RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy1832
         (111 letters)



>gnl|CDD|219530 pfam07714, Pkinase_Tyr, Protein tyrosine kinase. 
          Length = 258

 Score = 29.8 bits (68), Expect = 0.23
 Identities = 22/97 (22%), Positives = 36/97 (37%), Gaps = 27/97 (27%)

Query: 17  GNIFRGKYRIVEPVTHLRKAIK----------IEEFKIEERNMFLLRHPYL-------TE 59
           G +++G  +     T  + A+K           EEF  E   M  L HP +       T+
Sbjct: 13  GEVYKGTLKGDGEGTETKVAVKTLKEGASEEEREEFLEEASIMKKLSHPNIVRLLGVCTQ 72

Query: 60  EE------ELVHLKDLERNENF-RRERRALKLQKFIK 89
            E      E +   DL    +F R+    L L+  ++
Sbjct: 73  GEPLYIVTEYMPGGDL---LDFLRKHGEKLTLKDLLQ 106


>gnl|CDD|214568 smart00221, STYKc, Protein kinase; unclassified specificity.
          Phosphotransferases. The specificity of this class of
          kinases can not be predicted. Possible dual-specificity
          Ser/Thr/Tyr kinase.
          Length = 258

 Score = 27.5 bits (62), Expect = 1.1
 Identities = 14/51 (27%), Positives = 21/51 (41%), Gaps = 10/51 (19%)

Query: 17 GNIFRGKYRIVEPVTHLRKAIK----------IEEFKIEERNMFLLRHPYL 57
          G +++G  +       +  A+K          IEEF  E R M  L HP +
Sbjct: 13 GEVYKGTLKGKGDGKEVEVAVKTLKEDASEQQIEEFLREARIMRKLDHPNI 63


>gnl|CDD|197581 smart00219, TyrKc, Tyrosine kinase, catalytic domain.
          Phosphotransferases. Tyrosine-specific kinase
          subfamily.
          Length = 257

 Score = 27.1 bits (61), Expect = 1.9
 Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 10/51 (19%)

Query: 17 GNIFRGKYRIVEPVTHLRKAIK----------IEEFKIEERNMFLLRHPYL 57
          G +++GK +       +  A+K          IEEF  E R M  L HP +
Sbjct: 13 GEVYKGKLKGKGGKKKVEVAVKTLKEDASEQQIEEFLREARIMRKLDHPNV 63


>gnl|CDD|183017 PRK11177, PRK11177, phosphoenolpyruvate-protein phosphotransferase;
           Provisional.
          Length = 575

 Score = 26.9 bits (60), Expect = 2.7
 Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 7/32 (21%)

Query: 38  KIEEFKIEERNMFLLRHPYLTEEEELVHLKDL 69
            IEE K        ++  Y +E+ EL  LKDL
Sbjct: 235 VIEELK-------AVQEQYASEKAELAKLKDL 259


>gnl|CDD|133248 cd05148, PTKc_Srm_Brk, Catalytic domain of the Protein Tyrosine
          Kinases, Srm and Brk.  Protein Tyrosine Kinase (PTK)
          family; Src-related kinase lacking C-terminal
          regulatory tyrosine and N-terminal myristylation sites
          (Srm) and breast tumor kinase (Brk, also called protein
          tyrosine kinase 6); catalytic (c) domains. The PTKc
          family is part of a larger superfamily that includes
          the catalytic domains of other kinases such as protein
          serine/threonine kinases, RIO kinases, and
          phosphoinositide 3-kinase (PI3K). PTKs catalyze the
          transfer of the gamma-phosphoryl group from ATP to
          tyrosine (tyr) residues in protein substrates. Srm and
          Brk are a member of the Src subfamily of proteins,
          which are cytoplasmic (or non-receptor) tyr kinases.
          Src kinases in general contain an N-terminal SH4 domain
          with a myristoylation site, followed by SH3 and SH2
          domains, a tyr kinase domain, and a regulatory
          C-terminal region containing a conserved tyr; they are
          activated by autophosphorylation at the tyr kinase
          domain, but are negatively regulated by phosphorylation
          at the C-terminal tyr by Csk (C-terminal Src Kinase).
          Srm and Brk however, lack the N-terminal myristylation
          sites. Src proteins are involved in signaling pathways
          that regulate cytokine and growth factor responses,
          cytoskeleton dynamics, cell proliferation, survival,
          and differentiation. Brk has been found to be
          overexpressed in a majority of breast tumors.
          Length = 261

 Score = 25.9 bits (57), Expect = 4.6
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 14/50 (28%)

Query: 17 GNIFRGKYRIVEPVTHLRKAIKI---------EEFKIEERNMFLLRHPYL 57
          G ++ G ++       +R AIKI         ++F+ E + +  LRH +L
Sbjct: 20 GEVWEGLWK-----NRVRVAIKILKSDDLLKQQDFQKEVQALKRLRHKHL 64


>gnl|CDD|239662 cd03691, BipA_TypA_II, BipA_TypA_II: domain II of BipA (also
          called TypA) having homology to domain II of the
          elongation factors (EFs) EF-G and EF-Tu.  BipA is a
          highly conserved protein with global regulatory
          properties in Escherichia coli.  BipA is phosphorylated
          on a tyrosine residue under some cellular conditions.
          Mutants show altered regulation of some pathways. BipA
          functions as a translation factor that is required
          specifically for the expression of the transcriptional
          modulator Fis.  BipA binds to ribosomes at a site that
          coincides with that of EF-G and has a GTPase activity
          that is sensitive to high GDP:GTP ratios and, is
          stimulated  by 70S ribosomes programmed with mRNA and
          aminoacylated tRNAs. The growth rate-dependent
          induction of BipA allows the efficient expression of
          Fis, thereby modulating a range of downstream
          processes, including DNA metabolism and type III
          secretion.
          Length = 86

 Score = 25.1 bits (56), Expect = 5.0
 Identities = 11/28 (39%), Positives = 18/28 (64%)

Query: 17 GNIFRGKYRIVEPVTHLRKAIKIEEFKI 44
          G IFRG  ++ + V  +++  KIE+ KI
Sbjct: 20 GRIFRGTVKVGQQVAVVKRDGKIEKAKI 47


>gnl|CDD|235203 PRK04024, PRK04024, cofactor-independent phosphoglycerate mutase;
           Provisional.
          Length = 412

 Score = 25.6 bits (57), Expect = 6.9
 Identities = 10/21 (47%), Positives = 13/21 (61%)

Query: 6   ILLRGARKYPKGNIFRGKYRI 26
           ILLRGA + P+   F  KY +
Sbjct: 224 ILLRGAGEVPEIPKFTEKYGL 244


>gnl|CDD|132367 TIGR03324, alt_F1F0_F1_al, alternate F1F0 ATPase, F1 subunit alpha.
            A small number of taxonomically diverse prokaryotic
           species, including Methanosarcina barkeri, have what
           appears to be a second ATP synthase, in addition to the
           normal F1F0 ATPase in bacteria and A1A0 ATPase in
           archaea. These enzymes use ion gradients to synthesize
           ATP, and in principle may run in either direction. This
           model represents the F1 alpha subunit of this apparent
           second ATP synthase.
          Length = 497

 Score = 25.1 bits (55), Expect = 9.2
 Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 3/37 (8%)

Query: 2   HLTQILLR--GARKYPKGNIFRGKYRIVEPVTHLRKA 36
            L+ +L R  G   +P G+IF    R++E  THL + 
Sbjct: 272 ELSLLLRRPPGREAFP-GDIFYVHSRLLERSTHLNEE 307


  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
   0.325    0.142    0.414 

Gapped
Lambda     K      H
   0.267   0.0807    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,041,225
Number of extensions: 564790
Number of successful extensions: 770
Number of sequences better than 10.0: 1
Number of HSP's gapped: 766
Number of HSP's successfully gapped: 46
Length of query: 111
Length of database: 10,937,602
Length adjustment: 75
Effective length of query: 36
Effective length of database: 7,611,052
Effective search space: 273997872
Effective search space used: 273997872
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.0 bits)