RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3171
         (305 letters)



>gnl|CDD|215968 pfam00520, Ion_trans, Ion transport protein.  This family contains
           Sodium, Potassium, Calcium ion channels. This family is
           6 transmembrane helices in which the last two helices
           flank a loop which determines ion selectivity. In some
           sub-families (e.g. Na channels) the domain is repeated
           four times, whereas in others (e.g. K channels) the
           protein forms as a tetramer in the membrane. A bacterial
           structure of the protein is known for the last two
           helices but is not the Pfam family due to it lacking the
           first four helices.
          Length = 194

 Score = 66.5 bits (163), Expect = 4e-13
 Identities = 27/107 (25%), Positives = 51/107 (47%), Gaps = 20/107 (18%)

Query: 100 IETLCIIWFTFELSVRFLACPNKLNFFRDVMNIIDIIAIIPYFITLATVVAEEEDVLNLP 159
           ++ +  + FT E+ ++F+A   K  +FR   NI+D + ++P  ++L   +  E+  L   
Sbjct: 2   LDYVFTVIFTLEMLLKFIALGFKRKYFRSPWNILDFLVVLPSLVSLILFLLGEDSGL--- 58

Query: 160 KAPVSPQDKSTNQAMSLAILRVIRLVRVFRIFKLSR-HSKGLQILGR 205
                           L +LR++RL+R+ R+ +        LQ LGR
Sbjct: 59  ----------------LRVLRLLRLLRLLRLLRRFPGLRTLLQSLGR 89


>gnl|CDD|215343 PLN02638, PLN02638, cellulose synthase A (UDP-forming), catalytic
           subunit.
          Length = 1079

 Score = 32.6 bits (74), Expect = 0.29
 Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 17/55 (30%)

Query: 54  VILLSIVIFCLETLPEFKHYKVFNTTTNGTKIEEDEVPDITDPFFLIETLCIIWF 108
           VI+L +VI C+     F HY++ N   N                +LI  +C IWF
Sbjct: 274 VIVLRLVILCI-----FLHYRITNPVRNAY------------ALWLISVICEIWF 311


>gnl|CDD|221323 pfam11931, DUF3449, Domain of unknown function (DUF3449).  This
           presumed domain is functionally uncharacterized. This
           domain is found in eukaryotes. This domain is typically
           between 181 to 207 amino acids in length. This domain
           has two conserved sequence motifs: PIP and CEICG. The
           domain carries a zinc-finger domain of the C2H2-type.
          Length = 187

 Score = 29.2 bits (66), Expect = 2.3
 Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 10/39 (25%)

Query: 186 RVF-RIFKLSRHSKGLQILGRECQFILHIIPSSILFRGI 223
           + F + F   RH+ GL+ LG         IP++  F+ I
Sbjct: 107 KAFEKHFSEWRHAYGLKCLG---------IPNTRHFKEI 136


>gnl|CDD|198266 cd10403, SH2_STAP1, Src homology 2 domain found in
          Signal-transducing adaptor protein 1 (STAP1).  STAP1 is
          a signal-transducing adaptor protein. It is composed of
          a Pleckstrin homology (PH) and SH2 domains along with
          several tyrosine phosphorylation sites. STAP-1 is an
          ortholog of BRDG1 (BCR downstream signaling 1). STAP1
          protein functions as a docking protein acting
          downstream of Tec tyrosine kinase in B cell antigen
          receptor signaling. The protein is phosphorylated by
          Tec and participates in a positive feedback loop,
          increasing Tec activity. STAP1 has been shown to
          interact with C19orf2, an unconventional prefoldin RPB5
          interactor. In general SH2 domains are involved in
          signal transduction. They typically bind
          pTyr-containing ligands via two surface pockets, a pTyr
          and hydrophobic binding pocket, allowing proteins with
          SH2 domains to localize to tyrosine phosphorylated
          sites.
          Length = 94

 Score = 27.4 bits (61), Expect = 3.9
 Identities = 8/25 (32%), Positives = 10/25 (40%)

Query: 67 LPEFKHYKVFNTTTNGTKIEEDEVP 91
           P  KHY+V +     T   E  V 
Sbjct: 46 KPRIKHYRVMSRGQGYTIELEKPVT 70


>gnl|CDD|165225 PHA02902, PHA02902, putative IMV membrane protein; Provisional.
          Length = 70

 Score = 26.4 bits (58), Expect = 5.3
 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 49 IISVFVIL-LSIVIFCLETLPEFKHYKVFNTTTNGTKIEEDEVPDITDPFF 98
           I  FVIL + ++IFCL     +K YK   +  +  +   D + D  DP F
Sbjct: 2  AIDTFVILAVIVIIFCLLIYAAYKRYKCIPSPDDRDERFGDTLED--DPLF 50


>gnl|CDD|223642 COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Transcription].
          Length = 342

 Score = 27.6 bits (62), Expect = 9.3
 Identities = 17/42 (40%), Positives = 21/42 (50%), Gaps = 6/42 (14%)

Query: 171 NQAMSLAILRVIRLVR-----VFRIFKLSRHSKGL-QILGRE 206
            QA++ AI    R +R     V  I KL R  + L Q LGRE
Sbjct: 164 RQAITRAIADQARTIRIPVHQVELINKLRRVKRELLQELGRE 205


  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
   0.327    0.143    0.421 

Gapped
Lambda     K      H
   0.267   0.0754    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,144,100
Number of extensions: 1589715
Number of successful extensions: 1920
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1914
Number of HSP's successfully gapped: 25
Length of query: 305
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 208
Effective length of database: 6,635,264
Effective search space: 1380134912
Effective search space used: 1380134912
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 59 (26.5 bits)