RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11482
         (172 letters)



>gnl|CDD|114259 pfam05527, DUF758, Domain of unknown function (DUF758).  Family of
           eukaryotic proteins with unknown function, which are
           induced by tumour necrosis factor.
          Length = 186

 Score =  155 bits (393), Expect = 2e-48
 Identities = 70/159 (44%), Positives = 100/159 (62%), Gaps = 12/159 (7%)

Query: 7   TDRFKTNDLAMRVQKKLASKMSNKSMVKMYIDDRSGRLLDNLYRVIKTYVSFRHQSGNGK 66
            + F + DLA++ QKK+ SKM++KS+  M+IDD S  +LD LYRV K Y           
Sbjct: 1   METFSSKDLALQAQKKILSKMASKSVANMFIDDTSSEILDELYRVTKEY----------- 49

Query: 67  DTNNKKQSEKIIKTLIKIIIKTTLLVKNHQFSSTELTTCETLKAKFHTLLMSLISFYEVD 126
            T NKK+++K+IK LIKI +K  +L +N+QFS  EL   E  + K H L M+ ISFYEVD
Sbjct: 50  -TGNKKEAQKVIKNLIKIAVKIGVLYRNNQFSPEELALAERFRKKLHQLAMTAISFYEVD 108

Query: 127 FSYDAAYLIRQLTTLRSQLAGLLQRHLTSKNLTNLDNLY 165
           F++D   L + LT  R  L  L+QRHLT K+   +++++
Sbjct: 109 FTFDRNVLSKLLTECRDLLHQLVQRHLTPKSHGRINHVF 147


>gnl|CDD|201855 pfam01552, Pico_P2B, Picornavirus 2B protein.  Poliovirus infection
           leads to drastic alterations in membrane permeability
           late during infection. Proteins 2B and 2BC enhance
           membrane permeability.
          Length = 99

 Score = 29.1 bits (66), Expect = 0.38
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 75  EKIIKTLIKIIIKTTLLVKNHQFSSTELTT 104
           EKI+K LIKI+    ++V+N     T   T
Sbjct: 39  EKILKWLIKIVSALVIVVRNSSDLVTVTAT 68


>gnl|CDD|235774 PRK06292, PRK06292, dihydrolipoamide dehydrogenase; Validated.
          Length = 460

 Score = 28.2 bits (64), Expect = 2.4
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 28  SNKSMVKMYIDDRSGRLL 45
            N   VK+Y D ++GRLL
Sbjct: 386 KNDGFVKVYADKKTGRLL 403


>gnl|CDD|239549 cd03466, Nitrogenase_NifN_2, Nitrogenase_nifN_2: A subgroup of the
           NifN subunit of the NifEN complex: NifN forms an
           alpha2beta2 tetramer with NifE.  NifN and nifE are
           structurally homologous to nitrogenase MoFe protein beta
           and alpha subunits respectively.  NifEN participates in
           the synthesis of the iron-molybdenum cofactor (FeMoco)
           of the MoFe protein.  NifB-co (an iron and sulfur
           containing precursor of the FeMoco) from NifB is
           transferred to the NifEN complex where it is further
           processed to FeMoco. The nifEN bound precursor of FeMoco
           has been identified as a molybdenum-free, iron- and
           sulfur- containing analog of FeMoco. It has been
           suggested that this nifEN bound precursor also acts as a
           cofactor precursor in nitrogenase systems which require
           a cofactor other than FeMoco: i.e. iron-vanadium
           cofactor (FeVco) or iron only cofactor (FeFeco). This
           group also contains the Clostidium fused NifN-NifB
           protein.
          Length = 429

 Score = 27.7 bits (62), Expect = 3.2
 Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 11/41 (26%)

Query: 6   DTDRFKTNDLAMRVQKKLASKMSNKSMVKMYIDDRSGRLLD 46
            TD F            L SK++ K + + Y  +R GRLLD
Sbjct: 260 ATDEFM----------SLLSKLTGKPIPEKYTRER-GRLLD 289


>gnl|CDD|107285 cd06290, PBP1_LacI_like_9, Ligand-binding domain of uncharacterized
           DNA-binding regulatory proteins that are members of the
           LacI-GalR family of bacterial transcription repressors. 
           This group includes the ligand-binding domain of
           uncharacterized DNA-binding regulatory proteins that are
           members of the LacI-GalR family of bacterial
           transcription repressors. The LacI-GalR family
           repressors are composed of two functional domains: an
           N-terminal HTH (helix-turn-helix) domain, which is
           responsible for the DNA-binding specificity, and a
           C-terminal ligand-binding domain, which is homologous to
           the sugar-binding domain of ABC-type transport systems
           that contain the type I periplasmic binding protein-like
           fold.  As also observed in the periplasmic binding
           proteins, the C-terminal domain of the bacterial
           transcription repressor undergoes a conformational
           change upon ligand binding which in turn changes the DNA
           binding affinity of the repressor.
          Length = 265

 Score = 27.3 bits (61), Expect = 4.7
 Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 3/26 (11%)

Query: 117 MSLISFYEVDFSYDAAYLIRQLTTLR 142
           +SLI F ++  S   AY    LTT+R
Sbjct: 206 VSLIGFDDLPLS---AYTTPPLTTVR 228


  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    0.132    0.361 

Gapped
Lambda     K      H
   0.267   0.0626    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,037,656
Number of extensions: 706573
Number of successful extensions: 690
Number of sequences better than 10.0: 1
Number of HSP's gapped: 689
Number of HSP's successfully gapped: 27
Length of query: 172
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 82
Effective length of database: 6,945,742
Effective search space: 569550844
Effective search space used: 569550844
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: 55 (25.2 bits)