RPS-BLAST 2.2.18 [Mar-02-2008]

Database: CDD.v.2.12 
           24,291 sequences; 6,026,850 total letters

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

Query= orf10
         (129 letters)

 ***** No hits found ******


Query= orf20
         (765 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gnl|CDD|82074 PRK07003, PRK07003, DNA polymerase III subunits ga...    41   0.001

>gnl|CDD|82074 PRK07003, PRK07003, DNA polymerase III subunits gamma and tau.
          Length = 825

 Score = 41.0 bits (95), Expect = 0.001
 Identities = 51/212 (24%), Positives = 65/212 (30%)

Query: 101 GTGTTTCAGAAGATATAATAAAAAAAATAGAAAAAAAAAATTGGAAACTAATAGCAATTT 160
           G       GA+   A      A  AA    AAAA AA  A    AA    ATA      +
Sbjct: 384 GARAAAAVGASAVPAVTGATGATGAALAPKAAAARAATRAEAPPAAPARPATAERGDDAS 443

Query: 161 TATTAACTCATAATCATATTGATCATGTAGGAGGAGTAGAAGAAATTATAAGAAGATATC 220
                    A A   A +      A   A     +G A +A       +A  AA  +A  
Sbjct: 444 DGDAPVPAKANARASADSRCDERDAQPPADSGSASGAASSAPPDTAFESAPRAAAPSAAT 503

Query: 221 CAAACGTAACTGTTTTTGGTCCTGAAGAAACAAAAACAAGAAATGTAAATAAAATTGTAA 280
            AA     A    +          AA  +     AA A  + ATG AAA       G   
Sbjct: 504 PAAVPDARAPAAASAEDAVEAAAPAAPESRPPTPAAGAPVSRATGAAAALDVLRNAGMRV 563

Query: 281 AACAAGGAGATGTAATAAAATTGTTAAAAAGT 312
           ++    GA        A+       A  +  T
Sbjct: 564 SSGRGAGAARPAAGPAASPTKPAPRAQVSVPT 595


Query= orf30
         (225 letters)

 ***** No hits found ******


Query= orf40
         (858 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gnl|CDD|33678 COG3889, COG3889, Predicted solute binding protein...    47   2e-05

>gnl|CDD|33678 COG3889, COG3889, Predicted solute binding protein [General
           function prediction only].
          Length = 872

 Score = 47.3 bits (112), Expect = 2e-05
 Identities = 33/147 (22%), Positives = 48/147 (32%), Gaps = 3/147 (2%)

Query: 505 TTGGGTGTTTTTATTTTAATTTTATTTTATAGTGTAAAGATGAAGGGATTAATTGGTTTT 564
              G   T   +     A        TT                G   TT+ T       
Sbjct: 721 VKIGQALTVYGSLEVFPAGENWGFIPTTK--RVKVRIMDPASGTGTSITTSGTFTAEVPQ 778

Query: 565 TGTAAAGAACTTACTTTACAACCTTTTAATCATCCTGTATTTTTTATTTTTAATTTTTTA 624
           + T        +A + T+     TT+   T     T T T++ +   TT+   T+T+TT 
Sbjct: 779 SPTKTETTLSYSAYSNTSILIE-TTSVVITKTVTQTQTTTSSPSPTQTTSPTQTSTSTTT 837

Query: 625 TTAGAATTAGTTTCTTTATTATCAAAA 651
           TT+ + TT G   C         AA A
Sbjct: 838 TTSPSQTTTGGGICGPIVIIVGLAALA 864



 Score = 45.4 bits (107), Expect = 5e-05
 Identities = 30/134 (22%), Positives = 44/134 (32%), Gaps = 5/134 (3%)

Query: 522 AATTTTATTTTATAGTGTAAAGATGAAGGGATTAATTGGTTTTTGTAAAGAACTTACTTT 581
            A T   +     AG        T          A+  GT+ TT         T     +
Sbjct: 725 QALTVYGSLEVFPAGENWGFIPTTKRVKVRIMDPASGTGTSITTSGTF-----TAEVPQS 779

Query: 582 ACAACCTTTTAATCATCCTGTATTTTTTATTTTTAATTTTTTATTAGAATTAGTTTCTTT 641
                 T + +A   T      T+   T T T T  TT++ + T   + T   T+T TTT
Sbjct: 780 PTKTETTLSYSAYSNTSILIETTSVVITKTVTQTQTTTSSPSPTQTTSPTQTSTSTTTTT 839

Query: 642 ATTATCAAAACCAA 655
           + + T      C  
Sbjct: 840 SPSQTTTGGGICGP 853



 Score = 45.0 bits (106), Expect = 8e-05
 Identities = 28/132 (21%), Positives = 41/132 (31%)

Query: 105 AGATTTATGTAATTTTAAGTTTGTTGAACCAGGAAAAATTGTTTCTCATTTTTGGGTTTT 164
            G   T  G+              T           A+ TGT+  T  T T     + T 
Sbjct: 723 IGQALTVYGSLEVFPAGENWGFIPTTKRVKVRIMDPASGTGTSITTSGTFTAEVPQSPTK 782

Query: 165 AAATATTGATTCAATCATATTTTCTCTTGTATTAGGATGTTTTTTTTTGAGCATCTTTTA 224
              T +  A +  +     T+   T T     T   +   T TT+ T  +   T TT+ +
Sbjct: 783 TETTLSYSAYSNTSILIETTSVVITKTVTQTQTTTSSPSPTQTTSPTQTSTSTTTTTSPS 842

Query: 225 CACAGTGGCAAA 236
               G G C   
Sbjct: 843 QTTTGGGICGPI 854



 Score = 42.3 bits (99), Expect = 4e-04
 Identities = 26/96 (27%), Positives = 39/96 (40%)

Query: 368 TTGTTTGGGTTTTTTTAATGAATCTTATGGATTTAATTCCAATTGATTTTTTTCCATTTA 427
            +GT T   T+ T T     + T T  T   +  + T+    TT    T T T   TTT+
Sbjct: 759 ASGTGTSITTSGTFTAEVPQSPTKTETTLSYSAYSNTSILIETTSVVITKTVTQTQTTTS 818

Query: 428 TTTCTGAGAGGTTTTTTCATTTTCCAGCAATGCGTA 463
           + + T   +   T+T+T  TT+          CG  
Sbjct: 819 SPSPTQTTSPTQTSTSTTTTTSPSQTTTGGGICGPI 854


Query= orf50
         (189 letters)

 ***** No hits found ******


Query= orf60
         (387 letters)

 ***** No hits found ******


Query= orf70
         (600 letters)

 ***** No hits found ******


Query= orf80
         (270 letters)

 ***** No hits found ******


Query= orf90
         (987 letters)

 ***** No hits found ******


Query= orf100
         (624 letters)

 ***** No hits found ******


Query= orf110
         (435 letters)

 ***** No hits found ******


  Database: CDD.v.2.12
    Posted date:  Aug 13, 2008 12:02 PM
  Number of letters in database: 6,026,850
  Number of sequences in database:  24,291
  
Lambda     K      H
   0.320    0.134    0.503 

Gapped
Lambda     K      H
   0.267   0.0579    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24291
Number of Hits to DB: 98,336,059
Number of extensions: 7540086
Number of successful extensions: 79485
Number of sequences better than 1.0e-03: 11
Number of HSP's gapped: 59896
Number of HSP's successfully gapped: 1457
Length of database: 6,026,850
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: 86 (37.2 bits)