RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6410
         (169 letters)



>gnl|CDD|218165 pfam04597, Ribophorin_I, Ribophorin I.  Ribophorin I is an
           essential subunit of oligosaccharyltransferase (OST),
           which is also known as
           Dolichyl-diphosphooligosaccharide--protein
           glycosyltransferase, (EC:2.4.1.119). OST catalyzes the
           transfer of an oligosaccharide from dolichol
           pyrophosphate to selected asparagine residues of nascent
           polypeptides as they are translocated into the lumen of
           the rough endoplasmic reticulum. Ribophorin I and OST48
           are though to be responsible for OST catalytic activity.
           Both yeast and mammalian proteins are glycosylated but
           the sites are not conserved. Glycosylation may
           contribute towards general solubility but is unlikely to
           be involved in a specific biochemical function Most
           family members are predicted to have a transmembrane
           helix at the C terminus of this region.
          Length = 429

 Score =  142 bits (361), Expect = 3e-41
 Identities = 64/123 (52%), Positives = 79/123 (64%), Gaps = 13/123 (10%)

Query: 55  NIESFTSV--MPTTQVEQTITYGPYENVPPYTKANITIHYENNSPFLVVTRLVRQIEVSH 112
           NI S+T    +P T+   T+TYGPYENVP ++   IT+HYENN P + VT L R IEVSH
Sbjct: 147 NILSYTKTPNLPPTRQGNTLTYGPYENVPAFSLEPITVHYENNKPLITVTNLERDIEVSH 206

Query: 113 W------EHIHLKHDGAKLKGTFSRYDYQRDS-----AHGIKSFKTILPAAASDAYYRDE 161
           W      E+  L ++GAKLKG FSR DYQ+ S     +  +KS KT LPA A+D YY DE
Sbjct: 207 WGNIAVEEYYELTNNGAKLKGGFSRVDYQKGSYSTRNSSALKSLKTPLPAGATDVYYTDE 266

Query: 162 IGK 164
           IG 
Sbjct: 267 IGN 269


>gnl|CDD|236728 PRK10629, PRK10629, EnvZ/OmpR regulon moderator; Provisional.
          Length = 127

 Score = 30.0 bits (68), Expect = 0.28
 Identities = 19/54 (35%), Positives = 24/54 (44%), Gaps = 6/54 (11%)

Query: 97  PFLVVTRLVRQIEVSHWEHIHLKHDGAKLKGTFSRYDYQRDSAHGIKSFKTILP 150
             L  + L +Q E +    I   H GA L   F  Y YQ   A+GI   K+I P
Sbjct: 24  LLLAWSALRQQ-ESTL--AIRAVHQGASLPDGF--YVYQHLDANGI-HIKSITP 71


>gnl|CDD|221494 pfam12257, DUF3608, Protein of unknown function (DUF3608).  This
           domain family is found in eukaryotes, and is
           approximately 280 amino acids in length. The family is
           found in association with pfam00610.
          Length = 281

 Score = 28.1 bits (63), Expect = 2.2
 Identities = 22/91 (24%), Positives = 35/91 (38%), Gaps = 18/91 (19%)

Query: 26  ITIHYENNSPFLVVTRLVRQIEVSHWGTLNIESFTSVMPTTQVEQTITYGPYENVPPYTK 85
           I  H   NS F  + +  + I   H  ++ I  FTSV  +           + ++ P  +
Sbjct: 92  IMFHKLVNSLFPKIFKKWKDINTHH--SITIVLFTSVDLSDI--------SWTDLGPGER 141

Query: 86  ANITIHYENNSPFLVVTRLVRQIEVSHWEHI 116
                 Y     F VV   V Q+ + HW+ I
Sbjct: 142 PKNRRDY-----FRVV---VDQVNIIHWDEI 164


>gnl|CDD|197886 smart00809, Alpha_adaptinC2, Adaptin C-terminal domain.  Adaptins
           are components of the adaptor complexes which link
           clathrin to receptors in coated vesicles.
           Clathrin-associated protein complexes are believed to
           interact with the cytoplasmic tails of membrane
           proteins, leading to their selection and concentration.
           Gamma-adaptin is a subunit of the golgi adaptor. Alpha
           adaptin is a heterotetramer that regulates clathrin-bud
           formation. The carboxyl-terminal appendage of the alpha
           subunit regulates translocation of endocytic accessory
           proteins to the bud site. This Ig-fold domain is found
           in alpha, beta and gamma adaptins and consists of a
           beta-sandwich containing 7 strands in 2 beta-sheets in a
           greek-key topology.. The adaptor appendage contains an
           additional N-terminal strand.
          Length = 104

 Score = 26.1 bits (58), Expect = 4.6
 Identities = 17/83 (20%), Positives = 27/83 (32%), Gaps = 17/83 (20%)

Query: 22  TKANITIHYENNSPFLVVTRLVRQIEVSHWGTLNIESFTSVMPTTQVEQTITYGPYENVP 81
               IT+ + N SP   +T    Q  V     L ++  +S                  +P
Sbjct: 18  GLIRITLTFTNKSPS-PITNFSFQAAVPKSLKLQLQPPSS----------------PTLP 60

Query: 82  PYTKANITIHYENNSPFLVVTRL 104
           P  +    +  EN   F +  RL
Sbjct: 61  PGGQITQVLKVENPGKFPLRLRL 83


>gnl|CDD|212573 cd11700, DHR2_DOCK11, Dock Homology Region 2, a GEF domain, of
           Class D Dedicator of Cytokinesis 11.  Dock11, also
           called Zizimin2 or activated Cdc42-associated GEF (ACG),
           is an atypical guanine nucleotide exchange factor (GEF)
           that lacks the conventional Dbl homology (DH) domain. As
           a GEF, it activates the small GTPase Cdc42 by exchanging
           bound GDP for free GTP. Dock11 is predominantly
           expressed in lymphocytes and is found in high levels in
           germinal center B lymphocytes after T cell dependent
           antigen immunization. DOCK proteins are divided into
           four classes (A-D) based on sequence similarity and
           domain architecture; class D includes Dock9, 10 and 11.
           All DOCKs contain two homology domains: the DHR-1 (Dock
           homology region-1), also called CZH1 (CED-5, Dock180,
           and MBC-zizimin homology 1), and DHR-2 (also called CZH2
           or Docker). The DHR-1 domain binds
           phosphatidylinositol-3,4,5-triphosphate. This alignment
           model represents the DHR-2 domain of Dock11, which
           contains the catalytic GEF activity for Cdc42. Class D
           DOCKs also contain a Pleckstrin homology (PH) domain at
           the N-terminus.
          Length = 413

 Score = 27.3 bits (60), Expect = 4.7
 Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 19/92 (20%)

Query: 77  YENVPPYTKANITIHYENNSPFLVVTRLVRQIEVSHWEHIHLKHDGAKLKGTFSRYDYQR 136
           YE +   +K  I I YE    F  +T+L R +  ++ + + + H G +L GTF R     
Sbjct: 98  YELISEISKLIIPI-YEKRREFEKLTQLYRTLHGAYAKILEVMHTGKRLLGTFFRV---- 152

Query: 137 DSAHGIKSFKTILPAAASDAYYRDEIGKRFIY 168
                         A     ++ +E GK +IY
Sbjct: 153 --------------AFYGQGFFEEEDGKEYIY 170


>gnl|CDD|215560 PLN03076, PLN03076, ARF guanine nucleotide exchange factor (ARF-GEF);
            Provisional.
          Length = 1780

 Score = 27.1 bits (60), Expect = 5.7
 Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 1/42 (2%)

Query: 110  VSHWEHIHLKHDGAKLKGTFSRYDYQRDSAHGIKSFKTILPA 151
            VS +EH+HL  +GA    TF     Q +S    ++   ILP 
Sbjct: 975  VSRFEHLHLLGEGAPPDATFFAAP-QNESDKSKQAKSPILPV 1015


>gnl|CDD|168934 PRK07394, PRK07394, hypothetical protein; Provisional.
          Length = 342

 Score = 26.4 bits (59), Expect = 8.1
 Identities = 11/16 (68%), Positives = 11/16 (68%)

Query: 150 PAAASDAYYRDEIGKR 165
           P A S   YRDEIGKR
Sbjct: 169 PLAESLIPYRDEIGKR 184


  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
   0.317    0.133    0.400 

Gapped
Lambda     K      H
   0.267   0.0764    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,526,600
Number of extensions: 746231
Number of successful extensions: 522
Number of sequences better than 10.0: 1
Number of HSP's gapped: 520
Number of HSP's successfully gapped: 11
Length of query: 169
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 79
Effective length of database: 6,945,742
Effective search space: 548713618
Effective search space used: 548713618
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: 41 (21.7 bits)
S2: 55 (24.9 bits)