RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11011
         (134 letters)



>gnl|CDD|216245 pfam01015, Ribosomal_S3Ae, Ribosomal S3Ae family. 
          Length = 195

 Score =  161 bits (411), Expect = 1e-51
 Identities = 64/128 (50%), Positives = 78/128 (60%), Gaps = 18/128 (14%)

Query: 1   MFTNKQVGKTLVNRTQGTKIASEGLKHRVFEVSLADLQSDQDAERSFRKFRLIAEDVQGH 60
           MF ++++GKT  N         E LK RV EVSLADL    D  +S RK +   EDVQG 
Sbjct: 26  MFGSREIGKTPAND-------PEKLKGRVVEVSLADLT--GDYSKSNRKLKFKIEDVQGD 76

Query: 61  NVLTNFHGMDLTTDKLRSMVKKWQTLIEANVDVKTTDGYLLRLFCIGFTHKDQLSQRKTC 120
           N LTNFHG +LT D LRS+V++W + IEA VDVKT DGYLLR+F I FT K         
Sbjct: 77  NALTNFHGHELTRDYLRSLVRRWTSKIEAIVDVKTKDGYLLRVFVIAFTKKR-------- 128

Query: 121 YAQHNQIK 128
            AQ +Q +
Sbjct: 129 -AQTSQKR 135


>gnl|CDD|224802 COG1890, RPS1A, Ribosomal protein S3AE [Translation, ribosomal
           structure and biogenesis].
          Length = 214

 Score =  115 bits (290), Expect = 2e-33
 Identities = 48/119 (40%), Positives = 69/119 (57%), Gaps = 10/119 (8%)

Query: 1   MFTNKQVGKTLVNRTQGTKIASEGLKHRVFEVSLADLQSDQDAERSFRKFRLIAEDVQGH 60
            F   +VGKT  N         + L  RV EV+LADL  D    +S RK +   +DV+G 
Sbjct: 27  YFGGVEVGKTPAND-------PDKLIGRVVEVTLADLTGDFS--KSHRKLKFRIDDVEGD 77

Query: 61  NVLTNFHGMDLTTDKLRSMVKKWQTLIEANVDVKTTDGYLLRLFCIGFT-HKDQLSQRK 118
             LT F G +LT D +RS+V++  + I+A VDVKT DGY+LR+  + FT  + + SQ++
Sbjct: 78  KALTRFKGHELTRDYIRSLVRRRTSRIDAIVDVKTKDGYVLRVKAMAFTRRRAKTSQKR 136


>gnl|CDD|235216 PRK04057, PRK04057, 30S ribosomal protein S3Ae; Validated.
          Length = 203

 Score = 69.9 bits (172), Expect = 9e-16
 Identities = 32/84 (38%), Positives = 47/84 (55%), Gaps = 2/84 (2%)

Query: 28  RVFEVSLADLQSDQDAERSFRKFRLIAEDVQGHNVLTNFHGMDLTTDKLRSMVKKWQTLI 87
           RV E +L DL  D   +     F++   +V+G    T F G +LT D LRS+V++  + I
Sbjct: 39  RVVETTLGDLTGDFSKQNVKLYFKID--NVEGDKAYTRFIGHELTRDYLRSLVRRRTSKI 96

Query: 88  EANVDVKTTDGYLLRLFCIGFTHK 111
           +A VDV T DGY +R+  +  T K
Sbjct: 97  DAIVDVTTKDGYKVRVKPVALTTK 120


>gnl|CDD|143385 cd07880, STKc_p38gamma_MAPK12, Catalytic domain of the
          Serine/Threonine Kinase, p38gamma Mitogen-Activated
          Protein Kinase.  Serine/Threonine Kinases (STKs),
          p38gamma subfamily, catalytic (c) domain. STKs catalyze
          the transfer of the gamma-phosphoryl group from ATP to
          serine/threonine residues on protein substrates. The
          p38gamma subfamily is part of a larger superfamily that
          includes the catalytic domains of other protein STKs,
          protein tyrosine kinases, RIO kinases, aminoglycoside
          phosphotransferase, choline kinase, and
          phosphoinositide 3-kinase. p38 kinases are
          mitogen-activated protein kinases (MAPKs), serving as
          important mediators of cellular responses to
          extracellular signals. They are activated by the MAPK
          kinases MKK3 and MKK6, which in turn are activated by
          upstream MAPK kinase kinases including TAK1, ASK1, and
          MLK3, in response to cellular stresses or inflammatory
          cytokines. Vertebrates contain four isoforms of p38,
          named alpha, beta, gamma, and delta. p38gamma, also
          called MAPK12, is predominantly expressed in skeletal
          muscle. Unlike p38alpha and p38beta, p38gamma is
          insensitive to pyridinylimidazoles. It displays an
          antagonizing function compared to p38alpha. p38gamma
          inhibits, while p38alpha stimulates, c-Jun
          phosphorylation and AP-1 mediated transcription.
          p38gamma also plays a role in the signaling between Ras
          and the estrogen receptor and has been implicated to
          increase cell invasion and breast cancer progression.
          In Xenopus, p38gamma is critical in the meiotic
          maturation of oocytes.
          Length = 343

 Score = 27.2 bits (60), Expect = 3.1
 Identities = 20/67 (29%), Positives = 37/67 (55%), Gaps = 11/67 (16%)

Query: 12 VNRTQGTKIASEGLKHRVFEVSLADLQSDQDAERSFRKFRLIAEDVQGHNV--LTNFHGM 69
          ++R  G K+A + L +R F       QS+  A+R++R+ RL+ + ++  NV  L +    
Sbjct: 35 LDRRTGAKVAIKKL-YRPF-------QSELFAKRAYRELRLL-KHMKHENVIGLLDVFTP 85

Query: 70 DLTTDKL 76
          DL+ D+ 
Sbjct: 86 DLSLDRF 92


>gnl|CDD|232932 TIGR00345, GET3_arsA_TRC40, transport-energizing ATPase,
           TRC40/GET3/ArsA family.  Members of this family are
           ATPases that energize transport, although with different
           partner proteins for different functions. Recent
           findings show that TRC40 (GET3 in yeast) in involved in
           the insertion of tail-anchored membrane proteins in
           eukaryotes. A similar function is expected for members
           of this family in archaea. However, the earliest
           discovery of a function for this protein family is ArsA,
           an arsenic resistance protein that partners with ArsB
           (see pfam02040) for As(III) efflux [Hypothetical
           proteins, Conserved].
          Length = 284

 Score = 26.7 bits (59), Expect = 3.8
 Identities = 8/57 (14%), Positives = 23/57 (40%)

Query: 72  TTDKLRSMVKKWQTLIEANVDVKTTDGYLLRLFCIGFTHKDQLSQRKTCYAQHNQIK 128
            T +L  + +   + +E  + +++  G + +LF       + L + +    Q    +
Sbjct: 125 HTLRLLQLPEVLSSFLEKFIKIRSKLGPMAKLFMGAGEDDEALEKLEELKEQIEAAR 181


>gnl|CDD|217881 pfam04083, Abhydro_lipase, Partial alpha/beta-hydrolase lipase
           region.  This family corresponds to a N-terminal part of
           an alpha/beta hydrolase domain.
          Length = 62

 Score = 24.8 bits (55), Expect = 5.2
 Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 1/33 (3%)

Query: 93  VKTTDGYLLRLFCIGFTHKD-QLSQRKTCYAQH 124
           V T DGY+L L  I     +    ++     QH
Sbjct: 17  VTTEDGYILTLHRIPPGRNNRGRGKKPVVLLQH 49


>gnl|CDD|218703 pfam05700, BCAS2, Breast carcinoma amplified sequence 2 (BCAS2).
           This family consists of several eukaryotic sequences of
           unknown function. The mammalian members of this family
           are annotated as breast carcinoma amplified sequence 2
           (BCAS2) proteins. BCAS2 is a putative spliceosome
           associated protein.
          Length = 221

 Score = 25.9 bits (57), Expect = 7.8
 Identities = 7/25 (28%), Positives = 16/25 (64%)

Query: 71  LTTDKLRSMVKKWQTLIEANVDVKT 95
              +KLRS+ ++W  L+  N++++ 
Sbjct: 172 EAGEKLRSLEQRWVDLVSKNLEIEV 196


  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
   0.321    0.134    0.384 

Gapped
Lambda     K      H
   0.267   0.0742    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,236,381
Number of extensions: 524638
Number of successful extensions: 444
Number of sequences better than 10.0: 1
Number of HSP's gapped: 439
Number of HSP's successfully gapped: 13
Length of query: 134
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 48
Effective length of database: 7,123,158
Effective search space: 341911584
Effective search space used: 341911584
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: 54 (24.6 bits)