RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy9120
         (263 letters)



>gnl|CDD|214983 smart01027, Beta-Casp, Beta-Casp domain.  The beta-CASP domain is
           found C terminal to the beta-lactamase domain in
           pre-mRNA 3'-end-processing endonuclease. The active site
           of this enzyme is located at the interface of these two
           domains.
          Length = 126

 Score = 59.5 bits (145), Expect = 2e-11
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 6/78 (7%)

Query: 3   QSKVYLPEEPFPHAHLVKTGRLKHFKSIHDDAFNAEFRQPCIVFCGHPSLRFGDSVHFVQ 62
           + +      PF   +L     L+  K +       +++ P ++      L  G S H+++
Sbjct: 48  RKRFEQGRNPFDFKNLKFVKSLEESKRL------NDYKGPKVIIASSGMLTGGRSRHYLK 101

Query: 63  LWGSNPLHTIIFTEPDFP 80
               +P +T+I T     
Sbjct: 102 RLAPDPRNTVILTGYQAE 119


>gnl|CDD|220932 pfam10996, Beta-Casp, Beta-Casp domain.  The beta-CASP domain is
           found C terminal to the beta-lactamase domain in
           pre-mRNA 3'-end-processing endonuclease. The active site
           of this enzyme is located at the interface of these two
           domains.
          Length = 124

 Score = 49.5 bits (119), Expect = 8e-08
 Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 8/71 (11%)

Query: 10  EEPFPHAHLVKTGRLKHFKSIHDDAFNAEFRQPCIVFCGHPSLRFGDSVHFVQLWGSNPL 69
             PF +        LK  +S+ +         P ++      L  G S+H+++    +P 
Sbjct: 55  AFPFDN--------LKFVRSVDESKELNNLGGPKVIIASSGMLEGGRSLHYLKKLAPDPK 106

Query: 70  HTIIFTEPDFP 80
           +T+I T     
Sbjct: 107 NTVILTGYQAE 117


>gnl|CDD|237481 PRK13723, PRK13723, conjugal transfer pilus assembly protein TraH;
           Provisional.
          Length = 451

 Score = 33.2 bits (76), Expect = 0.12
 Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 8/76 (10%)

Query: 132 SGQGATYLGG----VVVKALPPRPMDQQALKNANVLLLSGLTQTPTSNPDAMLGELCMTV 187
           S QG T +GG    V  KA       ++ LKN N ++   L++    + +  L E  MT+
Sbjct: 186 SRQGCT-VGGQSDSVRDKA--SDKDKERVLKNIN-IMWDALSKNRMFDGNKELKEFVMTL 241

Query: 188 VGTLRANGKVDRKVLT 203
            GTL      +   L 
Sbjct: 242 TGTLIFGENGEITPLP 257


>gnl|CDD|130908 TIGR01849, PHB_depoly_PhaZ, polyhydroxyalkanoate depolymerase,
           intracellular.  This model represents an intracellular
           depolymerase for polyhydroxyalkanoate (PHA), a carbon
           and energy storing polyester that accumulates in
           granules in many bacterial species when carbon sources
           are abundant but other nutrients are limiting. This
           family is named for PHAs generally, rather than
           polyhydroxybutyrate (PHB) specificially as in Ralstonia
           eutropha H16, to avoid overcalling chemical specificity
           in other species. Note that this family lacks the
           classic GXSXG lipase motif and instead shows weak
           similarity to some [Fatty acid and phospholipid
           metabolism, Degradation].
          Length = 406

 Score = 31.3 bits (71), Expect = 0.46
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 8/65 (12%)

Query: 58  VHFVQLWGSNPLHTIIFTEPDFPYVEALA-------PFQPLAMKSIHCPIDTSLNFNQAN 110
           + F++  G +  H I   +P  P + A+A       P QP +M  +  PID   +    N
Sbjct: 160 IEFIRFLGPDI-HVIAVCQPAVPVLAAVALMAENEPPAQPRSMTLMGGPIDARASPTVVN 218

Query: 111 KLIRE 115
           +L RE
Sbjct: 219 ELARE 223


>gnl|CDD|181325 PRK08252, PRK08252, enoyl-CoA hydratase; Provisional.
          Length = 254

 Score = 30.7 bits (70), Expect = 0.54
 Identities = 15/51 (29%), Positives = 26/51 (50%), Gaps = 4/51 (7%)

Query: 201 VLTLKRGEVLKIPLKRKRTRVNMSAE----IAEAVEPCELRPGLAIASIKG 247
           VL  +RG VL I + R   R  ++A     +A A++  +  P L++  + G
Sbjct: 5   VLVERRGRVLIITINRPEARNAVNAAVAQGLAAALDELDADPDLSVGILTG 55


>gnl|CDD|226926 COG4553, DepA, Poly-beta-hydroxyalkanoate depolymerase [Lipid
           metabolism].
          Length = 415

 Score = 29.4 bits (66), Expect = 2.1
 Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 8/65 (12%)

Query: 58  VHFVQLWGSNPLHTIIFTEPDFPYVEALA-------PFQPLAMKSIHCPIDTSLNFNQAN 110
           +  +   G +  H +   +P  P + A++       P  P +M  +  PID   N    N
Sbjct: 161 IEMINFLGPDA-HVMAVCQPTVPVLAAISLMEEDGDPNVPSSMTLMGGPIDARKNPTAVN 219

Query: 111 KLIRE 115
           +L  E
Sbjct: 220 ELATE 224


>gnl|CDD|236658 PRK10153, PRK10153, DNA-binding transcriptional activator CadC;
           Provisional.
          Length = 517

 Score = 28.9 bits (65), Expect = 3.3
 Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 2/30 (6%)

Query: 55  GDSVHFVQLWGSNPLHTIIFTEPDFPYVEA 84
           GD+    +   S+ L  I+ +EPDF Y +A
Sbjct: 353 GDAKSLNK--ASDLLEEILKSEPDFTYAQA 380


>gnl|CDD|185335 PRK15438, PRK15438, erythronate-4-phosphate dehydrogenase PdxB;
           Provisional.
          Length = 378

 Score = 28.7 bits (64), Expect = 3.7
 Identities = 15/50 (30%), Positives = 27/50 (54%), Gaps = 4/50 (8%)

Query: 144 VKALPPRPMDQQALKNANVLLLSGLTQTPTSNPDAMLGELCMTVVGTLRA 193
           VKA+P RP+    L +A+ L++  +T+      +++L    +  VGT  A
Sbjct: 22  VKAVPGRPIPVAQLADADALMVRSVTKV----NESLLAGKPIKFVGTATA 67


>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 782

 Score = 28.3 bits (64), Expect = 5.7
 Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 10/53 (18%)

Query: 164 LLSGLTQTPTSNPDAMLGELCMTVVGTLRAN----GKVDRKVLTLKRGEVLKI 212
           L+S LT  P     AM GE+      TLR      G +  K+L   RG +  +
Sbjct: 690 LVSLLTGKPVRADVAMTGEI------TLRGRVLPIGGLKEKLLAAHRGGIKTV 736


>gnl|CDD|238343 cd00620, Methyltransferase_Sun, N-terminal RNA binding domain of
           the methyltransferase Sun. The rRNA-specific
           5-methylcytidine transferase Sun, also known as RrmB or
           Fmu shares the RNA-binding non-catalytic domain with the
           transcription termination factor NusB. The precise
           biological role of this domain in Sun is unknown,
           although it is likely to be involved in
           sequence-specific RNA binding. The C-terminal
           methyltransferase domain of Sun has been shown to
           catalyze formation of m5C at position 967 of 16S rRNA in
           Escherichia coli.
          Length = 126

 Score = 26.1 bits (58), Expect = 9.6
 Identities = 24/104 (23%), Positives = 37/104 (35%), Gaps = 15/104 (14%)

Query: 153 DQQALKNANVLLLSGLTQTPTSNPD-AMLGELCMTVVGTLRANGKVD---RKVLTLKRGE 208
           D      +   +LS L +   S+ D  +  EL     GTLR    +D     +L      
Sbjct: 13  DVLQRGASLNAVLSALQKKDKSDRDRGLATELV---YGTLRWLALLDWIINPLLKKPDVG 69

Query: 209 V-------LKIPL-KRKRTRVNMSAEIAEAVEPCELRPGLAIAS 244
                   L++ L +     V   A + E VE  ++R  L  A 
Sbjct: 70  KDPDVRNLLRLGLYQLLYLDVPPHAAVDETVEIAKIRKDLGRAG 113


  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    0.137    0.427 

Gapped
Lambda     K      H
   0.267   0.0812    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,396,218
Number of extensions: 1249716
Number of successful extensions: 998
Number of sequences better than 10.0: 1
Number of HSP's gapped: 997
Number of HSP's successfully gapped: 15
Length of query: 263
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 168
Effective length of database: 6,723,972
Effective search space: 1129627296
Effective search space used: 1129627296
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: 58 (26.0 bits)