RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy7405
         (87 letters)



>gnl|CDD|236332 PRK08668, PRK08668, NADH dehydrogenase subunit M; Validated.
          Length = 610

 Score = 29.2 bits (66), Expect = 0.19
 Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 3/33 (9%)

Query: 4   PEVHHYHPPPRGFYRPFISEYPTYPSFKSIYDD 36
            +++HY    R FY P    Y  +PSF+ +Y+ 
Sbjct: 543 EDLYHYA---RNFYAPLERAYAFWPSFEKLYEM 572


>gnl|CDD|224787 COG1875, COG1875, NYN ribonuclease and ATPase of PhoH family
           domains [General    function prediction only].
          Length = 436

 Score = 25.8 bits (57), Expect = 3.1
 Identities = 14/53 (26%), Positives = 19/53 (35%), Gaps = 14/53 (26%)

Query: 29  SFKSIYDDPVNPH-----------ERINIPGYRYLPIS---RETYGISPRNIQ 67
           S     D P  P             R+N  G   L +    +E +GI PRN +
Sbjct: 180 STNDKLDLPCYPGFRLLGSSSSALGRVNPNGKVILLLKHEDQEVWGIRPRNAE 232


>gnl|CDD|234013 TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit,
            Firmicutes type.  AddAB, also called RexAB, substitutes
            for RecBCD in several bacterial lineages. These DNA
            recombination proteins act before synapse and are
            particularly important for DNA repair of double-stranded
            breaks by homologous recombination. The term AddAB is
            used broadly, with AddA homologous between the Firmicutes
            (as modeled here) and the alphaproteobacteria, while the
            partner AddB proteins show no strong homology across the
            two groups of species [DNA metabolism, DNA replication,
            recombination, and repair].
          Length = 1230

 Score = 25.8 bits (57), Expect = 3.2
 Identities = 12/40 (30%), Positives = 16/40 (40%), Gaps = 3/40 (7%)

Query: 22   SEYPTYPS---FKSIYDDPVNPHERINIPGYRYLPISRET 58
            +E P   S    K I++D     ER  +   R   IS E 
Sbjct: 1005 TETPAKQSVSEIKRIFEDEDEGSERAPVKQSRGKSISLER 1044


>gnl|CDD|237256 PRK12901, secA, preprotein translocase subunit SecA; Reviewed.
          Length = 1112

 Score = 25.8 bits (57), Expect = 3.8
 Identities = 8/23 (34%), Positives = 14/23 (60%)

Query: 25  PTYPSFKSIYDDPVNPHERINIP 47
             +P  K +Y++  N +ERI +P
Sbjct: 899 IAFPVIKQVYEEQGNMYERIVVP 921


>gnl|CDD|214363 CHL00099, ilvB, acetohydroxyacid synthase large subunit.
          Length = 585

 Score = 25.0 bits (55), Expect = 5.4
 Identities = 6/20 (30%), Positives = 8/20 (40%)

Query: 34  YDDPVNPHERINIPGYRYLP 53
           Y  P   +  I I G R + 
Sbjct: 181 YYPPEPGNTIIKILGCRPIY 200


>gnl|CDD|130691 TIGR01630, psiM2_ORF9, phage uncharacterized protein (putative
           large terminase), C-terminal domain.  This model
           represents the C-terminal region of a set of phage
           proteins typically about 400-500 amino acids in length,
           although some members are considerably shorter. An
           article on Methanobacterium phage Psi-M2 (PMID:9791169)
           calls the member from that phage, ORF9, a putative large
           terminase subunit, and ORF8 a candidate terminase small
           subunit. Most proteins in this family have an apparent
           P-loop nucleotide-binding sequence toward the N-terminus
           [Mobile and extrachromosomal element functions, Prophage
           functions].
          Length = 142

 Score = 24.8 bits (54), Expect = 6.2
 Identities = 8/37 (21%), Positives = 15/37 (40%), Gaps = 1/37 (2%)

Query: 5   EVHHYHPP-PRGFYRPFISEYPTYPSFKSIYDDPVNP 40
           E  +  PP    ++   I     +P  K+ +DD  + 
Sbjct: 96  EAGNVFPPNWAPWWPDLIQALEAFPREKAAHDDDPDA 132


>gnl|CDD|220990 pfam11124, Pho86, Inorganic phosphate transporter Pho86.  Pho86p is
           an ER protein which is produced in response to phosphate
           starvation. It is essential for growth when phosphate
           levels are limiting. Pho86p is also involved in the
           regulation of Pho84p, a high-affinity phosphate
           transporter which is localised to the endoplasmic
           reticulum (ER) in low phosphate medium. When the level
           of phosphate increases Pho84p is transported to the
           vacuole. Pho86p is required for packaging of Pho84p in
           to COPII vesicles.
          Length = 296

 Score = 25.0 bits (55), Expect = 6.4
 Identities = 8/33 (24%), Positives = 16/33 (48%), Gaps = 4/33 (12%)

Query: 29  SFKSIYDDPVNPHERINIPGYRYLPISRETYGI 61
            FK I    +N +  +     +   I+R+T+G+
Sbjct: 266 GFKKIDSYTLNENRLL----GKLFGITRDTWGL 294


>gnl|CDD|182292 PRK10188, PRK10188, DNA-binding transcriptional activator SdiA;
          Provisional.
          Length = 240

 Score = 24.7 bits (54), Expect = 7.8
 Identities = 10/19 (52%), Positives = 12/19 (63%), Gaps = 2/19 (10%)

Query: 10 HPPPRGFYRPFISEYPTYP 28
          HP P  F RP ++ Y TYP
Sbjct: 48 HPVP--FTRPKVAFYTTYP 64


  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
   0.323    0.147    0.505 

Gapped
Lambda     K      H
   0.267   0.0779    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,026,971
Number of extensions: 415189
Number of successful extensions: 401
Number of sequences better than 10.0: 1
Number of HSP's gapped: 401
Number of HSP's successfully gapped: 23
Length of query: 87
Length of database: 10,937,602
Length adjustment: 55
Effective length of query: 32
Effective length of database: 8,498,132
Effective search space: 271940224
Effective search space used: 271940224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.1 bits)