RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12830
         (94 letters)



>gnl|CDD|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase
          II.  The eukaryotic RPB3 subunit of RNA polymerase
          (RNAP) II is involved in the assembly of RNAP subunits.
          RNAP is a large multi-subunit complex responsible for
          the synthesis of RNA. It is the principal enzyme of the
          transcription process, and is a final target in many
          regulatory pathways that control gene expression in all
          living cells. At least three distinct RNAP complexes
          are found in eukaryotic nuclei: RNAP I, RNAP II, and
          RNAP III. RNAP II is responsible for the synthesis of
          mRNA precursor. The RPB3 subunit is similar to the
          bacterial RNAP alpha subunit in that it contains two
          subdomains: one subdomain is similar the eukaryotic
          Rpb11/AC19/archaeal L subunit which is involved in
          dimerization, and the other is an inserted beta sheet
          subdomain. The RPB3 subunit heterodimerizes with the
          RPB11 subunit, and together with RPB10 and RPB12,
          anchors the two largest subunits, RPB1 and RPB2, and
          stabilizes their association.
          Length = 265

 Score = 37.2 bits (87), Expect = 3e-04
 Identities = 14/23 (60%), Positives = 19/23 (82%)

Query: 7  PSVHITDLTDENVKFQVEDTELS 29
          P V IT+LTD+ VKF +E+T+LS
Sbjct: 1  PRVEITELTDDKVKFILENTDLS 23


>gnl|CDD|218767 pfam05827, ATP-synt_S1, Vacuolar ATP synthase subunit S1
          (ATP6S1).  This family consists of eukaryotic vacuolar
          ATP synthase subunit S1 proteins.
          Length = 277

 Score = 28.5 bits (64), Expect = 0.42
 Identities = 6/21 (28%), Positives = 10/21 (47%)

Query: 3  YANQPSVHITDLTDENVKFQV 23
          + +QP +  +D T E   F  
Sbjct: 50 FISQPGLSASDFTTEKDNFPN 70


>gnl|CDD|233176 TIGR00898, 2A0119, cation transport protein.  [Transport and
           binding proteins, Cations and iron carrying compounds].
          Length = 505

 Score = 25.7 bits (57), Expect = 4.2
 Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 3/25 (12%)

Query: 39  NMEWKGLSAQLLLCSRPSFLFAFLC 63
             +W+ L    L  S P+FLF  L 
Sbjct: 239 IPDWRWL---QLAVSLPTFLFFLLS 260


>gnl|CDD|151313 pfam10864, DUF2663, Protein of unknown function (DUF2663).  Some
          members in this family of proteins are annotated as
          YpbF however currently no function is known.
          Length = 131

 Score = 25.0 bits (55), Expect = 5.2
 Identities = 10/37 (27%), Positives = 12/37 (32%), Gaps = 1/37 (2%)

Query: 41 EWKGLSAQLLLCSRPSFLFAFL-CIYENRLALSQTGF 76
          +W  L  Q L     S +   L CIY          F
Sbjct: 12 KWDRLEKQHLFWQWASLICLCLFCIYLYAKVTGSYSF 48


>gnl|CDD|216355 pfam01195, Pept_tRNA_hydro, Peptidyl-tRNA hydrolase. 
          Length = 183

 Score = 24.8 bits (55), Expect = 7.5
 Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 1/42 (2%)

Query: 18 NVKFQVEDTELSKRTNGNWKENMEWKGLSAQLLLCSRPSFLF 59
          NV F V D  L++R   + K+  ++KGL A+  +      L 
Sbjct: 18 NVGFMVID-RLAERLGVSLKKKKKFKGLIAKGRIEGEKVILL 58


>gnl|CDD|224460 COG1543, COG1543, Uncharacterized conserved protein [Function
           unknown].
          Length = 504

 Score = 24.6 bits (54), Expect = 8.9
 Identities = 9/36 (25%), Positives = 14/36 (38%), Gaps = 3/36 (8%)

Query: 9   VHITDLTDENVKFQVEDTELSKRTNGNWKENMEWKG 44
           +  +DL    V  QVE    S  + G+ +    W  
Sbjct: 360 ITPSDLLRHFVGVQVELPPSSWGSGGDHQ---VWLN 392


  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
   0.317    0.132    0.411 

Gapped
Lambda     K      H
   0.267   0.0705    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,512,749
Number of extensions: 336517
Number of successful extensions: 217
Number of sequences better than 10.0: 1
Number of HSP's gapped: 217
Number of HSP's successfully gapped: 11
Length of query: 94
Length of database: 10,937,602
Length adjustment: 61
Effective length of query: 33
Effective length of database: 8,232,008
Effective search space: 271656264
Effective search space used: 271656264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)