RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8283
         (285 letters)



>gnl|CDD|218280 pfam04825, Rad21_Rec8_N, N terminus of Rad21 / Rec8 like protein.
           This family represents a conserved N-terminal region
           found in eukaryotic cohesins of the Rad21, Rec8 and Scc1
           families. Members of this family mediate sister
           chromatid cohesion during mitosis and meiosis, as part
           of the cohesin complex. Cohesion is necessary for
           homologous recombination (including double-strand break
           repair) and correct chromatid segregation. These
           proteins may also be involved in chromosome
           condensation. Dissociation at the metaphase to anaphase
           transition causes loss of cohesion and chromatid
           segregation.
          Length = 110

 Score =  179 bits (456), Expect = 2e-57
 Identities = 65/112 (58%), Positives = 83/112 (74%), Gaps = 3/112 (2%)

Query: 1   MFYAQFVLAKKGPLARIWLAAHWDKKLTKAHVFETNIEKSVDGILQPKVKMALRTSGHLL 60
           MFY+  +L KKGPLA +WLAA  +KKL++  + E +I KS + IL P+  +ALR SG LL
Sbjct: 1   MFYSHELLTKKGPLATVWLAATLEKKLSRKQILEVDIPKSCEEILNPEAPIALRLSGQLL 60

Query: 61  LGVVRIYSRKAKYLLADCNEAFVKIKMAFR-PGMVDLPEDNREAAVNAITLP 111
            GVVRIYSRK +YLL DCNEA  ++K AFR PG +DLPE  R+A+ NA+TLP
Sbjct: 61  YGVVRIYSRKVEYLLEDCNEALSRLKKAFRIPGQLDLPE--RKASPNALTLP 110


>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
          Length = 3151

 Score = 32.6 bits (74), Expect = 0.26
 Identities = 17/37 (45%), Positives = 19/37 (51%), Gaps = 5/37 (13%)

Query: 238 PAPPSVPPPAP-----ESDDDDHFGGPASPMGHPRSR 269
           PAPP  PPPAP     E DD+D      SP+  PR  
Sbjct: 310 PAPPDPPPPAPAGDAEEEDDEDGAMEVVSPLPRPRQH 346


>gnl|CDD|165700 PLN00131, PLN00131, hypothetical protein; Provisional.
          Length = 218

 Score = 29.6 bits (66), Expect = 1.6
 Identities = 13/31 (41%), Positives = 17/31 (54%)

Query: 224 FDDTPIGGVDMNEPPAPPSVPPPAPESDDDD 254
            + TP   +D+N+P A    P PAP  DD D
Sbjct: 100 LNSTPQPELDLNQPAAHEQEPEPAPPLDDQD 130


>gnl|CDD|219404 pfam07415, Herpes_LMP2, Gammaherpesvirus latent membrane protein
           (LMP2) protein.  This family consists of several
           Gammaherpesvirus latent membrane protein (LMP2)
           proteins. Epstein-Barr virus is a human Gammaherpesvirus
           that infects and establishes latency in B lymphocytes in
           vivo. The latent membrane protein 2 (LMP2) gene is
           expressed in latently infected B cells and encodes two
           protein isoforms, LMP2A and LMP2B, that are identical
           except for an additional N-terminal 119 aa cytoplasmic
           domain which is present in the LMP2A isoform. LMP2A is
           thought to play a key role in either the establishment
           or the maintenance of latency and/or the reactivation of
           productive infection from the latent state. The
           significance of LMP2B and its role in pathogenesis
           remain unclear.
          Length = 489

 Score = 29.4 bits (66), Expect = 2.4
 Identities = 18/62 (29%), Positives = 22/62 (35%), Gaps = 5/62 (8%)

Query: 203 DGDAFSGNLNADAPHMFGLKLFDDTPIGGVDMNEPPAPPSVPPPAPESDDDDHFGGPASP 262
             D   G+ N   P  FG       P       +  AP   PPP   S+ D H  G   P
Sbjct: 19  GPDGDEGDSNPYYPSSFGSSWDRPGP---PVPEDYDAPSHRPPPYGGSNGDRH--GGYQP 73

Query: 263 MG 264
           +G
Sbjct: 74  LG 75


>gnl|CDD|183740 PRK12779, PRK12779, putative bifunctional glutamate synthase
           subunit beta/2-polyprenylphenol hydroxylase;
           Provisional.
          Length = 944

 Score = 29.4 bits (66), Expect = 2.6
 Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 1/33 (3%)

Query: 177 DGPLGRVCDPPQFMSSSTSMMNQMEIDGDAFSG 209
           D   G +    Q M +S+  +N+M I GDAFSG
Sbjct: 702 DAEKGTIDLVVQGMGTSSLEINRMAI-GDAFSG 733


>gnl|CDD|233605 TIGR01865, cas_Csn1, CRISPR-associated protein Cas9/Csn1, subtype
           II/NMEMI.  CRISPR loci appear to be mobile elements with
           a wide host range. This model represents a protein found
           only in CRISPR-containing species, near other
           CRISPR-associated proteins (cas), as part of the NMENI
           subtype of CRISPR/Cas locus. The species range so far
           for this protein is animal pathogens and commensals only
           [Mobile and extrachromosomal element functions, Other].
          Length = 805

 Score = 29.3 bits (66), Expect = 2.9
 Identities = 14/47 (29%), Positives = 22/47 (46%)

Query: 26  KLTKAHVFETNIEKSVDGILQPKVKMALRTSGHLLLGVVRIYSRKAK 72
                 + + NI K+ D IL P VK AL  +  ++  +V+ Y    K
Sbjct: 471 INDSQLLPKINITKAKDEILNPVVKRALLQARKVVNELVKKYGPPDK 517


>gnl|CDD|233692 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D.  This
           model represents one of two ATPase subunits of the
           trimeric magnesium chelatase responsible for insertion
           of magnesium ion into protoporphyrin IX. This is an
           essential step in the biosynthesis of both chlorophyll
           and bacteriochlorophyll. This subunit is found in green
           plants, photosynthetic algae, cyanobacteria and other
           photosynthetic bacteria. Unlike subunit I (TIGR02030),
           this subunit is not found in archaea [Biosynthesis of
           cofactors, prosthetic groups, and carriers, Chlorophyll
           and bacteriochlorphyll].
          Length = 589

 Score = 29.0 bits (65), Expect = 3.6
 Identities = 9/19 (47%), Positives = 11/19 (57%)

Query: 236 EPPAPPSVPPPAPESDDDD 254
            PP PP   PP PE + D+
Sbjct: 273 PPPPPPPPEPPEPEEEPDE 291


>gnl|CDD|225588 COG3046, COG3046, Uncharacterized protein related to
           deoxyribodipyrimidine photolyase [General function
           prediction only].
          Length = 505

 Score = 27.8 bits (62), Expect = 8.7
 Identities = 20/72 (27%), Positives = 25/72 (34%), Gaps = 21/72 (29%)

Query: 219 FGLKLFDDTPIGGV----DMNEPPAPPSVPPPAP----------------ESDDDDHFGG 258
            G+ + DD P GG       N    PP + PP P                E    D+FG 
Sbjct: 158 TGILMEDDQPEGGRWNFDAENRKKLPPDLLPPKPLKFPPDEIVQEVKERVERLFPDNFGQ 217

Query: 259 PASPMGHPRSRT 270
                G P +RT
Sbjct: 218 VEG-FGWPVTRT 228


  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
   0.319    0.137    0.418 

Gapped
Lambda     K      H
   0.267   0.0539    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,078,968
Number of extensions: 1464804
Number of successful extensions: 1891
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1852
Number of HSP's successfully gapped: 34
Length of query: 285
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 189
Effective length of database: 6,679,618
Effective search space: 1262447802
Effective search space used: 1262447802
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 (21.8 bits)
S2: 58 (26.6 bits)