RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13863
         (261 letters)



>gnl|CDD|217939 pfam04176, TIP41, TIP41-like family.  The TOR signalling pathway
           activates a cell-growth program in response to
           nutrients. TIP41 interacts with TAP42 and negatively
           regulates the TOR signaling pathway.
          Length = 180

 Score =  246 bits (630), Expect = 4e-83
 Identities = 87/179 (48%), Positives = 121/179 (67%), Gaps = 4/179 (2%)

Query: 57  MVFAGNILKLSHAG-GCSLEFNAFDALSSV-IVGEMPLQIACSEAWKSSRRSTGFTESHI 114
           M+F  N L++ H   G S+EFNA DAL  V   G   L++A ++ W+ SR  T      I
Sbjct: 1   MIFGDNFLRIEHEKSGWSIEFNALDALKLVDKTGLPMLKVAYAKEWQESREKTSSGIEVI 60

Query: 115 HPFDWTYSTDYAGTLVGDWAI--EKTSLQIDLEKLKQREKIHFYQDLILYEDELHDNGIA 172
            PFDWTY+TDY GT+ G   +  E T+ +I +EKLK+R+ I F+ ++IL+EDEL DNGI+
Sbjct: 61  KPFDWTYTTDYKGTVTGASGLLVEPTTERIPIEKLKRRDPILFFDEVILFEDELADNGIS 120

Query: 173 KCSVKIRVMSSGFFILLRFFLRVDDVLVRMNDTRLYHEYKNNFVLREISTRQASVKELR 231
             SVKIRVM S   +LLRFFLRVD+VL R+ DTR+Y E+  ++VLRE + R+A+  +L+
Sbjct: 121 MLSVKIRVMPSRLLLLLRFFLRVDNVLFRIRDTRIYVEFGKDYVLREYTHREATYDKLK 179


>gnl|CDD|233947 TIGR02600, Verru_Chthon_A, Verru_Chthon cassette protein A.  In
            Verrucomicrobium spinosum and Chthoniobacter flavus, a
            four-gene operon that includes proteins with an
            N-terminal signal sequence for cleavage and methylation
            recurs many times. Each operon is likely to encode a
            membrane complex, the function of which is unknown. This
            model represents a long protein from this putative
            membrame complex, with members averaging about 1300 amino
            acids. The N-terminal region includes an apparent signal
            sequence. The function is unknown. Most cassettes are
            adjacent to an unusually large protein with both an outer
            membrane autotransporter region and PEP-CTERM putative
            protein-sorting motif [Cell envelope, Surface
            structures].
          Length = 1265

 Score = 33.3 bits (76), Expect = 0.14
 Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 2/53 (3%)

Query: 81   ALSSVIVGEMPLQIACSEAWKS-SRRSTGFTES-HIHPFDWTYSTDYAGTLVG 131
             L +V+   +P  I  S          TG+  + + +  +WT    Y  TL G
Sbjct: 1059 GLHAVLKSVLPTAIPLSGVGNYNFTTETGYKYTANSYRAEWTADNIYNRTLAG 1111


>gnl|CDD|214835 smart00824, PKS_TE, Thioesterase.  Peptide synthetases are involved
           in the non-ribosomal synthesis of peptide antibiotics.
           Next to the operons encoding these enzymes, in almost
           all cases, are genes that encode proteins that have
           similarity to the type II fatty acid thioesterases of
           vertebrates. There are also modules within the peptide
           synthetases that also share this similarity. With
           respect to antibiotic production, thioesterases are
           required for the addition of the last amino acid to the
           peptide antibiotic, thereby forming a cyclic antibiotic.
           Thioesterases (non-integrated) have molecular masses of
           25-29 kDa.
          Length = 212

 Score = 30.3 bits (69), Expect = 0.73
 Identities = 9/20 (45%), Positives = 11/20 (55%)

Query: 188 LLRFFLRVDDVLVRMNDTRL 207
           LLR     +D  V M+D RL
Sbjct: 115 LLRGVFEREDSFVPMDDARL 134


>gnl|CDD|173636 cd05057, PTKc_EGFR_like, Catalytic domain of Epidermal Growth
           Factor Receptor-like Protein Tyrosine Kinases.  Protein
           Tyrosine Kinase (PTK) family; Epidermal Growth Factor
           Receptor (EGFR) subfamily; catalytic (c) domain. EGFR
           (HER, ErbB) subfamily members include EGFR (HER1,
           ErbB1), HER2 (ErbB2), HER3 (ErbB3), HER4 (ErbB4), and
           similar proteins. 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.
           The EGFR proteins are receptor tyr kinases (RTKs)
           containing an extracellular EGF-related ligand-binding
           region, a transmembrane helix, and a cytoplasmic region
           with a tyr kinase domain and a regulatory C-terminal
           tail. Unlike other tyr kinases, phosphorylation of the
           activation loop of EGFR proteins is not critical to
           their activation. Instead, they are activated by
           ligand-induced dimerization, resulting in the
           phosphorylation of tyr residues in the C-terminal tail,
           which serve as binding sites for downstream signaling
           molecules. Collectively, they can recognize a variety of
           ligands including EGF, TGFalpha, and neuregulins, among
           others. All four subfamily members can form homo- or
           heterodimers. HER3 contains an impaired kinase domain
           and depends on its heterodimerization partner for
           activation. EGFR subfamily members are involved in
           signaling pathways leading to a broad range of cellular
           responses including cell proliferation, differentiation,
           migration, growth inhibition, and apoptosis. Gain of
           function alterations, through their overexpression,
           deletions, or point mutations in their kinase domains,
           have been implicated in various cancers. These receptors
           are targets of many small molecule inhibitors and
           monoclonal antibodies used in cancer therapy.
          Length = 279

 Score = 30.1 bits (68), Expect = 0.94
 Identities = 14/46 (30%), Positives = 26/46 (56%)

Query: 216 VLREISTRQASVKELRIPQSMISDEEPNLVNMLPLIKSETHKLMFQ 261
           VLRE ++ +A+ + L     M S + P++V +L +  S   +L+ Q
Sbjct: 43  VLREETSPKANKEILDEAYVMASVDHPHVVRLLGICLSSQVQLITQ 88


>gnl|CDD|226355 COG3835, CdaR, Sugar diacid utilization regulator [Transcription /
           Signal transduction mechanisms].
          Length = 376

 Score = 28.1 bits (63), Expect = 4.4
 Identities = 16/92 (17%), Positives = 30/92 (32%), Gaps = 10/92 (10%)

Query: 80  DALSSVIVGEMPLQIACSEAWKSSRRSTGFTESHIHPFDWTYSTDYAGTLVGDWAIEKTS 139
           + ++ + + E  +      A +  R         +      Y         G++ +   S
Sbjct: 191 NDVAILSLNERVVLKPALSAERWDREVHSKRIEKLLARAKAYGRLSLRIGAGNYFVGPDS 250

Query: 140 LQIDLE----------KLKQREKIHFYQDLIL 161
           L    E          K K   +I+FY+DL L
Sbjct: 251 LARSYESAKKTLEVGLKRKPESRIYFYEDLRL 282


>gnl|CDD|111033 pfam02091, tRNA-synt_2e, Glycyl-tRNA synthetase alpha subunit. 
          Length = 284

 Score = 27.4 bits (61), Expect = 8.3
 Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 14/55 (25%)

Query: 63  ILKLSHAGGCSLEFNAFDALSSVIVGEMPLQIA--------CSEAWKSSRRSTGF 109
           +LK SHA      FN  DA  ++ V E    I          ++ +   R S GF
Sbjct: 234 VLKASHA------FNLLDARGAISVTERTRYILRIRQLARAVADLYYEQRESLGF 282


  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    0.403 

Gapped
Lambda     K      H
   0.267   0.0774    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,887,297
Number of extensions: 1190351
Number of successful extensions: 875
Number of sequences better than 10.0: 1
Number of HSP's gapped: 872
Number of HSP's successfully gapped: 10
Length of query: 261
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 166
Effective length of database: 6,723,972
Effective search space: 1116179352
Effective search space used: 1116179352
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: 58 (26.0 bits)