RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy9775
         (133 letters)



>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit
           [Transcription / DNA replication, recombination, and
           repair / Chromatin structure and dynamics].
          Length = 1001

 Score =  138 bits (349), Expect = 4e-39
 Identities = 55/103 (53%), Positives = 78/103 (75%)

Query: 7   ASMVEHVTKQEIEFDTPFRELGFPGAPYRSTVLLQPTSGCLVNLTEWPPFVISLEDVELV 66
           AS +   ++  IEF   FR+LGF G P+RS+V+++PT+ CLV L E P FVI+LE+VE+V
Sbjct: 782 ASSIAEASEGRIEFKVQFRKLGFYGVPFRSSVMIKPTTDCLVQLDEAPFFVITLEEVEIV 841

Query: 67  HFERVQFQLKNFDMVFVFKDYHRKVVMINAIPMNMLDHVKEWL 109
           + ERVQF LKNFD+VF+ +D++R +V IN +P+  LD +KEWL
Sbjct: 842 NLERVQFGLKNFDVVFILRDFYRPLVHINTVPVESLDKLKEWL 884


>gnl|CDD|219876 pfam08512, Rtt106, Histone chaperone Rttp106-like.  This family
           includes Rttp106, a histone chaperone involved in
           heterochromatin-mediated silencing. This domain belongs
           to the Pleckstrin homology domain superfamily.
          Length = 93

 Score =  100 bits (252), Expect = 5e-29
 Identities = 38/85 (44%), Positives = 49/85 (57%), Gaps = 4/85 (4%)

Query: 29  FPGAPYR---STVLLQPTSGCLVNLTEWPPFVISLEDVELVHFERVQFQLKNFDMVFVFK 85
           FPG P     S  LL P    L+ L E PP VI+L+D+E V FERV   L+ FD+V VFK
Sbjct: 1   FPGVPCSYKASEGLLYPLEKGLLFLFEKPPLVITLDDIESVSFERVSGGLRTFDLVVVFK 60

Query: 86  DYHRKVVMINAIPMNMLDHVKEWLK 110
            Y   V   ++I    LD +K++LK
Sbjct: 61  -YSGPVHEFSSIDREELDVLKDFLK 84


>gnl|CDD|241385 cd13231, PH2_SSRP1-like, Structure Specific Recognition protein 1
           (SSRP1) Pleckstrin homology (PH) domain, repeat 2.
           SSRP1 is a component of FACT (facilitator of chromatin
           transcription), an essential chromatin reorganizing
           factor. In yeast FACT (yFACT) is composed of three
           proteins: Spt16/Cdc68, Pob3, and Nhp6. In metazoans the
           Pob3 and Nhp6 orthologs are fused to form SSRP1/T160 in
           human and mouse, respectively.The middle domain of the
           Pob3 subunit (Pob3-M) has an unusual double pleckstrin
           homology (PH) architecture. yFACT interacts in a
           physiologically important way with the central
           single-strand DNA binding factor RPA to promote a step
           in DNA Replication. Coordinated function by yFACT and
           RPA is important during nucleosome deposition. These
           results support the model that the FACT family has an
           essential role in constructing nucleosomes during DNA
           replication, and suggest that RPA contributes to this
           process. Members of this cd are composed of the second
           PH-like repeat. PH domains have diverse functions, but
           in general are involved in targeting proteins to the
           appropriate cellular location or in the interaction with
           a binding partner. They share little sequence
           conservation, but all have a common fold, which is
           electrostatically polarized. Less than 10% of PH domains
           bind phosphoinositide phosphates (PIPs) with high
           affinity and specificity. PH domains are distinguished
           from other PIP-binding domains by their specific
           high-affinity binding to PIPs with two vicinal phosphate
           groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3
           which results in targeting some PH domain proteins to
           the plasma membrane. A few display strong specificity in
           lipid binding. Any specificity is usually determined by
           loop regions or insertions in the N-terminus of the
           domain, which are not conserved across all PH domains.
           PH domains are found in cellular signaling proteins such
           as serine/threonine kinase, tyrosine kinases, regulators
           of G-proteins, endocytotic GTPases, adaptors, as well as
           cytoskeletal associated molecules and in lipid
           associated enzymes.
          Length = 100

 Score = 32.9 bits (76), Expect = 0.012
 Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 5/60 (8%)

Query: 54  PPFVISLEDVELVHFERV---QFQLKNFDMVFVFKDYHRKVVMINAIPMNMLDHVKEWLK 110
           PP +I  +D+  V F RV       + FD+    K         ++I       ++++LK
Sbjct: 34  PPILIRFDDISSVEFSRVGGSSTSSRTFDLEIELKG--GTEHTFSSIDREEYGPLEDFLK 91


>gnl|CDD|182035 PRK09699, PRK09699, D-allose transporter subunit; Provisional.
          Length = 312

 Score = 29.7 bits (67), Expect = 0.41
 Identities = 11/22 (50%), Positives = 14/22 (63%)

Query: 39  LLQPTSGCLVNLTEWPPFVISL 60
            L   +GCLVN T   PF+I+L
Sbjct: 104 ALGAINGCLVNWTGLHPFIITL 125


>gnl|CDD|215228 PLN02408, PLN02408, phospholipase A1.
          Length = 365

 Score = 27.9 bits (62), Expect = 1.6
 Identities = 12/32 (37%), Positives = 13/32 (40%), Gaps = 2/32 (6%)

Query: 22 TPFRELGFPGAPYRSTVLLQPTSGCLVNLTEW 53
          T     G P   YR T  L+ TSG    L  W
Sbjct: 56 TLLERSGLPNTGYRLTKHLRATSGI--QLPRW 85


>gnl|CDD|200491 cd11354, AmyAc_bac_CMD_like, Alpha amylase catalytic domain found
          in bacterial cyclomaltodextrinases and related
          proteins.  Cyclomaltodextrinase (CDase; EC3.2.1.54),
          neopullulanase (NPase; EC 3.2.1.135), and maltogenic
          amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of
          alpha-(1,4) glycosidic linkages on a number of
          substrates including cyclomaltodextrins (CDs),
          pullulan, and starch. These enzymes hydrolyze CDs and
          starch to maltose and pullulan to panose by cleavage of
          alpha-1,4 glycosidic bonds whereas alpha-amylases
          essentially lack activity on CDs and pullulan. They
          also catalyze transglycosylation of oligosaccharides to
          the C3-, C4- or C6-hydroxyl groups of various acceptor
          sugar molecules. Since these proteins are nearly
          indistinguishable from each other, they are referred to
          as cyclomaltodextrinases (CMDs). This group of CMDs is
          bacterial. The Alpha-amylase family comprises the
          largest family of glycoside hydrolases (GH), with the
          majority of enzymes acting on starch, glycogen, and
          related oligo- and polysaccharides. These proteins
          catalyze the transformation of alpha-1,4 and alpha-1,6
          glucosidic linkages with retention of the anomeric
          center. The protein is described as having 3 domains:
          A, B, C. A is a (beta/alpha) 8-barrel; B is a loop
          between the beta 3 strand and alpha 3 helix of A; C is
          the C-terminal extension characterized by a Greek key.
          The majority of the enzymes have an active site cleft
          found between domains A and B where a triad of
          catalytic residues (Asp, Glu and Asp) performs
          catalysis. Other members of this family have lost the
          catalytic activity as in the case of the human 4F2hc,
          or only have 2 residues that serve as the catalytic
          nucleophile and the acid/base, such as Thermus A4
          beta-galactosidase with 2 Glu residues (GH42) and human
          alpha-galactosidase with 2 Asp residues (GH31). The
          family members are quite extensive and include: alpha
          amylase, maltosyltransferase, cyclodextrin
          glycotransferase, maltogenic amylase, neopullulanase,
          isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
          4-alpha-glucotransferase, oligo-1,6-glucosidase,
          amylosucrase, sucrose phosphorylase, and amylomaltase.
          Length = 357

 Score = 27.3 bits (61), Expect = 2.4
 Identities = 11/34 (32%), Positives = 13/34 (38%)

Query: 27 LGFPGAPYRSTVLLQPTSGCLVNLTEWPPFVISL 60
          LGF GAP R           L  L  W  + + L
Sbjct: 10 LGFVGAPIRPREPEAAVEHRLDRLEPWLDYAVEL 43


>gnl|CDD|218827 pfam05960, DUF885, Bacterial protein of unknown function (DUF885). 
           This family consists of several hypothetical bacterial
           proteins several of which are putative membrane
           proteins.
          Length = 539

 Score = 26.5 bits (59), Expect = 5.0
 Identities = 8/28 (28%), Positives = 17/28 (60%), Gaps = 1/28 (3%)

Query: 82  FVFKDYHRKVVMINAIPMNML-DHVKEW 108
           F  +++H  V+   A+P+++L + V  W
Sbjct: 511 FDLREFHDAVLSQGALPLDLLEEAVDGW 538


>gnl|CDD|183369 PRK11902, ampG, muropeptide transporter; Reviewed.
          Length = 402

 Score = 26.4 bits (58), Expect = 6.4
 Identities = 10/21 (47%), Positives = 12/21 (57%)

Query: 38  VLLQPTSGCLVNLTEWPPFVI 58
           V + PTSG LV    WP F +
Sbjct: 353 VYVGPTSGYLVEAYGWPGFYL 373


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.322    0.134    0.405 

Gapped
Lambda     K      H
   0.267   0.0763    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,655,786
Number of extensions: 576108
Number of successful extensions: 488
Number of sequences better than 10.0: 1
Number of HSP's gapped: 487
Number of HSP's successfully gapped: 13
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.1 bits)