RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy1900
         (293 letters)



>gnl|CDD|217720 pfam03770, IPK, Inositol polyphosphate kinase.  ArgRIII has has
           been demonstrated to be an inositol polyphosphate
           kinase.
          Length = 183

 Score =  158 bits (403), Expect = 2e-48
 Identities = 61/183 (33%), Positives = 90/183 (49%), Gaps = 11/183 (6%)

Query: 109 FLILSNLIGDLHEPRVMDIKIGYQTHEPGAPKEKVLAEESKYAG-TKKPWGFCIPGFQIY 167
           +L+L +L     +P V+D+K+G + +   A +EK   ++ K A  T    GF I G ++Y
Sbjct: 1   YLLLEDLTAGFKKPCVLDLKMGTRQYGDDASEEKKRRQQRKCAQSTSASLGFRICGMKVY 60

Query: 168 NKDTGKREKYGKEFGKHLKKDSVLNVFKMFVDQYSSPSVSIETVKSFLYSLKQIQSWFET 227
           N D        K +G+ L  + V    K F     S     + +  FL  L+++++W E+
Sbjct: 61  NVDEDGYIFRDKYYGRSLSAEEVKEALKRFFSNGKSLRRKKKLIPRFLERLQELRNWLES 120

Query: 228 QRIYHFYSSSLLFSYD---------EHKAYVHMIDFAHVVPATDN-NLDSNYLGGLNNII 277
           Q  Y FYSSSLLF YD           K  V +IDFAH  P T     D  YL GL ++I
Sbjct: 121 QESYRFYSSSLLFVYDGDPSAEEDPPPKVKVKLIDFAHTTPLTPGGGPDEGYLFGLRSLI 180

Query: 278 KLF 280
           K+ 
Sbjct: 181 KIL 183


>gnl|CDD|215359 PLN02667, PLN02667, inositol polyphosphate multikinase.
          Length = 286

 Score =  155 bits (394), Expect = 9e-46
 Identities = 84/280 (30%), Positives = 132/280 (47%), Gaps = 31/280 (11%)

Query: 33  QVGGHEFIAGKQTMSMLKDKDGHVLKYINKPILGERETKFYEVLQS-TEDPELLKLKKFV 91
           QV GH    GK  +  L D  G   K +     GERE  FYE   S T  P+   +++F 
Sbjct: 8   QVAGHRASDGK--LGPLVDDSGRFYKPLQDDSRGEREAAFYESFSSDTRVPD--HIRRFF 63

Query: 92  PQYFGTTTLKMSNQDVKFLILSNLIGDLHEPRVMDIKIGYQTHEPGAPKEKVLAEESKYA 151
           P + GT  ++ S+     L+L +L+    +P VMD+K+G +T  P A +E +     K  
Sbjct: 64  PVFHGTQLVEASD-GSGLLVLEDLLAGYTKPCVMDVKMGSRTWYPEASEEYIQKCLKKDR 122

Query: 152 GTKK-PWGFCIPGFQIYNKDTGKREKYGKEFGKHLKKDSVLNVFKMFVDQYSSPSVSIET 210
            T     GF + GF++Y+    +  K  ++  K L  D V    + FV   S+       
Sbjct: 123 ETTTVSLGFRVSGFKVYDHKESEFWKAERKLVKGLDADGVRLALRKFVS--SNSPADPNP 180

Query: 211 VKSF-----------LYSLKQIQSWFETQRIYHFYSSSLLFSYDEH----------KAYV 249
             +F           L  L +++SWFE Q +YHF+S+S+L  Y+            +  V
Sbjct: 181 DCAFASAVYGGSHGILAQLLELKSWFEEQTLYHFFSASILIVYEGEAILKGNPEDSRVEV 240

Query: 250 HMIDFAHVVPATDNNLDSNYLGGLNNIIKLFQTILDDLEQ 289
            ++DFAHV+   +  +D N+LGGL ++IK    IL   ++
Sbjct: 241 KLVDFAHVLDG-NGVIDHNFLGGLCSLIKFISEILTSPDE 279


>gnl|CDD|221870 pfam12950, TaqI_C, TaqI-like C-terminal specificity domain.  This
           domain is found at the C-terminus of the TaqI protein
           and is involved in DNA-binding and substrate
           recognition.
          Length = 118

 Score = 32.9 bits (76), Expect = 0.059
 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 6/74 (8%)

Query: 224 WFETQRI-YHFYSSSLLFSYDEHKAYVHMIDFAHVVPATDNNLDSNYLGGLNN---IIKL 279
           +FE  +I        L+ +YDE + Y  +    +++   D N+   YL G+ N   I   
Sbjct: 36  FFEKPKILVRQIGGRLVAAYDE-EQYYWLNSL-YLLIPKDENISLKYLLGILNSKLIQFY 93

Query: 280 FQTILDDLEQGTVH 293
           ++ I  +      H
Sbjct: 94  YRKIYPEQRGLFPH 107


>gnl|CDD|184643 PRK14354, glmU, bifunctional N-acetylglucosamine-1-phosphate
          uridyltransferase/glucosamine-1-phosphate
          acetyltransferase; Provisional.
          Length = 458

 Score = 31.7 bits (73), Expect = 0.46
 Identities = 17/45 (37%), Positives = 21/45 (46%), Gaps = 10/45 (22%)

Query: 14 VMEDGTRFAIPQGTELLAEQVG-GHEFIAGKQTMSMLKDKDGHVL 57
          V+ D + FA      L  EQ+G GH   A  Q    L DK+G  L
Sbjct: 62 VLGDRSEFA------LQEEQLGTGH---AVMQAEEFLADKEGTTL 97


>gnl|CDD|218816 pfam05936, DUF876, Bacterial protein of unknown function
          (DUF876).  This family consists of a series of
          hypothetical bacterial sequences of unknown function.
          Length = 427

 Score = 29.5 bits (67), Expect = 2.4
 Identities = 8/22 (36%), Positives = 9/22 (40%)

Query: 11 AECVMEDGTRFAIPQGTELLAE 32
          A  +  DGT F IP    L   
Sbjct: 47 ASGIFPDGTPFDIPGDDPLPPP 68


>gnl|CDD|241109 cd12665, RRM2_RAVER1, RNA recognition motif 2 found in vertebrate
           ribonucleoprotein PTB-binding 1 (raver-1).  This
           subgroup corresponds to the RRM2 of raver-1, a
           ubiquitously expressed heterogeneous nuclear
           ribonucleoprotein (hnRNP) that serves as a co-repressor
           of the nucleoplasmic splicing repressor polypyrimidine
           tract-binding protein (PTB)-directed splicing of select
           mRNAs. It shuttles between the cytoplasm and the nucleus
           and can accumulate in the perinucleolar compartment, a
           dynamic nuclear substructure that harbors PTB. Raver-1
           also modulates focal adhesion assembly by binding to the
           cytoskeletal proteins, including alpha-actinin,
           vinculin, and metavinculin (an alternatively spliced
           isoform of vinculin) at adhesion complexes, particularly
           in differentiated muscle tissue. Raver-1 contains three
           N-terminal RNA recognition motifs (RRMs), also termed
           RBDs (RNA binding domains) or RNPs (ribonucleoprotein
           domains), two putative nuclear localization signals
           (NLS) at the N- and C-termini, a central leucine-rich
           region, and a C-terminal region harboring two
           PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB
           through the PTB-binding motifs at its C-terminal half,
           and binds to other partners, such as RNA having the
           sequence UCAUGCAGUCUG, through its N-terminal RRMs.
           Interestingly, the 12-nucleotide RNA having the sequence
           UCAUGCAGUCUG with micromolar affinity is found in
           vinculin mRNA. Additional research indicates that the
           RRM1 of raver-1 directs its interaction with the tail
           domain of activated vinculin. Then the raver1/vinculin
           tail (Vt) complex binds to vinculin mRNA, which is
           permissive for vinculin binding to F-actin. .
          Length = 77

 Score = 27.2 bits (60), Expect = 2.7
 Identities = 13/35 (37%), Positives = 22/35 (62%), Gaps = 2/35 (5%)

Query: 155 KPWGFCIPGFQIYNKDTGKREKYGKEFGKHLKKDS 189
           +P+G     F +Y++ TG  + YG  F +++KKDS
Sbjct: 21  RPFGNLERCFLVYSETTGHSKGYG--FVEYMKKDS 53


>gnl|CDD|236639 PRK10002, PRK10002, outer membrane protein F; Provisional.
          Length = 362

 Score = 27.5 bits (61), Expect = 7.8
 Identities = 11/20 (55%), Positives = 13/20 (65%)

Query: 165 QIYNKDTGKREKYGKEFGKH 184
           +IYNKD  K + YGK  G H
Sbjct: 24  EIYNKDGNKVDLYGKAVGLH 43


>gnl|CDD|218268 pfam04793, Herpes_BBRF1, BRRF1-like protein.  Family of herpesvirus
           proteins including Epstein-barr virus protein BBRF1.
          Length = 284

 Score = 27.7 bits (62), Expect = 7.8
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 4/58 (6%)

Query: 193 VFKMF--VDQYSSPSVSIETVKSFL-YSLKQIQSWFETQRIYHFYSSSLLFSYDEHKA 247
           V KMF           SI  + + L   +K   +W+++Q   H Y    +  Y EH  
Sbjct: 200 VLKMFSSCIYNDYLLDSIACISALLKNEVKAFCAWYDSQTFPH-YVPLAMVKYLEHLL 256


>gnl|CDD|227358 COG5025, COG5025, Transcription factor of the Forkhead/HNF3 family
           [Transcription].
          Length = 610

 Score = 27.9 bits (62), Expect = 9.0
 Identities = 11/46 (23%), Positives = 15/46 (32%)

Query: 14  VMEDGTRFAIPQGTELLAEQVGGHEFIAGKQTMSMLKDKDGHVLKY 59
               G  ++I  G E    + G      GKQ M  L       + Y
Sbjct: 153 AKVKGHFWSIGPGHETQFLKSGLRLDGGGKQMMFTLPSSTEIKITY 198


>gnl|CDD|211382 cd11010, S1-P1_nuclease, S1/P1 nucleases and related enzymes.  This
           family summarizes both S1 and P1 nucleases (EC:3.1.30.1)
           which cleave RNA and single stranded DNA with no base
           specificity. S1 nuclease is more active on DNA than RNA.
           Its reaction products are oligonucleotides or single
           nucleotides with 5' phosphoryl groups. Although its
           primary substrate is single-stranded, it may also
           introduce single-stranded breaks in double-stranded DNA
           or RNA, or DNA-RNA hybrids. It is used as a reagent in
           nuclease protection assays and in removing single
           stranded tails from DNA molecules to create blunt ended
           molecules and opening hairpin loops generated during
           synthesis of double stranded cDNA. P1 nuclease cleaves
           its substrate at every position yielding nucleoside 5'
           monophosphates, and it does not recognize or act on
           double-stranded DNA. It is useful at removing single
           stranded strands hanging off the end of double stranded
           DNA and at completely cleaving melted DNA for simple DNA
           composition analysis.
          Length = 249

 Score = 27.3 bits (61), Expect = 9.9
 Identities = 8/26 (30%), Positives = 16/26 (61%), Gaps = 2/26 (7%)

Query: 97  TTTLKMSNQDVKFLILSNLIGDLHEP 122
           + +     + +KFLI  + +GD+H+P
Sbjct: 98  SLSDAERAEALKFLI--HFVGDIHQP 121


  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
   0.319    0.136    0.402 

Gapped
Lambda     K      H
   0.267   0.0788    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,814,512
Number of extensions: 1396049
Number of successful extensions: 1149
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1140
Number of HSP's successfully gapped: 18
Length of query: 293
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 197
Effective length of database: 6,679,618
Effective search space: 1315884746
Effective search space used: 1315884746
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 (21.7 bits)
S2: 59 (26.4 bits)