RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4833
         (141 letters)



>gnl|CDD|239154 cd02753, MopB_Formate-Dh-H, Formate dehydrogenase H (Formate-Dh-H)
           catalyzes the reversible oxidation of formate to CO2
           with the release of a proton and two electrons. It is a
           component of the anaerobic formate hydrogen lyase
           complex. The E. coli formate dehydrogenase H (Fdh-H) is
           a monomer composed of a single polypeptide chain with a 
           Mo active site region and a [4Fe-4S] center. Members of
           the MopB_Formate-Dh-H CD belong to the
           molybdopterin_binding (MopB) superfamily of proteins.
          Length = 512

 Score = 27.9 bits (63), Expect = 2.0
 Identities = 9/23 (39%), Positives = 12/23 (52%), Gaps = 1/23 (4%)

Query: 88  KMQLSDASDIFREVASGVTPSYA 110
               S   +IF E+A  +TP YA
Sbjct: 442 PGFYSHPEEIFDEIAR-LTPQYA 463


>gnl|CDD|240845 cd12399, RRM_HP0827_like, RNA recognition motif in Helicobacter
          pylori HP0827 protein and similar proteins.  This
          subfamily corresponds to the RRM of H. pylori HP0827, a
          putative ssDNA-binding protein 12rnp2 precursor,
          containing one RNA recognition motif (RRM), also termed
          RBD (RNA binding domain) or RNP (ribonucleoprotein
          domain). The ssDNA binding may be important in
          activation of HP0827. .
          Length = 78

 Score = 26.4 bits (59), Expect = 2.2
 Identities = 13/43 (30%), Positives = 23/43 (53%), Gaps = 12/43 (27%)

Query: 1  MTDDELRVAVVR-GQVLSVQGLGITGIRVSVDKDSGR---FGF 39
          +T+++L+    + G+V S         RV  D+++GR   FGF
Sbjct: 11 VTEEDLKDLFGQFGEVTSA--------RVITDRETGRSRGFGF 45


>gnl|CDD|222268 pfam13620, CarboxypepD_reg, Carboxypeptidase regulatory-like
          domain. 
          Length = 81

 Score = 25.3 bits (56), Expect = 5.5
 Identities = 21/77 (27%), Positives = 29/77 (37%), Gaps = 2/77 (2%)

Query: 10 VVRGQVLSVQGLGITGIRVSV-DKDSGRFGFTLTRGGGWFDMLVNGGGAVTLQFQRSPYR 68
           + G V    G  I G  V++ + D+G    T T   G F +     G  TL      Y+
Sbjct: 1  TISGTVTDASGAPIPGATVTLTNADTGTVRGTTTDADGRFSLTGLPPGTYTLTVSAPGYK 60

Query: 69 PQTRT-VFIPWNQIVVL 84
           QT   V +   Q   L
Sbjct: 61 SQTVKDVTVTAGQTTTL 77


>gnl|CDD|205225 pfam13044, DUF3904, Protein of unknown function (DUF3904).  This
           family of proteins is functionally uncharacterized. This
           family of proteins is found in viruses. Proteins in this
           family are typically between 437 and 448 amino acids in
           length.
          Length = 436

 Score = 26.5 bits (58), Expect = 5.7
 Identities = 10/17 (58%), Positives = 11/17 (64%)

Query: 38  GFTLTRGGGWFDMLVNG 54
           GFTL  GG WF   +NG
Sbjct: 273 GFTLGIGGAWFQAYLNG 289


>gnl|CDD|215193 PLN02337, PLN02337, lipoxygenase.
          Length = 866

 Score = 26.2 bits (58), Expect = 7.1
 Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 7/45 (15%)

Query: 99  REVASGVTP-------SYAPKGNSDLQHYGPRSSNKTVRHCESSL 136
           RE+ +GV P        + PK   D + YG ++S+ T  H E +L
Sbjct: 370 REMLAGVNPVVIRRLTEFPPKSKLDPKKYGDQNSSITEEHIEKNL 414


  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
   0.319    0.136    0.408 

Gapped
Lambda     K      H
   0.267   0.0744    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,051,761
Number of extensions: 625454
Number of successful extensions: 518
Number of sequences better than 10.0: 1
Number of HSP's gapped: 518
Number of HSP's successfully gapped: 10
Length of query: 141
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 54
Effective length of database: 7,078,804
Effective search space: 382255416
Effective search space used: 382255416
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: 54 (24.5 bits)