128
           +S F+ G+ E +  +  +     +  KV S    +EL  D++ + LK   + + + 
Sbjct: 22  VSSFLCGVAEDDDPESDKPSVFYSFCKVGSGFSDEEL--DEIRRKLKPHWKPFDKK 75


>gnl|CDD|163692 cd08061, MPN_NPL4, Mov34/MPN/PAD-1 family: nuclear protein
           localization-4 (Npl4) domain.  Npl4p (nuclear protein
           localization-4) is identical to Hmg-CoA reductase
           degradation 4 (HRD4) protein and contains a domain that
           is part of the pfam clan MPN/Mov34-like. Npl4 plays an
           intermediate role between endoplasmic
           reticulum-associated degradation (ERAD) substrate
           ubiquitylation and proteasomal degradation. Npl4p
           associates with Cdc48p (Cdc48 in yeast and p97 or
           valosin-containing protein (VCP) in higher eukaryotes),
           the highly conserved ATPase of the AAA family, via
           ubiquitin fusion degradation-1 protein (Ufd1p) to form a
           Cdc48p-Ufd1p-Npl4p complex which then functions in the
           recognition of several polyubiquitin-tagged proteins and
           facilitates their presentation to the 26S proteasome for
           processive degradation. This family of eukaryotic
           MPN-like domains lacks the key residues that coordinate
           a metal ion and therefore does not show catalytic
           isopeptidase activity.
          Length = 274

 Score = 26.2 bits (58), Expect = 5.8
 Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 5/58 (8%)

Query: 25  CEALYSPESYSNTYREQKLRDKIIELRRKFAKENGLKTV----TEVCPKPKDITYSLS 78
            EA+Y P         + L D   +     A   GL+ V    T++  + KD  Y LS
Sbjct: 58  VEAIYEPPQEGTPDGFELLEDPNADTVDAIAAALGLERVGWIFTDLPREDKD-GYFLS 114


>gnl|CDD|63877 cd04408, RhoGAP_GMIP, RhoGAP_GMIP: RhoGAP (GTPase-activator
          protein [GAP] for Rho-like small GTPases) domain of
          GMIP (Gem interacting protein). GMIP plays important
          roles in neurite growth and axonal guidance, and
          interacts with Gem, a member of the RGK subfamily of
          the Ras small GTPase superfamily, through the
          N-terminal half of the protein. GMIP contains a
          C-terminal RhoGAP domain. GMIP inhibits RhoA function,
          but is inactive towards Rac1 and Cdc41. Small GTPases
          cluster into distinct families, and all act as
          molecular switches, active in their GTP-bound form but
          inactive when GDP-bound. The Rho family of GTPases
          activates effectors involved in a wide variety of
          developmental processes, including regulation of
          cytoskeleton formation, cell proliferation and the JNK
          signaling pathway. GTPases generally have a low
          intrinsic GTPase hydrolytic activity but there are
          family-specific groups of GAPs that enhance the rate of
          GTP hydrolysis by several orders of magnitude..
          Length = 200

 Score = 26.1 bits (57), Expect = 7.6
 Identities = 21/81 (25%), Positives = 33/81 (40%), Gaps = 3/81 (3%)

Query: 8  QFKNYLHEDVKFYLDKWCEALYSPE-SYSNTYREQKLRDKIIELRRKFAKENGLKTVTEV 66
          Q      E+V F + +    + +        YR    + ++ +L + F  ENG   V   
Sbjct: 7  QLPRDFPEEVPFVVVRCTAEIENRALGVQGIYRISGSKARVEKLCQAF--ENGRDLVDLS 64

Query: 67 CPKPKDITYSLSHFIEGLIES 87
             P DIT  L HF++ L E 
Sbjct: 65 GHSPHDITSVLKHFLKELPEP 85


>gnl|CDD|145366 pfam02171, Piwi, Piwi domain.  This domain is found in the protein
           Piwi and its relatives. The function of this domain is
           the dsRNA guided hydrolysis of ssRNA. Determination of
           the crystal structure of Argonaute reveals that PIWI is
           an RNase H domain, and identifies Argonaute as Slicer,
           the enzyme that cleaves mRNA in the RNAi RISC complex.
           In addition, Mg+2 dependence and production of 3'-OH and
           5' phosphate products are shared characteristics of
           RNaseH and RISC. The PIWI domain core has a tertiary
           structure belonging to the RNase H family of enzymes.
           RNase H fold proteins all have a five-stranded mixed
           beta-sheet surrounded by helices. By analogy to RNase H
           enzymes which cleave single-stranded RNA guided by the
           DNA strand in an RNA/DNA hybrid, the PIWI domain can be
           inferred to cleave single-stranded RNA, for example
           mRNA, guided by double stranded siRNA.
          Length = 296

 Score = 25.7 bits (57), Expect = 7.9
 Identities = 8/36 (22%), Positives = 18/36 (50%)

Query: 104 VVSDELLHDKLNKILKKSVRNYSRDSGHLNRDVIFH 139
             S + L + L  I+K+S+R++ +        +I +
Sbjct: 113 QASGQELIESLKDIIKESLRSFYKSRKKKPERIIIY 148


  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
   0.318    0.135    0.387 

Gapped
Lambda     K      H
   0.267   0.0737    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,453,725
Number of extensions: 127267
Number of successful extensions: 447
Number of sequences better than 10.0: 1
Number of HSP's gapped: 447
Number of HSP's successfully gapped: 30
Length of query: 200
Length of database: 6,263,737
Length adjustment: 89
Effective length of query: 111
Effective length of database: 4,340,536
Effective search space: 481799496
Effective search space used: 481799496
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: 55 (24.9 bits)