RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16969
         (77 letters)



>gnl|CDD|233931 TIGR02565, cas_Csy2, CRISPR type I-F/YPEST-associated protein Csy2.
            CRISPR (Clustered Regularly Interspaced Short
           Palindromic Repeats) is a widespread family of
           prokaryotic direct repeats with spacers of unique
           sequence between consecutive repeats. This protein
           family, typified by YPO2464 of Yersinia pestis, is a
           CRISPR-associated (Cas) family strictly associated with
           the Ypest subtype of CRISPR/Cas locus. This family is
           designated Csy2, for CRISPR/Cas Subtype Ypest protein 2
           [Mobile and extrachromosomal element functions, Other].
          Length = 296

 Score = 27.9 bits (62), Expect = 0.42
 Identities = 18/63 (28%), Positives = 28/63 (44%), Gaps = 7/63 (11%)

Query: 7   PHLGLGLGIGILDSALVPLLAS-VVDSRHTAHYGSIYALQQTAVSLAYSLGKFVVPTKIM 65
              G  + I +   A+ PL A   VD+    HY   +          YSLG++V P +I+
Sbjct: 222 KGRGWLVPIPVGYQAISPLYAPGQVDNARDPHYPFQFVEA------LYSLGEWVFPHRIV 275

Query: 66  DLS 68
           D+ 
Sbjct: 276 DID 278


>gnl|CDD|187807 cd09676, Csy2_I-F, CRISPR/Cas system-associated RAMP superfamily
           protein Csy2.  CRISPR (Clustered Regularly Interspaced
           Short Palindromic Repeats) and associated Cas proteins
           comprise a system for heritable host defense by
           prokaryotic cells against phage and other foreign DNA;
           RAMP superfamily protein; predicted Cas5 ortholog.
          Length = 292

 Score = 27.4 bits (61), Expect = 0.62
 Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 7/68 (10%)

Query: 2   SGLIGPHLGLGLGIGILDSALVPLLAS-VVDSRHTAHYGSIYALQQTAVSLAYSLGKFVV 60
           S  +    G  + I +   A+ PL A   VD+    HY   +          YSLG++V 
Sbjct: 214 SWSVKKGRGWLVPIPVGYQAISPLYAPGQVDNARDPHYPFQFVEA------LYSLGEWVF 267

Query: 61  PTKIMDLS 68
           P +I+D+ 
Sbjct: 268 PHRIVDID 275


>gnl|CDD|237086 PRK12386, PRK12386, fumarate reductase iron-sulfur subunit;
           Provisional.
          Length = 251

 Score = 27.4 bits (61), Expect = 0.73
 Identities = 9/21 (42%), Positives = 14/21 (66%)

Query: 14  GIGILDSALVPLLASVVDSRH 34
            I I D+AL+P+   VVD ++
Sbjct: 215 HIKITDNALIPMKERVVDRKY 235


>gnl|CDD|223481 COG0404, GcvT, Glycine cleavage system T protein
           (aminomethyltransferase) [Amino acid transport and
           metabolism].
          Length = 379

 Score = 25.3 bits (56), Expect = 3.3
 Identities = 10/40 (25%), Positives = 14/40 (35%), Gaps = 4/40 (10%)

Query: 1   MSGLIGPHLGLGLGIGILDSALV----PLLASVVDSRHTA 36
            SG   P LG  + +  +DS        L   +   R  A
Sbjct: 323 TSGTFSPTLGKSIALAYVDSDYAKPGTELEVEIRGKRVPA 362


>gnl|CDD|178695 PLN03150, PLN03150, hypothetical protein; Provisional.
          Length = 623

 Score = 25.5 bits (56), Expect = 3.4
 Identities = 16/69 (23%), Positives = 24/69 (34%), Gaps = 13/69 (18%)

Query: 6   GPHLGLGLGIGILDSALVPLLASVVDS-------------RHTAHYGSIYALQQTAVSLA 52
           GPHL +G  IGI     V  L  V+ +             +  A   + YA  +T  S  
Sbjct: 538 GPHLSVGAKIGIAFGVSVAFLFLVICAMCWWKRRQNILRAQRIAAREAPYAKARTHFSRD 597

Query: 53  YSLGKFVVP 61
             + +    
Sbjct: 598 VQMTRHHRQ 606


  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
   0.320    0.136    0.384 

Gapped
Lambda     K      H
   0.267   0.0674    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,764,326
Number of extensions: 288112
Number of successful extensions: 287
Number of sequences better than 10.0: 1
Number of HSP's gapped: 287
Number of HSP's successfully gapped: 24
Length of query: 77
Length of database: 10,937,602
Length adjustment: 46
Effective length of query: 31
Effective length of database: 8,897,318
Effective search space: 275816858
Effective search space used: 275816858
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 (21.8 bits)
S2: 53 (24.3 bits)