RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6931
         (81 letters)



>gnl|CDD|147159 pfam04857, CAF1, CAF1 family ribonuclease.  The major pathways of
          mRNA turnover in eukaryotes initiate with shortening of
          the polyA tail. CAF1 encodes a critical component of
          the major cytoplasmic deadenylase in yeast. Both Caf1p
          is required for normal mRNA deadenylation in vivo and
          localises to the cytoplasm. Caf1p copurifies with a
          Ccr4p-dependent polyA-specific exonuclease activity.
          Some members of this family include and inserted RNA
          binding domain pfam01424. This family of proteins is
          related to other exonucleases pfam00929 (Bateman A
          pers. obs.). The crystal structure of Saccharomyces
          cerevisiae Pop2 has been resolved at 2.3
          Angstrom#resolution.
          Length = 235

 Score = 52.6 bits (127), Expect = 7e-10
 Identities = 18/55 (32%), Positives = 25/55 (45%)

Query: 20 KAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFK 74
          +AI S  F+ ID EF G+   P  +   T    Y  +R+      +IQ GL  F 
Sbjct: 17 QAIDSYDFIAIDTEFPGVVARPIGSFRSTSDYRYQALRKNVDRLKIIQLGLTLFD 71


>gnl|CDD|178601 PLN03033, PLN03033, 2-dehydro-3-deoxyphosphooctonate aldolase;
           Provisional.
          Length = 290

 Score = 29.1 bits (65), Expect = 0.19
 Identities = 10/30 (33%), Positives = 19/30 (63%)

Query: 23  KSALFVTIDGEFTGLNNGPNTTPYDTPAQY 52
           ++A+ V +DG F  +++ P + P D P Q+
Sbjct: 227 RTAVAVGVDGIFMEVHDDPLSAPVDGPTQW 256


>gnl|CDD|193492 cd09838, CBM6_FsXyn10D-like, Carbohydrate Binding Module Family 6
           (CBM6), Fibrobacter succinogenes S85 Xyn10D-like;
           appended mainly to glycoside hydrolase (GH) family 5 and
           GH43 domains.  This family includes carbohydrate binding
           module 6 (CBM6) domains that are appended mainly to
           several glycoside hydrolase (GH) families, including GH5
           (cellulase) and GH43. CBM6s are non-catalytic
           carbohydrate binding domains that facilitate the strong
           binding of the GH catalytic modules with their
           dedicated, insoluble substrates. For this subgroup,
           little information is available about the specific
           substrates of the appended GH domains; it includes the
           CBM6 of Fibrobacter succinogenes S85 Xyn10D xylanase,
           appended to a GH10 domain, and the CBM6 of Cellvibrio
           japonicas Cel5G appended to a GH5 (cellulase) domain.
           The GH5 (cellulase) family includes enzymes with several
           known activities such as endoglucanase, beta-mannanase,
           and xylanase, which are involved in the degradation of
           cellulose and xylans. GH43 includes beta-xylosidases and
           beta-xylanases, using aryl-glycosides as substrates.
           CBM6 is an unusual CBM as it represents a chimera of two
           distinct binding sites with different modes of binding:
           binding site I within the loop regions and binding site
           II on the concave face of the beta-sandwich fold.
          Length = 139

 Score = 28.4 bits (64), Expect = 0.29
 Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 1/37 (2%)

Query: 13  NITTRYAKAIKSALF-VTIDGEFTGLNNGPNTTPYDT 48
            ++ R A       F + +DG  TG  + PNT  + T
Sbjct: 70  TVSFRVASPNSGGSFRLEVDGALTGSVDVPNTGGWQT 106


>gnl|CDD|221056 pfam11277, Med24_N, Mediator complex subunit 24 N-terminal.  This
           subunit of the Mediator complex appears to be conserved
           only from insects to humans. It is essential for correct
           retinal development in fish. Subunit composition of the
           mediator contributes to the control of differentiation
           in the vertebrate CNS as there are divergent functions
           of the mediator subunits Crsp34/Med27, Trap100/Med24,
           and Crsp150/Med14.
          Length = 991

 Score = 25.2 bits (55), Expect = 4.5
 Identities = 15/49 (30%), Positives = 18/49 (36%), Gaps = 5/49 (10%)

Query: 1   MAPT--QHPMILQHNITTRYAKAIKSALFV--TIDGEFTGLNNGPNTTP 45
           M PT    P + Q  +  R  K I             FTGL N P T+ 
Sbjct: 255 MNPTGDTQPYVEQLMMLKRL-KGIPLPRLYLEIWRACFTGLINVPETSE 302


>gnl|CDD|236387 PRK09130, PRK09130, NADH dehydrogenase subunit G; Validated.
          Length = 687

 Score = 24.8 bits (55), Expect = 6.0
 Identities = 8/12 (66%), Positives = 10/12 (83%)

Query: 55 KIRQGSMDFLLI 66
          K R+G M+FLLI
Sbjct: 82 KAREGVMEFLLI 93


>gnl|CDD|223874 COG0803, LraI, ABC-type metal ion transport system, periplasmic
           component/surface adhesin [Inorganic ion transport and
           metabolism].
          Length = 303

 Score = 24.6 bits (54), Expect = 7.1
 Identities = 9/46 (19%), Positives = 19/46 (41%), Gaps = 3/46 (6%)

Query: 13  NITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQ 58
           N++++ A+ +     V I G     + G   +  DT   Y   ++ 
Sbjct: 250 NVSSKSAETLAKETGVKILGLLYLDSLGDKDSKGDT---YISMMKA 292


  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
   0.322    0.136    0.413 

Gapped
Lambda     K      H
   0.267   0.0637    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,028,439
Number of extensions: 306083
Number of successful extensions: 249
Number of sequences better than 10.0: 1
Number of HSP's gapped: 249
Number of HSP's successfully gapped: 7
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
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 (21.9 bits)
S2: 53 (24.4 bits)