RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3792
         (224 letters)



>gnl|CDD|219667 pfam07962, Swi3, Replication Fork Protection Component Swi3.
           Replication fork pausing is required to initiate a
           recombination events. More specifically, Swi1 is
           required for recombination near the mat1 locus. Swi3 has
           been found to co-purify with Swi1 Swi3, together with
           Swi1, define a fork protection complex that coordinates
           leading- and lagging-strand synthesis and stabilises
           stalled replication forks. The Swi1-Swi3 complex is
           required for accurate replication, fork protection and
           replication checkpoint signalling.
          Length = 84

 Score =  106 bits (267), Expect = 4e-30
 Identities = 37/84 (44%), Positives = 55/84 (65%)

Query: 63  KLNAQRLTGPRGIQCIEQYFKDVKFKGKGHELADLNTIMSNLEHWANRLYPKSNFVDVLK 122
           KL+ +RL  P+GI  + + FKD KFKGKGHE +DL  ++   + WA+ L+PK+ F D L 
Sbjct: 1   KLDEERLLSPKGIPALRKTFKDFKFKGKGHEYSDLARLLQFYQLWAHDLFPKAKFKDFLN 60

Query: 123 RLEVLGHKRPVMTHIKKIRLGMIE 146
            +E LGHK+ V T+ +++RL    
Sbjct: 61  LVEKLGHKKQVQTYRRELRLEEKG 84


>gnl|CDD|220725 pfam10383, Clr2, Transcription-silencing protein Clr2.  Clr2 is a
           chromatin silencing protein, one of a quartet of
           proteins forming the core of SHREC, a multienzyme
           effector complex that mediates hetero-chromatic
           transcriptional gene silencing in fission yeast. Clr2
           does not have any obvious well-conserved domains but,
           along with the other core proteins, binds to the histone
           deacetylase Clr3, and on its own might also have a role
           in chromatin organisation at the cnt domain, the site of
           kinetochore assembly.
          Length = 133

 Score = 28.5 bits (64), Expect = 1.6
 Identities = 18/91 (19%), Positives = 28/91 (30%), Gaps = 11/91 (12%)

Query: 46  DAVRVAPKKKVIRNPQPKLNAQ--------RLTGPRGIQCIEQYFKDVKFKGKGHELADL 97
           D VR+ P    +   +   +          +L     IQC       V+FKGK +  +  
Sbjct: 17  DPVRLKPTGYSLGASRLGPDVTDVMVIDEIQL---DLIQCDPDLKSQVRFKGKIYTTSRQ 73

Query: 98  NTIMSNLEHWANRLYPKSNFVDVLKRLEVLG 128
                N               +V  R E +G
Sbjct: 74  RAYDENNSPIPPGTPKPLMREEVASRFEYVG 104


>gnl|CDD|180177 PRK05636, PRK05636, replicative DNA helicase; Provisional.
          Length = 505

 Score = 27.9 bits (62), Expect = 4.8
 Identities = 13/46 (28%), Positives = 17/46 (36%)

Query: 29 SQDEDEQPPPNPSEPSEDAVRVAPKKKVIRNPQPKLNAQRLTGPRG 74
          S D+D  PPP PS+  +  V V        +P          G R 
Sbjct: 8  SFDDDYVPPPEPSDADDAHVDVPAPAFEDFSPAQAFGQGTRGGDRR 53


>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
          Length = 333

 Score = 27.3 bits (61), Expect = 7.9
 Identities = 12/55 (21%), Positives = 15/55 (27%), Gaps = 4/55 (7%)

Query: 8   DELVDDPEPMLNEDHHPEARESQDEDEQPPPNPSEPSEDAVRVAPKKKVIRNPQP 62
                 P P        +    Q + EQP   P  P          + V   PQP
Sbjct: 113 VPPQHAPRPAQPAPQPVQQPAYQPQPEQPLQQPVSPQVA----PAPQPVHSAPQP 163


>gnl|CDD|221275 pfam11861, DUF3381, Domain of unknown function (DUF3381).  This
           domain is functionally uncharacterized. This domain is
           found in eukaryotes. This presumed domain is typically
           between 156 to 174 amino acids in length. This domain is
           found associated with pfam07780, pfam01728.
          Length = 154

 Score = 26.5 bits (59), Expect = 8.4
 Identities = 11/35 (31%), Positives = 21/35 (60%)

Query: 190 VKEITEAQRERMLRNRQIAEEKRLARLAMEAEQKK 224
           V+E+ E ++   L  +++A+ KR  R   E +QK+
Sbjct: 111 VEELDEEEQIDELLEKELAKLKREKRRENERKQKE 145


>gnl|CDD|218328 pfam04921, XAP5, XAP5, circadian clock regulator.  This protein
          is found in a wide range of eukaryotes. It is a nuclear
          protein and is suggested to be DNA binding. In plants,
          this family is essential for correct circadian clock
          functioning by acting as a light-quality regulator
          coordinating the activities of blue and red light
          signalling pathways during plant growth - inhibiting
          growth in red light but promoting growth in blue light.
          Length = 233

 Score = 26.5 bits (59), Expect = 9.7
 Identities = 13/36 (36%), Positives = 19/36 (52%)

Query: 25 EARESQDEDEQPPPNPSEPSEDAVRVAPKKKVIRNP 60
          E  E + EDE+  P  S   ++A     KKK+ +NP
Sbjct: 19 EEDEDEGEDEKKVPKESSEPDEANVNPNKKKIGKNP 54


  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
   0.313    0.132    0.375 

Gapped
Lambda     K      H
   0.267   0.0778    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,968,757
Number of extensions: 1141354
Number of successful extensions: 1237
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1224
Number of HSP's successfully gapped: 49
Length of query: 224
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 131
Effective length of database: 6,812,680
Effective search space: 892461080
Effective search space used: 892461080
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 (21.9 bits)
S2: 57 (25.6 bits)