RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4476
         (266 letters)



>gnl|CDD|221912 pfam13086, AAA_11, AAA domain.  This family of domains contain a
           P-loop motif that is characteristic of the AAA
           superfamily. Many of the proteins in this family are
           conjugative transfer proteins.
          Length = 220

 Score = 31.9 bits (73), Expect = 0.21
 Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%)

Query: 133 DLNRSQVYAVKHAIQRP-LSLIQGM 156
           +LN SQ  A+K A+    ++LIQG 
Sbjct: 1   ELNDSQREAIKKALSSSDITLIQGP 25


>gnl|CDD|232945 TIGR00376, TIGR00376, DNA helicase, putative.  The gene product may
           represent a DNA helicase. Eukaryotic members of this
           family have been characterized as binding certain
           single-stranded G-rich DNA sequences (GGGGT and GGGCT).
           A number of related proteins are characterized as
           helicases [DNA metabolism, DNA replication,
           recombination, and repair].
          Length = 637

 Score = 32.1 bits (73), Expect = 0.30
 Identities = 23/75 (30%), Positives = 33/75 (44%), Gaps = 9/75 (12%)

Query: 82  SFDRMQLALRKFAVDDQSVSAYIYHRLLGHNVDEVLFRCHLPKHFSAPNLPDLNRSQVYA 141
           +F RM+ ALR      ++ S  +   +LG          H  + F     P+LN SQ  A
Sbjct: 114 TFKRMKEALRALT---ENHSRLLE-FILGREAPSKASEIHDFQFFD----PNLNESQKEA 165

Query: 142 VKHAI-QRPLSLIQG 155
           V  A+  + L LI G
Sbjct: 166 VLFALSSKDLFLIHG 180


>gnl|CDD|220633 pfam10214, Rrn6, RNA polymerase I-specific transcription-initiation
           factor.  RNA polymerase I-specific
           transcription-initiation factor Rrn6 and Rrn7 represent
           components of a multisubunit transcription factor
           essential for the initiation of rDNA transcription by
           Pol I. These proteins are found in fungi.
          Length = 753

 Score = 30.5 bits (69), Expect = 0.92
 Identities = 15/80 (18%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 169 GAGIGNSANTNRLRNKSNLNHRPSGANKLSQGHLSQGNNSQEITQPYSQVMSQGGGFSLS 228
            + + + +    +R+   ++    G + +     +      + +QP +   S     S S
Sbjct: 659 SSQLESQSQIPTIRSSQQVSQTRKGGSSVVP--SAPAPRLAQSSQPPTSQSSSDLPPSSS 716

Query: 229 QADLSQDSLMMSQLDGMLSQ 248
           QA    D  M SQ +  LS 
Sbjct: 717 QAFSLSDLPMQSQSESGLSG 736


>gnl|CDD|235895 PRK06945, flgK, flagellar hook-associated protein FlgK; Validated.
          Length = 651

 Score = 29.2 bits (66), Expect = 2.3
 Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 5/65 (7%)

Query: 192 SGANKLSQGHLSQGNNSQEITQPYSQVMS---QGGGFSLSQADLSQDSLMMSQLDGMLSQ 248
           +G      G+L QG N   + + YSQ +S        + S   LS     +SQL+  L+ 
Sbjct: 44  AGGQYTGSGYLGQGVNVVTVKRQYSQYLSAQLNNAQAASSS--LSTYYSQISQLNNYLAD 101

Query: 249 ESAYL 253
            +A L
Sbjct: 102 PTAGL 106


>gnl|CDD|130673 TIGR01612, 235kDa-fam, reticulocyte binding/rhoptry protein.  This
            model represents a group of paralogous families in
            plasmodium species alternately annotated as reticulocyte
            binding protein, 235-kDa family protein and rhoptry
            protein. Rhoptry protein is localized on the cell surface
            and is extremely large (although apparently lacking in
            repeat structure) and is important for the process of
            invasion of the RBCs by the parasite. These proteins are
            found in P. falciparum, P. vivax and P. yoelii.
          Length = 2757

 Score = 28.5 bits (63), Expect = 4.8
 Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 4/80 (5%)

Query: 131  LPDLNRSQVYAVKHAIQRPLSLIQGMNQRSNGLHHQPGGAGIGNSANTNRLRNKSNLNHR 190
            + DLN+SQ   + H I +   +I+ +    +G+H+      I      +++++ +N +H 
Sbjct: 2610 ILDLNKSQ-NILNHLIHKNKKIIEDLGNIKHGIHNNNNLHTINKHEEISKIKHPNNTSHN 2668

Query: 191  PSGANKLSQGHLSQGNNSQE 210
             +   K    H S   NS E
Sbjct: 2669 NNDDAKYKNHHHS---NSDE 2685


>gnl|CDD|223052 PHA03346, PHA03346, US22 family homolog; Provisional.
          Length = 520

 Score = 27.8 bits (62), Expect = 6.2
 Identities = 15/55 (27%), Positives = 22/55 (40%), Gaps = 7/55 (12%)

Query: 218 VMSQGGGFSLSQADLSQDSLMM--SQLD-----GMLSQESAYLDHRPPYSNTHYS 265
           V+  G    L   + SQD L++    LD     G+L  E  Y   + PY+     
Sbjct: 117 VLCMGAETRLYIYEPSQDILILVAPHLDELARYGLLHSECVYRQPQTPYATRVPH 171


>gnl|CDD|182974 PRK11115, PRK11115, transcriptional regulator PhoU; Provisional.
          Length = 236

 Score = 27.3 bits (61), Expect = 7.6
 Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 4/56 (7%)

Query: 201 HLSQGNNSQEITQPYSQVMSQGGGFSLSQADLSQDSLMMSQLDGMLSQESAYLDHR 256
           H+S G  + E+    +QV++ GG   L +  LS     M   D  L++     DH+
Sbjct: 9   HIS-GQFNAELESIRTQVLTMGG---LVEQQLSDAITAMHNQDAELAKRVIEGDHK 60


  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
   0.315    0.131    0.386 

Gapped
Lambda     K      H
   0.267   0.0766    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,907,116
Number of extensions: 1162856
Number of successful extensions: 812
Number of sequences better than 10.0: 1
Number of HSP's gapped: 811
Number of HSP's successfully gapped: 10
Length of query: 266
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 171
Effective length of database: 6,723,972
Effective search space: 1149799212
Effective search space used: 1149799212
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 (21.6 bits)
S2: 58 (26.0 bits)