RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8972
         (170 letters)



>gnl|CDD|217862 pfam04051, TRAPP, Transport protein particle (TRAPP) component.
           TRAPP plays a key role in the targeting and/or fusion of
           ER-to-Golgi transport vesicles with their acceptor
           compartment. TRAPP is a large multimeric protein that
           contains at least 10 subunits. This family contains many
           TRAPP family proteins. The Bet3 subunit is one of the
           better characterized TRAPP proteins and has a dimeric
           structure with hydrophobic channels. The channel
           entrances are located on a putative membrane-interacting
           surface that is distinctively flat, wide and decorated
           with positively charged residues. Bet3 is proposed to
           localise TRAPP to the Golgi.
          Length = 148

 Score =  105 bits (265), Expect = 1e-29
 Identities = 35/96 (36%), Positives = 58/96 (60%), Gaps = 6/96 (6%)

Query: 4   AKFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKDKGSLNCAIFVAG 63
            KF+  +LWK +FGK+ D LE ++D E  Y LI+ ++ +++F+ +P D   LN   F+ G
Sbjct: 55  LKFICKDLWKMLFGKQADVLETSHDGE--YVLIDNDNPLSQFVELPPDYSGLNYLNFLCG 112

Query: 64  IVEAVLNNCGFKSTVTAH----WHKGTTYMIQFDEQ 95
           I+   L++ GF + VTAH       GT + I+F++ 
Sbjct: 113 IIRGALSSLGFPAKVTAHSDPLRGPGTVFEIKFEKS 148


>gnl|CDD|227457 COG5128, COG5128, Transport protein particle (TRAPP) complex
           subunit [Intracellular trafficking and secretion].
          Length = 208

 Score = 83.8 bits (207), Expect = 2e-20
 Identities = 30/99 (30%), Positives = 55/99 (55%), Gaps = 6/99 (6%)

Query: 3   LAKFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKDKGSLNCAIFVA 62
           + + +  +LW  +FG   D+LE++ + +R Y +++ + L+++FISVP +   L+C   V 
Sbjct: 101 ILQRIHFDLWSYLFGDSDDRLEKSREVDREYMIVDNDPLLSRFISVPDEWNGLSCDSIVC 160

Query: 63  GIVEAVLNNCGFKSTVTAH------WHKGTTYMIQFDEQ 95
           GI++  L   GF   VTAH          T ++I+ D+ 
Sbjct: 161 GIIQGFLMAAGFPCEVTAHPEPSENLPNRTVFLIRIDDL 199


>gnl|CDD|240398 PTZ00391, PTZ00391, transport protein particle component (TRAPP)
           superfamily; Provisional.
          Length = 168

 Score = 81.8 bits (202), Expect = 3e-20
 Identities = 39/94 (41%), Positives = 57/94 (60%), Gaps = 7/94 (7%)

Query: 6   FVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKDKGSLNCAIFVAGIV 65
           F+  ++WK +FG   D L ++ D +  Y + ++  L+NKFISVPKD G +NCA F AGIV
Sbjct: 65  FISKHVWKYLFGHSSDLL-KSQDSDDEYMINDKNLLLNKFISVPKDLGHINCAAFAAGIV 123

Query: 66  EAVLNNCGFKSTVTAHW------HKGTTYMIQFD 93
           E +L +  F + VTAH       +  TT +I+F 
Sbjct: 124 EGILCSAEFPANVTAHTVEDTPKNFSTTILIKFY 157


>gnl|CDD|227432 COG5101, CRM1, Importin beta-related nuclear transport receptor
           [Nuclear structure / Intracellular trafficking and
           secretion].
          Length = 1053

 Score = 27.2 bits (60), Expect = 5.9
 Identities = 8/34 (23%), Positives = 20/34 (58%), Gaps = 2/34 (5%)

Query: 82  WHKGTTYMIQFDE-QEGKFTALQIMEENIASQWR 114
           W K   Y++   +  + K+ AL ++++ I ++W+
Sbjct: 48  WTK-ADYILNNSKLPQSKYIALSLLDKLITTKWK 80


>gnl|CDD|185129 PRK15207, PRK15207, long polar fimbrial outer membrane usher
           protein LpfC; Provisional.
          Length = 842

 Score = 26.4 bits (58), Expect = 9.2
 Identities = 16/45 (35%), Positives = 19/45 (42%)

Query: 108 NIASQWRRGAGKVGRGACKGNQQLNYNLMAKPSGHDFCIILEPPL 152
           N+  Q   G   VG    K NQQ+NY +      H   I L  PL
Sbjct: 631 NLGYQGGSGNISVGYNYSKDNQQVNYGVRGGVIVHSEGITLSQPL 675


  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
   0.320    0.136    0.421 

Gapped
Lambda     K      H
   0.267   0.0761    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,337,594
Number of extensions: 724978
Number of successful extensions: 472
Number of sequences better than 10.0: 1
Number of HSP's gapped: 469
Number of HSP's successfully gapped: 8
Length of query: 170
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 80
Effective length of database: 6,945,742
Effective search space: 555659360
Effective search space used: 555659360
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 (21.8 bits)
S2: 55 (24.9 bits)