RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy15694
         (81 letters)



>gnl|CDD|218295 pfam04858, TH1, TH1 protein.  TH1 is a highly conserved but
          uncharacterized metazoan protein. No homologue has been
          identified in Caenorhabditis elegans. TH1 binds
          specifically to A-Raf kinase.
          Length = 582

 Score = 93.4 bits (232), Expect = 4e-24
 Identities = 43/79 (54%), Positives = 48/79 (60%), Gaps = 6/79 (7%)

Query: 1  MNDDYDDEQTHRWDQDMVDV----DSDGGDDPMENPQEVLNECLEKFSTPDYIMEPGIFS 56
          M +DY  E T  WD+         D D   +  ENP  VL ECL +FST DYIMEP IF 
Sbjct: 1  MEEDY--EVTSGWDRSDGRGTAQGDDDARAEVDENPTAVLQECLRRFSTKDYIMEPSIFD 58

Query: 57 QLKRYFQAGGNPEQVIELM 75
           LKRYFQAGG PE VIEL+
Sbjct: 59 DLKRYFQAGGAPETVIELL 77


>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA.  This model describes
           a univeral, mostly one-gene-per-genome GTP-binding
           protein that associates with ribosomal subunits and
           appears to play a role in ribosomal RNA maturation. This
           GTPase, related to the nucleolar protein Obg, is
           designated CgtA in bacteria. Mutations in this gene are
           pleiotropic, but it appears that effects on cellular
           functions such as chromosome partition may be secondary
           to the effect on ribosome structure. Recent work done in
           Vibrio cholerae shows an essential role in the stringent
           response, in which RelA-dependent ability to synthesize
           the alarmone ppGpp is required for deletion of this
           GTPase to be lethal [Protein synthesis, Other].
          Length = 329

 Score = 27.8 bits (63), Expect = 0.44
 Identities = 10/28 (35%), Positives = 20/28 (71%), Gaps = 1/28 (3%)

Query: 17  MVDVDSDGGDDPMENPQEVLNECLEKFS 44
           ++D+  + G DP+E+ + + NE L+K+S
Sbjct: 242 LIDISPEDGSDPIEDYEIIRNE-LKKYS 268


>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
          Length = 390

 Score = 27.1 bits (61), Expect = 0.92
 Identities = 12/28 (42%), Positives = 20/28 (71%), Gaps = 1/28 (3%)

Query: 17  MVDVDSDGGDDPMENPQEVLNECLEKFS 44
           ++D+    G DP+EN + ++NE LEK+S
Sbjct: 244 LIDIAPIDGSDPVENARIIINE-LEKYS 270


>gnl|CDD|185231 PRK15331, PRK15331, chaperone protein SicA; Provisional.
          Length = 165

 Score = 26.9 bits (59), Expect = 0.94
 Identities = 11/25 (44%), Positives = 13/25 (52%)

Query: 39 CLEKFSTPDYIMEPGIFSQLKRYFQ 63
          C+  F  PDY M      QLK+ FQ
Sbjct: 64 CIYDFYNPDYTMGLAAVCQLKKQFQ 88


>gnl|CDD|144532 pfam00973, Paramyxo_ncap, Paramyxovirus nucleocapsid protein.  The
           nucleocapsid protein is referred to as NP. NP is is the
           major structural component of the nucleocapsid. The
           protein is approx. 58 kDa. 2600 NP molecules go to
           tightly encapsidate the RNA. NP interacts with several
           other viral encoded proteins, all of which are involved
           in controlling replication. {NP-NP, NP-P, NP-(PL), and
           NP-V}.
          Length = 524

 Score = 26.7 bits (59), Expect = 1.4
 Identities = 8/32 (25%), Positives = 18/32 (56%), Gaps = 2/32 (6%)

Query: 4   DYDDEQTHRWDQDMVDVD--SDGGDDPMENPQ 33
             DDE +    + ++D+D  S+   DP+++ +
Sbjct: 459 YTDDEPSSLSTETLLDIDTTSESDQDPLDSQK 490


>gnl|CDD|183567 PRK12515, PRK12515, RNA polymerase sigma factor; Provisional.
          Length = 189

 Score = 26.2 bits (58), Expect = 1.4
 Identities = 10/36 (27%), Positives = 12/36 (33%), Gaps = 5/36 (13%)

Query: 14  DQDMVDVDSDGGDDP-----MENPQEVLNECLEKFS 44
           D +      DG D P       +    L  CL K S
Sbjct: 98  DDEAAAAIEDGADTPEVALQKSDTSAALRACLAKLS 133


>gnl|CDD|216917 pfam02177, APP_N, Amyloid A4 N-terminal heparin-binding.  This
          N-terminal domain of APP, amyloid precursor protein, is
          the heparin-binding domain of the protein. this region
          is also responsible for stimulation of neurite
          outgrowth. The structure reveals both a highly charged
          basic surface that may interact with glycosaminoglycans
          in the brain and an abutting hydrophobic surface that
          is proposed to play an important functional role such
          as in dimerisation or ligand-binding. Structural
          similarities with cysteine-rich growth factors, taken
          together with its known growth-promoting properties,
          suggest the APP N-terminal domain could function as a
          growth factor in vivo.
          Length = 102

 Score = 25.8 bits (57), Expect = 2.0
 Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 5/43 (11%)

Query: 5  YDDEQTHRWDQDMVDVDSDGGDDPMENPQEVLNECLEKFSTPD 47
          Y D QT RW  D       G    +++  E+L  C + +   D
Sbjct: 15 YMDLQTGRWVPDP-----SGIATCLKDKLEILKYCRKVYPELD 52


>gnl|CDD|225144 COG2235, ArcA, Arginine deiminase [Amino acid transport and
           metabolism].
          Length = 409

 Score = 26.1 bits (58), Expect = 2.2
 Identities = 7/47 (14%), Positives = 20/47 (42%)

Query: 30  ENPQEVLNECLEKFSTPDYIMEPGIFSQLKRYFQAGGNPEQVIELMI 76
           +      N+ +E +     I   G   +++ Y  +    +++I ++I
Sbjct: 78  DKANAARNQFIETYLDEAEIKGTGTADEVRAYLLSLDKNKELISVLI 124


>gnl|CDD|219337 pfam07217, Het-C, Heterokaryon incompatibility protein Het-C.  In
           filamentous fungi, het loci (for heterokaryon
           incompatibility) are believed to regulate
           self/nonself-recognition during vegetative growth. As
           filamentous fungi grow, hyphal fusion occurs within an
           individual colony to form a network. Hyphal fusion can
           occur also between different individuals to form a
           heterokaryon, in which genetically distinct nuclei
           occupy a common cytoplasm. However, heterokaryotic cells
           are viable only if the individuals involved have
           identical alleles at all het loci.
          Length = 602

 Score = 25.8 bits (57), Expect = 2.5
 Identities = 7/21 (33%), Positives = 12/21 (57%)

Query: 26  DDPMENPQEVLNECLEKFSTP 46
           D+P  +  +VL++ L  F  P
Sbjct: 497 DNPGVDVDQVLDDILRVFHHP 517


>gnl|CDD|206685 cd01898, Obg, Obg GTPase.  The Obg nucleotide binding protein
           subfamily has been implicated in stress response,
           chromosome partitioning, replication initiation,
           mycelium development, and sporulation. Obg proteins are
           among a large group of GTP binding proteins conserved
           from bacteria to humans. The E. coli homolog, ObgE is
           believed to function in ribosomal biogenesis. Members of
           the subfamily contain two equally and highly conserved
           domains, a C-terminal GTP binding domain and an
           N-terminal glycine-rich domain.
          Length = 170

 Score = 25.1 bits (56), Expect = 3.7
 Identities = 10/25 (40%), Positives = 17/25 (68%), Gaps = 1/25 (4%)

Query: 20  VDSDGGDDPMENPQEVLNECLEKFS 44
           +D  G DDP+E+ + + NE LE ++
Sbjct: 86  IDLSGEDDPVEDYETIRNE-LEAYN 109


>gnl|CDD|223610 COG0536, Obg, Predicted GTPase [General function prediction only].
          Length = 369

 Score = 25.2 bits (56), Expect = 4.4
 Identities = 12/28 (42%), Positives = 19/28 (67%), Gaps = 1/28 (3%)

Query: 17  MVDVDSDGGDDPMENPQEVLNECLEKFS 44
           ++D+    G DP+E+ Q + NE LEK+S
Sbjct: 244 VIDLSPIDGRDPIEDYQTIRNE-LEKYS 270


>gnl|CDD|218458 pfam05136, Phage_portal_2, Phage portal protein, lambda family.
           This protein forms a hole, or portal, that enables DNA
           passage during packaging and ejection. It also forms the
           junction between the phage capsid and the tail proteins.
          Length = 352

 Score = 24.9 bits (55), Expect = 5.6
 Identities = 9/36 (25%), Positives = 13/36 (36%)

Query: 23  DGGDDPMENPQEVLNECLEKFSTPDYIMEPGIFSQL 58
           DG D   E       E  +     +  +EPG   +L
Sbjct: 249 DGTDGAGEGLGGPQGERGDADGEREIELEPGTVQEL 284


>gnl|CDD|236696 PRK10458, PRK10458, DNA cytosine methylase; Provisional.
          Length = 467

 Score = 24.6 bits (54), Expect = 7.4
 Identities = 7/16 (43%), Positives = 12/16 (75%)

Query: 5   YDDEQTHRWDQDMVDV 20
           Y D  THR+++D+ D+
Sbjct: 131 YCDPATHRFNEDIRDI 146


>gnl|CDD|237462 PRK13665, PRK13665, hypothetical protein; Provisional.
          Length = 316

 Score = 24.1 bits (53), Expect = 9.3
 Identities = 8/21 (38%), Positives = 17/21 (80%)

Query: 56 SQLKRYFQAGGNPEQVIELMI 76
          +QL+ ++ AGGN ++V++ +I
Sbjct: 75 NQLEAHYLAGGNVDRVVDALI 95


  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    0.137    0.413 

Gapped
Lambda     K      H
   0.267   0.0709    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,427,256
Number of extensions: 355178
Number of successful extensions: 240
Number of sequences better than 10.0: 1
Number of HSP's gapped: 240
Number of HSP's successfully gapped: 20
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
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: 42 (21.9 bits)
S2: 53 (24.2 bits)