RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy9260
         (217 letters)



>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and
            modification].
          Length = 2365

 Score =  296 bits (759), Expect = 8e-93
 Identities = 133/214 (62%), Positives = 144/214 (67%), Gaps = 41/214 (19%)

Query: 24   SRLKQEKASGFEESMKYKKLTNAQRSGLNQIPNRRFTLWWSPTINRANVYVGFQVQLDLT 83
              L  EKASGFEESMK+KKLTNAQR GL+QIPNRRFTLWWSPTINRANVYVGFQVQLDLT
Sbjct: 1528 EGLFWEKASGFEESMKFKKLTNAQRMGLSQIPNRRFTLWWSPTINRANVYVGFQVQLDLT 1587

Query: 84   GIFMHGKIPTLKISLIQIFRAHLWQKVHESIVMDLCQ----------------------- 120
            GI MHGKIPTLKISLIQIFR HLWQK+HES+V DLCQ                       
Sbjct: 1588 GILMHGKIPTLKISLIQIFRNHLWQKIHESVVGDLCQVLDKELDVLQIETVQKETVHPRK 1647

Query: 121  ----------------HSINFSP--LMFISRDTMDSTTTQKYWLDVQLRWGDYDSHDIER 162
                            +    S   L+   RD   +  T K W+DVQLRWGDYDSHDI R
Sbjct: 1648 SYKMNSSCADILLSGAYDWCVSSPSLLLEERDGGSNVRTNKLWIDVQLRWGDYDSHDIHR 1707

Query: 163  YARAKFLDYTTDNMSIYPSPTGVLIAIDLAYNLH 196
            YARAKFLDYTTD  S+YPSPTGV+I IDL YN+ 
Sbjct: 1708 YARAKFLDYTTDPQSMYPSPTGVVIGIDLCYNMW 1741


>gnl|CDD|151125 pfam10596, U6-snRNA_bdg, U6-snRNA interacting domain of PrP8.  This
           domain incorporates the interacting site for the
           U6-snRNA as part of the U4/U6.U5 tri-snRNPs complex of
           the spliceosome, and is the prime candidate for the role
           of cofactor for the spliceosome's RNA core. The
           essential spliceosomal protein Prp8 interacts with U5
           and U6 snRNAs and with specific pre-mRNA sequences that
           participate in catalysis. This close association with
           crucial RNA sequences, together with extensive genetic
           evidence, suggests that Prp8 could directly affect the
           function of the catalytic core, perhaps acting as a
           splicing cofactor.
          Length = 160

 Score =  200 bits (510), Expect = 6e-66
 Identities = 85/92 (92%), Positives = 91/92 (98%)

Query: 29  EKASGFEESMKYKKLTNAQRSGLNQIPNRRFTLWWSPTINRANVYVGFQVQLDLTGIFMH 88
           EKASGFEESMK+KKLTNAQRSGL+QIPNRRFTLWWSPTINRANVY+GFQVQLDLTG+FMH
Sbjct: 63  EKASGFEESMKFKKLTNAQRSGLSQIPNRRFTLWWSPTINRANVYIGFQVQLDLTGVFMH 122

Query: 89  GKIPTLKISLIQIFRAHLWQKVHESIVMDLCQ 120
           GKIPTLKISLIQIFRAHLWQK+HES+VMDL Q
Sbjct: 123 GKIPTLKISLIQIFRAHLWQKIHESLVMDLAQ 154


>gnl|CDD|237815 PRK14781, PRK14781, lipoprotein signal peptidase; Provisional.
          Length = 153

 Score = 30.5 bits (69), Expect = 0.32
 Identities = 12/31 (38%), Positives = 16/31 (51%)

Query: 63  WSPTINRANVYVGFQVQLDLTGIFMHGKIPT 93
           W PT N A+V+V   V L + G+    K P 
Sbjct: 120 WFPTFNLADVFVTTGVALLVLGMLRPPKDPE 150


>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein.  The
           Ligand-gated Ion Channel (LIC) Family of
           Neurotransmitter Receptors TC 1.A.9)Members of the LIC
           family of ionotropic neurotransmitter receptors are
           found only in vertebrate and invertebrate animals. They
           exhibit receptor specificity for (1)acetylcholine, (2)
           serotonin, (3) glycine, (4) glutamate and (5)
           g-aminobutyric acid (GABA). All of these receptor
           channels are probably hetero- orhomopentameric. The best
           characterized are the nicotinic acetyl-choline receptors
           which are pentameric channels of a2bgd subunit
           composition. All subunits arehomologous. The three
           dimensional structures of the protein complex in both
           the open and closed configurations have been solved at
           0.9 nm resolution.The channel protein complexes of the
           LIC family preferentially transport cations or anions
           depending on the channel (e.g., the acetylcholine
           receptors are cationselective while glycine receptors
           are anion selective) [Transport and binding proteins,
           Cations and iron carrying compounds].
          Length = 459

 Score = 29.3 bits (66), Expect = 1.8
 Identities = 9/36 (25%), Positives = 17/36 (47%), Gaps = 3/36 (8%)

Query: 128 LMFISRDTMDSTTT---QKYWLDVQLRWGDYDSHDI 160
           +M +    MD TT    ++ W D +L+W   +   +
Sbjct: 66  IMDVDEKNMDYTTNIWLRQEWTDERLQWNPEEYPGV 101


>gnl|CDD|239051 cd02136, Nitroreductase, Nitroreductase family. Members of this
           family utilize FMN as a cofactor and catalyze reduction
           of a variety of nitroaromatic compounds, including
           nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate
           and quinones by using either NADH or NADPH as a source
           of reducing equivalents in an obligatory two-election
           transfer mechanism.  The enzyme is typically a
           homodimer. Members of this family are also called NADH
           dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or
           dihydropteridine reductase.
          Length = 178

 Score = 27.5 bits (62), Expect = 3.5
 Identities = 10/47 (21%), Positives = 16/47 (34%)

Query: 155 YDSHDIERYARAKFLDYTTDNMSIYPSPTGVLIAIDLAYNLHRYIDY 201
           Y +  I R  +A        N   + +P G+   ID        +D 
Sbjct: 60  YGALGIAREDKAGRARQALRNFRFFGAPVGLFFTIDRRLGPGSALDL 106


>gnl|CDD|223385 COG0308, PepN, Aminopeptidase N [Amino acid transport and
           metabolism].
          Length = 859

 Score = 27.4 bits (61), Expect = 6.3
 Identities = 13/46 (28%), Positives = 17/46 (36%)

Query: 13  SQIYLFVHLLKSRLKQEKASGFEESMKYKKLTNAQRSGLNQIPNRR 58
             I L +++   +L   K   F E  K K L    R  L  I  R 
Sbjct: 805 GVIVLELNIFNPQLALRKIEEFLELKKLKALERLIREALETIAARE 850


>gnl|CDD|165574 PHA03330, PHA03330, putative primase; Provisional.
          Length = 771

 Score = 27.4 bits (60), Expect = 8.0
 Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 5/59 (8%)

Query: 48  RSGLNQIPNRRFTLWWSPTINRANVYVG-----FQVQLDLTGIFMHGKIPTLKISLIQI 101
           + G   IP   FT W     + A +        F +QL  +   +   +  L +  ++ 
Sbjct: 67  KEGEKIIPKNHFTWWPEEFHDPAALEAAGALQDFALQLGKSQASLEDFVSELFVEHVKT 125


>gnl|CDD|219342 pfam07227, DUF1423, Protein of unknown function (DUF1423).  This
           family represents a conserved region approximately 500
           residues long within a number of Arabidopsis thaliana
           proteins of unknown function.
          Length = 446

 Score = 27.0 bits (60), Expect = 9.9
 Identities = 30/111 (27%), Positives = 46/111 (41%), Gaps = 35/111 (31%)

Query: 1   MIHNKTQQSVEESQIYLFVHLLKSRLKQ--EKASGFEESMKYKKLTNAQRSGLNQIPNRR 58
            +H    + +EE         LK  L+   E A   +E +  +K     RS L       
Sbjct: 11  RMHEMPDEYLEE---------LKEALRGILEGAQKRDELVFLQKAVQ-SRSDLT------ 54

Query: 59  FTLWWSPTINRANVYVGFQVQLDL-----TGI--FMHGKIPTLKISLIQIF 102
                S T+ RA+     +VQL++     TGI  F+H  I   + SL++IF
Sbjct: 55  -----SETLIRAH-----RVQLEILVAIKTGIQAFLHPSISISQSSLVEIF 95


  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    0.135    0.412 

Gapped
Lambda     K      H
   0.267   0.0651    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,768,408
Number of extensions: 975642
Number of successful extensions: 920
Number of sequences better than 10.0: 1
Number of HSP's gapped: 920
Number of HSP's successfully gapped: 13
Length of query: 217
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 124
Effective length of database: 6,812,680
Effective search space: 844772320
Effective search space used: 844772320
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: 40 (21.5 bits)
S2: 57 (25.9 bits)