RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781213|ref|YP_003065626.1| head-to-tail joining protein,
putative [Candidatus Liberibacter asiaticus str. psy62]
         (556 letters)



>gnl|CDD|147306 pfam05056, DUF674, Protein of unknown function (DUF674).  This
           family is found in Arabidopsis thaliana and contains
           several uncharacterized proteins.
          Length = 462

 Score = 30.6 bits (69), Expect = 1.1
 Identities = 11/29 (37%), Positives = 16/29 (55%)

Query: 113 RSRSGFVGCLQSFYTSVVEFGTGCFYMEA 141
           +S+   +GC  + Y SVV+ G   F  EA
Sbjct: 56  KSQPVTIGCFNNLYKSVVDMGIDNFETEA 84


>gnl|CDD|99967 cd03793, GT1_Glycogen_synthase_GSY2_like, Glycogen synthase, which
           is most closely related to the GT1 family of
           glycosyltransferases, catalyzes the transfer of a
           glucose molecule from UDP-glucose to a terminal branch
           of a glycogen molecule, a rate-limit step of glycogen
           biosynthesis. GSY2, the member of this family in S.
           cerevisiae, has been shown to possess glycogen synthase
           activity..
          Length = 590

 Score = 30.0 bits (68), Expect = 2.0
 Identities = 10/30 (33%), Positives = 15/30 (50%)

Query: 86  LYKEDARSKKVREWCDQVTDTLFGFRERSR 115
           +Y  D R K   E   Q+T  ++ F + SR
Sbjct: 525 IYIVDRRFKSPDESVQQLTQYMYEFCQLSR 554


>gnl|CDD|33095 COG3285, COG3285, Predicted eukaryotic-type DNA primase [DNA
           replication, recombination, and repair].
          Length = 299

 Score = 29.9 bits (67), Expect = 2.1
 Identities = 20/84 (23%), Positives = 29/84 (34%), Gaps = 10/84 (11%)

Query: 241 VDENRFFEEKQIATFPYIVGRYRVRADEIYGRSPAMEALPTIRRLNETVNELAQFGRLSL 300
           +    FF++      P  V   RV        S   +    I      +  LAQ G L  
Sbjct: 58  IGGEAFFQKHAPRGAPPWVQTVRV-----TKDSGRTKPYLVIDDA-AGLAWLAQQGALEF 111

Query: 301 HPPTIAVSEAKQRN----FDLKPG 320
           HP    + + +  +    FDL PG
Sbjct: 112 HPWGATIDDLEHPDERIVFDLDPG 135


>gnl|CDD|173958 cd08199, EEVS, 2-epi-5-epi-valiolone synthase (EEVS).
           2-epi-5-epi-valiolone synthases catalyze the cyclization
           of sedoheptulose 7-phosphate to 2-epi-5-epi-valiolone in
           the biosynthesis of C(7)N-aminocyclitol-containing
           products. The cyclization product, 2-epi-5-epi-valiolone
           ((2S,3S,4S,5R)-5-(hydroxymethyl)cyclohexanon-2,3,4,
           5-tetrol), is a precursor of the valienamine moiety. The
           valienamine unit is responsible for their biological
           activities as various glycosidic hydrolases inhibitors. 
           Two important microbial secondary metabolites, i.e.,
           validamycin and acarbose, are used in agricultural and
           biomedical applications. Validamycine A is an antifungal
           antibiotic which has a strong trehalase inhibitory
           activity and has been used to control sheath blight
           disease in rice caused by Rhizoctonia solani. Acarbose
           is an alpha-glucosidase inhibitor used for the treatment
           of type II insulin-independent diabetes.  Salbostatin
           produced by Streptomyces albus also belongs to this
           family.  It exhibits strong trehalase inhibitory
           activity.
          Length = 354

 Score = 28.8 bits (65), Expect = 4.7
 Identities = 20/86 (23%), Positives = 31/86 (36%), Gaps = 24/86 (27%)

Query: 232 KGFHSKFVSVDEN----------RFFEEKQIATFPYIVGRYRVRADEIYGRSPAMEALPT 281
           +G   +FV VD+N           +F    I     +V R             A EA  T
Sbjct: 24  EGSGRRFVVVDQNVDKLYGKKLREYFAHHNI-PLTILVLR-------------AGEAAKT 69

Query: 282 IRRLNETVNELAQFGRLSLHPPTIAV 307
           +  + + V+ L  FG      P +A+
Sbjct: 70  MDTVLKIVDALDAFGISRRREPVLAI 95


>gnl|CDD|147186 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
           This family represents Cwf15/Cwc15 (from
           Schizosaccharomyces pombe and Saccharomyces cerevisiae
           respectively) and their homologues. The function of
           these proteins is unknown, but they form part of the
           spliceosome and are thus thought to be involved in mRNA
           splicing.
          Length = 241

 Score = 28.5 bits (64), Expect = 5.4
 Identities = 7/33 (21%), Positives = 19/33 (57%)

Query: 501 AEVEDIRQQREVQRRVMEEQHLQQQLQQTSQDI 533
            E+E I+++R  ++   EE+   ++ +   ++I
Sbjct: 149 RELEKIKKERAEEKEREEEEKAAEEEKAREEEI 181


>gnl|CDD|38725 KOG3516, KOG3516, KOG3516, Neurexin IV [Signal transduction
           mechanisms].
          Length = 1306

 Score = 28.4 bits (63), Expect = 6.0
 Identities = 13/62 (20%), Positives = 25/62 (40%), Gaps = 8/62 (12%)

Query: 71  KWHGLAESFSAYQAFLYKEDARSKKVRE-------WCDQVTDTLFGFRERSRSGFVGCLQ 123
           +WH +    ++ +A L + D   K +R             +    G     + GF+GC++
Sbjct: 871 QWHQVRAERNSKEASL-QVDGLPKSIRTSPIPGTRLLQLYSSLFVGGTVSRQRGFLGCIR 929

Query: 124 SF 125
           S 
Sbjct: 930 SL 931


>gnl|CDD|132748 cd06950, NR_LBD_Tlx_PNR_like, The ligand binding domain of
           Tailless-like proteins,  orphan nuclear receptors.  The
           ligand binding domain of the photoreceptor cell-specific
           nuclear receptor (PNR)  like family: This family
           includes photoreceptor cell-specific nuclear receptor
           (PNR), Tailless (TLX), and related receptors. TLX is an
           orphan receptor that is expressed by neural
           stem/progenitor cells in the adult brain of the
           subventricular zone (SVZ) and the dentate gyrus (DG). It
           plays a key role in neural development by promoting cell
           cycle progression and preventing apoptosis in the
           developing brain. PNR is expressed only in the outer
           layer of retinal photoreceptor cells. It may be involved
           in the signaling pathway regulating photoreceptor
           differentiation and/or maintenance. Like other members
           of the nuclear receptor (NR) superfamily of
           ligand-activated transcription factors, TLX and PNR
           have  a central well conserved DNA binding domain (DBD),
           a variable N-terminal domain, a flexible hinge and a
           C-terminal ligand binding domain (LBD).
          Length = 206

 Score = 28.4 bits (64), Expect = 6.0
 Identities = 11/24 (45%), Positives = 15/24 (62%)

Query: 344 LPYHEELNRLKESIRSLFLLDLFQ 367
           LP+ ++L  L+ES   LFLL   Q
Sbjct: 55  LPFRDQLILLEESWSELFLLGAAQ 78


>gnl|CDD|37150 KOG1939, KOG1939, KOG1939, Oxoprolinase [Amino acid transport and
           metabolism].
          Length = 1247

 Score = 28.0 bits (62), Expect = 6.5
 Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 8/58 (13%)

Query: 140 EADVDEKGL--------EEGIRYISVPLSNVYMSVNHQNVVDSVYREFTFTVDQIVSK 189
           E  VDE+ L        ++G++ I+V L + Y   +H+  V  + +E  F+   + SK
Sbjct: 162 EKKVDEEALRQDLKELYDKGVKSIAVVLLHSYTYPDHELEVGKIAKEIGFSHVSLSSK 219


>gnl|CDD|80311 cd04861, LigD_Pol_like, LigD_Pol_like: Polymerase (Pol) domain of
           bacterial LigD proteins similar to Pseudomonas
           aeruginosa (Pae) LigD. The LigD Pol domain belongs to
           the archaeal/eukaryal primase (AEP) superfamily. In
           prokaryotes, LigD along with Ku is required for
           non-homologous end joining (NHEJ)-mediated repair of DNA
           double-strand breaks (DSB). NHEJ-mediated DNA DSB repair
           is error-prone. PaeLigD is monomeric, containing an
           N-terminal phosphoesterase module, a central polymerase
           (Pol) domain, and a C-terminal ATP-dependent ligase
           domain. Mycobacterium tuberculosis (Mt)LigD, also found
           in this group, is monomeric and contains the same
           modules but these are arranged differently: an
           N-terminal Pol domain, a central phosphoesterase module,
           and a C-terminal ligase domain. It has been suggested
           that LigD Pol contributes to NHEJ-mediated DNA DSB
           repair in vivo, by filling in short 5'-overhangs with
           ribonucleotides; the filled in termini would then be
           sealed by the associated LigD ligase domain, resulting
           in short stretches of RNA incorporated into the genomic
           DNA. The PaeLigD Pol domain in vitro, in a
           manganese-dependent fashion, catalyzes templated
           extensions of 5'-overhang duplex DNA, and nontemplated
           single-nucleotide additions to blunt-end duplex DNA; it
           preferentially adds single ribonucleotides at blunt DNA
           ends. PaeLigD Pol adds a correctly paired rNTP to the
           DNA primer termini more rapidly than it does a correctly
           paired dNTP; it has higher infidelity as an RNA
           polymerase than it does as a DNA polymerase, which is in
           keeping with the mutagenic property of NHEJ-mediated DNA
           DSB repair. The MtLigD Pol domain similarly is
           stimulated by manganese, is error-prone, and prefers
           adding rNTPs to dNTPs in vitro. The MtLigD Pol domain
           has been shown to prefer DNA gapped substrates
           containing a 5'-phosphate group at the gap..
          Length = 227

 Score = 27.8 bits (62), Expect = 7.2
 Identities = 18/83 (21%), Positives = 28/83 (33%), Gaps = 10/83 (12%)

Query: 241 VDENRFFEEKQIATFPYIVGRYRVRADEIYGRSPAMEALPTIRRLNETVNELAQFGRLSL 300
           +D   FF++   A  P  V    V                 +      +  LA  G + L
Sbjct: 33  IDGESFFQKHAPAGAPDWVRTVEVE------SEGGTINYLLVNDA-AGLVWLANLGAIEL 85

Query: 301 HPPTIAVSEAKQRN---FDLKPG 320
           HP      + ++ +   FDL PG
Sbjct: 86  HPWLSRADDLERPDRLVFDLDPG 108


>gnl|CDD|114419 pfam05693, Glycogen_syn, Glycogen synthase.  This family consists
           of the eukaryotic glycogen synthase proteins GYS1, GYS2
           and GYS3. Glycogen synthase (GS) is the enzyme
           responsible for the synthesis of -1,4-linked glucose
           chains in glycogen. It is the rate limiting enzyme in
           the synthesis of the polysaccharide, and its activity is
           highly regulated through phosphorylation at multiple
           sites and also by allosteric effectors, mainly glucose
           6-phosphate (G6P).
          Length = 633

 Score = 27.8 bits (62), Expect = 9.3
 Identities = 9/30 (30%), Positives = 15/30 (50%)

Query: 86  LYKEDARSKKVREWCDQVTDTLFGFRERSR 115
           +Y  D R K   E   Q+   ++ F ++SR
Sbjct: 520 IYIVDRRFKSPDESVQQLAQFMYEFCQQSR 549


  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
   0.317    0.133    0.384 

Gapped
Lambda     K      H
   0.267   0.0670    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 6,514,020
Number of extensions: 339429
Number of successful extensions: 974
Number of sequences better than 10.0: 1
Number of HSP's gapped: 968
Number of HSP's successfully gapped: 23
Length of query: 556
Length of database: 6,263,737
Length adjustment: 99
Effective length of query: 457
Effective length of database: 4,124,446
Effective search space: 1884871822
Effective search space used: 1884871822
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: 60 (27.0 bits)