RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8965
         (193 letters)



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

 Score =  153 bits (389), Expect = 7e-48
 Identities = 75/166 (45%), Positives = 108/166 (65%), Gaps = 7/166 (4%)

Query: 34  ISINLYALLFSELVQYCQNKSLSVPEFQSKLHEVGQSIGAKLIDINFYREKNGKREIKLL 93
           +S++ +A LFSE+VQYC +KS      + KLHE+G  +G KL ++  YREKN KRE K+L
Sbjct: 1   VSLSSFAFLFSEIVQYCLSKSKRGYRLEDKLHEMGLRVGYKLNELLPYREKNQKRETKIL 60

Query: 94  NILQFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKDKGSLNCAIFV 153
           +IL F+  ++WK +FG   D L ++ D +  Y + ++  L+NKFISVPKD G +NCA F 
Sbjct: 61  SILTFISKHVWKYLFGHSSDLL-KSQDSDDEYMINDKNLLLNKFISVPKDLGHINCAAFA 119

Query: 154 AGIVEAVLNNCGFKSTVTAHW------HKGTTYMIQFDEQVIARDK 193
           AGIVE +L +  F + VTAH       +  TT +I+F  +VI R+K
Sbjct: 120 AGIVEGILCSAEFPANVTAHTVEDTPKNFSTTILIKFYPEVIEREK 165


>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 =  152 bits (386), Expect = 1e-47
 Identities = 54/154 (35%), Positives = 89/154 (57%), Gaps = 10/154 (6%)

Query: 38  LYALLFSELVQYCQNKSLSVPEFQSKLHEVGQSIGAKLIDINFYREKNGKREIKLLNILQ 97
           L+ALL+ ELV Y         +  ++L ++G +IG +LI+    R    KR   LL +L+
Sbjct: 1   LFALLYGELVSYLLRDV---EDVNARLEKMGYNIGQRLIERLLARS-GSKRCTDLLEVLK 56

Query: 98  FVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKDKGSLNCAIFVAGIV 157
           F+  +LWK +FGK+ D LE ++D E  Y LI+ ++ +++F+ +P D   LN   F+ GI+
Sbjct: 57  FICKDLWKMLFGKQADVLETSHDGE--YVLIDNDNPLSQFVELPPDYSGLNYLNFLCGII 114

Query: 158 EAVLNNCGFKSTVTAH----WHKGTTYMIQFDEQ 187
              L++ GF + VTAH       GT + I+F++ 
Sbjct: 115 RGALSSLGFPAKVTAHSDPLRGPGTVFEIKFEKS 148


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

 Score =  141 bits (357), Expect = 1e-42
 Identities = 56/168 (33%), Positives = 102/168 (60%), Gaps = 6/168 (3%)

Query: 31  KHDISINLYALLFSELVQYCQNKSLSVPEFQSKLHEVGQSIGAKLIDINFYREKNGKREI 90
           K ++ ++  A LF E+++Y   +   + +F++KL  +G  +G KL+++  +R +N KRE+
Sbjct: 37  KREVPLSTMAFLFCEMIEYLMEQRSGIQDFEAKLKSIGYEVGIKLLELCNFRRRNPKREV 96

Query: 91  KLLNILQFVKINLWKNIFGKECDKLERANDDERTYYLIEQESLVNKFISVPKDKGSLNCA 150
           ++L ILQ +  +LW  +FG   D+LE++ + +R Y +++ + L+++FISVP +   L+C 
Sbjct: 97  RILTILQRIHFDLWSYLFGDSDDRLEKSREVDREYMIVDNDPLLSRFISVPDEWNGLSCD 156

Query: 151 IFVAGIVEAVLNNCGFKSTVTAH------WHKGTTYMIQFDEQVIARD 192
             V GI++  L   GF   VTAH          T ++I+ D+ VIAR+
Sbjct: 157 SIVCGIIQGFLMAAGFPCEVTAHPEPSENLPNRTVFLIRIDDLVIARE 204


>gnl|CDD|199835 cd10277, PQQ_ADH_I, Ethanol dehydrogenase, a bacterial quinoprotein
           (PQQ-dependent type I alcohol dehydrogenase).  This
           bacterial family of homodimeric ethanol dehydrogenases
           utilize pyrroloquinoline quinone (PQQ) as a cofactor. It
           represents proteins whose expression may be induced by
           ethanol, and which are similar to quinoprotein methanol
           dehydrogenases, but have higher specificities for
           ethanol and other primary and secondary alcohols.
           Dehydrogenases with PQQ cofactors, such as ethanol,
           methanol, and membrane-bound glucose dehydrogenases,
           form an 8-bladed beta-propeller.
          Length = 529

 Score = 29.2 bits (66), Expect = 1.5
 Identities = 10/35 (28%), Positives = 14/35 (40%), Gaps = 6/35 (17%)

Query: 84  KNG------KREIKLLNILQFVKINLWKNIFGKEC 112
           +NG      +   KL+    FVK   W +I  K  
Sbjct: 301 RNGFFYVLDRTNGKLIWATPFVKKITWASIDLKTG 335


>gnl|CDD|217478 pfam03294, Pox_Rap94, RNA polymerase-associated transcription
           specificity factor, Rap94. 
          Length = 796

 Score = 28.5 bits (64), Expect = 2.8
 Identities = 23/97 (23%), Positives = 42/97 (43%), Gaps = 7/97 (7%)

Query: 19  TSILDKPINTKVKHDISINLYALLFSELVQYCQNKSLSVPEFQSKLHEVGQSIGAKLIDI 78
           +S L       +  D++ NLY L F+ L  Y + K ++V        +   +I  +  D+
Sbjct: 93  SSSLSIKEKNSITDDMTYNLYNLFFNTLDMYLRQKRINVLVNDDLNGDN--NINYRTSDL 150

Query: 79  NFYREKNGKREIK-----LLNILQFVKINLWKNIFGK 110
               E   + EI+     + ++L +V  NL +  F K
Sbjct: 151 TTNFEPASEPEIREIPFNMKDLLSYVSKNLDQLRFSK 187


>gnl|CDD|241537 cd13386, PH1_FGD2, FYVE, RhoGEF and PH domain
           containing/faciogenital dysplasia protein 2 pleckstrin
           homology (PH), N-terminal domain.  In general, FGDs have
           a RhoGEF (DH) domain, followed by an N-terminal PH
           domain, a FYVE domain and a C-terminal PH domain. All
           FGDs are guanine nucleotide exchange factors that
           activates the Rho GTPase Cdc42, an important regulator
           of membrane trafficking. The RhoGEF domain is
           responsible for GEF catalytic activity, while the
           N-terminal PH domain is involved in intracellular
           targeting of the DH domain. Not much is known about
           FGD2.  FGD1 is the best characterized member of the
           group with mutations here leading to the X-linked
           disorder known as faciogenital dysplasia (FGDY). PH
           domains have diverse functions, but in general are
           involved in targeting proteins to the appropriate
           cellular location or in the interaction with a binding
           partner. They share little sequence conservation, but
           all have a common fold, which is electrostatically
           polarized. Less than 10% of PH domains bind
           phosphoinositide phosphates (PIPs) with high affinity
           and specificity. PH domains are distinguished from other
           PIP-binding domains by their specific high-affinity
           binding to PIPs with two vicinal phosphate groups:
           PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which
           results in targeting some PH domain proteins to the
           plasma membrane. A few display strong specificity in
           lipid binding. Any specificity is usually determined by
           loop regions or insertions in the N-terminus of the
           domain, which are not conserved across all PH domains.
           PH domains are found in cellular signaling proteins such
           as serine/threonine kinase, tyrosine kinases, regulators
           of G-proteins, endocytotic GTPases, adaptors, as well as
           cytoskeletal associated molecules and in lipid
           associated enzymes.
          Length = 107

 Score = 26.5 bits (58), Expect = 5.2
 Identities = 22/94 (23%), Positives = 41/94 (43%), Gaps = 4/94 (4%)

Query: 31  KHDISINLYALLFSELVQYCQNKSLSV-PEFQSKLH-EVGQSIGAKLIDINFYRE--KNG 86
           + + ++  Y  LF+ ++ YC  K + V  EFQ +   +V      +L+D  F      +G
Sbjct: 12  RRNSTMEKYLFLFNNMLLYCVPKVIQVGAEFQVRTRIDVAGMKVRELMDAEFPHSFLVSG 71

Query: 87  KREIKLLNILQFVKINLWKNIFGKECDKLERAND 120
           K+    L      ++  W   F    D+ E+ N+
Sbjct: 72  KQRTLELQARSQEEMIAWIKAFQAAIDQKEKRNE 105


>gnl|CDD|227078 COG4735, COG4735, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 211

 Score = 27.1 bits (60), Expect = 6.0
 Identities = 20/88 (22%), Positives = 26/88 (29%), Gaps = 25/88 (28%)

Query: 46  LVQYCQNKSLSVPEFQSKLHEVGQSIGAKLIDINFYREKNGKREIKLLNILQFVKINLWK 105
           L+Q C+       E Q      G S    L D+                        L+K
Sbjct: 17  LIQVCKYLKRIAEELQ---TTGGLSAANFLRDLGQ----------------------LYK 51

Query: 106 NIFGKECDKLERANDDERTYYLIEQESL 133
            I   E DKL+     E     IE+  L
Sbjct: 52  KILCDEKDKLKVKVQKELGTTEIEEPLL 79


>gnl|CDD|236945 PRK11644, PRK11644, sensory histidine kinase UhpB; Provisional.
          Length = 495

 Score = 26.9 bits (60), Expect = 7.3
 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 5/39 (12%)

Query: 20  SILDKPINTKVKHDISINLYALLF--SELVQYCQNKSLS 56
           S++ +P+N + +H   I  Y LLF  S  +Q      LS
Sbjct: 170 SLVSQPVNWRGRH---IVWYLLLFVLSIWLQLGLPDELS 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
   0.319    0.135    0.387 

Gapped
Lambda     K      H
   0.267   0.0739    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,355,417
Number of extensions: 843691
Number of successful extensions: 635
Number of sequences better than 10.0: 1
Number of HSP's gapped: 628
Number of HSP's successfully gapped: 20
Length of query: 193
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 101
Effective length of database: 6,857,034
Effective search space: 692560434
Effective search space used: 692560434
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: 56 (25.3 bits)