RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13877
         (114 letters)



>gnl|CDD|214631 smart00350, MCM, minichromosome maintenance proteins. 
          Length = 509

 Score = 36.1 bits (84), Expect = 0.002
 Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 3/36 (8%)

Query: 1  MCPSEDCQVNKSGGRLYLQTRGSKFVKFQELKVQEH 36
          +CP  +CQ            R S F+ FQ++K+QE 
Sbjct: 61 VCPPRECQSPTP--FSLNHER-STFIDFQKIKLQES 93


>gnl|CDD|224162 COG1241, MCM2, Predicted ATPase involved in replication control,
           Cdc46/Mcm family [DNA replication, recombination, and
           repair].
          Length = 682

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 3/35 (8%)

Query: 1   MCPSEDCQVNKSGGRLYLQTRGSKFVKFQELKVQE 35
            C +         G L L  R S+F+ FQ++K+QE
Sbjct: 153 ECENCGK---FGKGPLKLVPRKSEFIDFQKVKIQE 184


>gnl|CDD|238735 cd01458, vWA_ku, Ku70/Ku80 N-terminal domain. The Ku78 heterodimer
           (composed of Ku70 and Ku80) contributes to genomic
           integrity through its ability to bind DNA double-strand
           breaks (DSB) in a preferred orientation. DSB's are
           repaired by either homologues recombination or
           non-homologues end joining and facilitate repair by the
           non-homologous end-joining pathway (NHEJ). The Ku
           heterodimer is required for accurate process that tends
           to preserve the sequence at the junction. Ku78 is found
           in all three kingdoms of life. However, only the
           eukaryotic proteins have a vWA domain fused to them at
           their N-termini. The vWA domain is not involved in DNA
           binding but may very likey mediate Ku78's interactions
           with other proteins. Members of this subgroup lack the
           conserved MIDAS motif.
          Length = 218

 Score = 26.6 bits (59), Expect = 3.0
 Identities = 9/41 (21%), Positives = 18/41 (43%), Gaps = 5/41 (12%)

Query: 63  QKMIVLTNNSNPPALEEKKFDRGIYNNEGLIASKLMKKGGQ 103
           +++ + TNN +P   +  K  +       + A  L  KG +
Sbjct: 129 KRIFLFTNNDDPHGGDSIKDSQAA-----VKAEDLKDKGIE 164


>gnl|CDD|183150 PRK11468, PRK11468, dihydroxyacetone kinase subunit DhaK;
           Provisional.
          Length = 356

 Score = 26.1 bits (58), Expect = 4.3
 Identities = 8/20 (40%), Positives = 13/20 (65%)

Query: 52  VKLTNPPVQTGQKMIVLTNN 71
            + T  P+Q+G ++I L NN
Sbjct: 265 EEQTKQPLQSGDRVIALVNN 284


>gnl|CDD|233816 TIGR02302, aProt_lowcomp, TIGR02302 family protein.  Members of
           this family are long (~850 residue) bacterial proteins
           from the alpha Proteobacteria. Each has 2-3 predicted
           transmembrane helices near the N-terminus and a long
           C-terminal region that includes stretches of
           Gln/Gly-rich low complexity sequence, predicted by TMHMM
           to be outside the membrane. In Bradyrhizobium japonicum,
           two tandem reading frames are together homologous the
           single members found in other species; the cutoffs
           scores are set low enough that the longer scores above
           the trusted cutoff and the shorter above the noise
           cutoff for this model.
          Length = 851

 Score = 26.1 bits (57), Expect = 4.6
 Identities = 13/35 (37%), Positives = 17/35 (48%)

Query: 39  NQPLQMGSSPAQVVKLTNPPVQTGQKMIVLTNNSN 73
           +    M  S A++     PPV TG+  I LT  SN
Sbjct: 169 DWKPAMSPSTARIDAWVTPPVYTGRAPIFLTAASN 203


>gnl|CDD|182767 PRK10836, PRK10836, lysine transporter; Provisional.
          Length = 489

 Score = 25.9 bits (57), Expect = 5.1
 Identities = 6/20 (30%), Positives = 13/20 (65%)

Query: 17  YLQTRGSKFVKFQELKVQEH 36
           Y   +G+ FV++ E+K  ++
Sbjct: 467 YKLIKGTHFVRYSEMKFPQN 486


>gnl|CDD|226956 COG4590, COG4590, ABC-type uncharacterized transport system,
           permease component [General function prediction only].
          Length = 733

 Score = 26.0 bits (57), Expect = 6.0
 Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 15/66 (22%)

Query: 33  VQEHTSNQPLQMGSSPAQ----VVKLTNPP-----------VQTGQKMIVLTNNSNPPAL 77
           V +  S+  L +G++P Q    VV LT  P              G+ MIVL    N P L
Sbjct: 610 VPKSLSDGSLALGATPWQTLIYVVLLTASPGIFSAIMIGLGRAVGETMIVLMATGNTPLL 669

Query: 78  EEKKFD 83
           +   F+
Sbjct: 670 DWNIFE 675


  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
   0.310    0.128    0.360 

Gapped
Lambda     K      H
   0.267   0.0754    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,309,855
Number of extensions: 415613
Number of successful extensions: 236
Number of sequences better than 10.0: 1
Number of HSP's gapped: 236
Number of HSP's successfully gapped: 13
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
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 (21.8 bits)
S2: 53 (24.1 bits)