RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10144
         (88 letters)



>gnl|CDD|233155 TIGR00860, LIC, Cation transporter family protein.  The
           Ligand-gated Ion Channel (LIC) Family of
           Neurotransmitter Receptors TC 1.A.9)Members of the LIC
           family of ionotropic neurotransmitter receptors are
           found only in vertebrate and invertebrate animals. They
           exhibit receptor specificity for (1)acetylcholine, (2)
           serotonin, (3) glycine, (4) glutamate and (5)
           g-aminobutyric acid (GABA). All of these receptor
           channels are probably hetero- orhomopentameric. The best
           characterized are the nicotinic acetyl-choline receptors
           which are pentameric channels of a2bgd subunit
           composition. All subunits arehomologous. The three
           dimensional structures of the protein complex in both
           the open and closed configurations have been solved at
           0.9 nm resolution.The channel protein complexes of the
           LIC family preferentially transport cations or anions
           depending on the channel (e.g., the acetylcholine
           receptors are cationselective while glycine receptors
           are anion selective) [Transport and binding proteins,
           Cations and iron carrying compounds].
          Length = 459

 Score = 65.5 bits (160), Expect = 3e-14
 Identities = 24/42 (57%), Positives = 34/42 (80%)

Query: 14  YLPTILIVIISWVSFWMDVDSVPGRTTLGVTTLLAVSSQSSG 55
           Y+P+ILIVI+SWVSFW+  D+   R +LG+TTLL +++ SSG
Sbjct: 248 YIPSILIVILSWVSFWLPADASGARVSLGITTLLTMTTFSSG 289


>gnl|CDD|202474 pfam02932, Neur_chan_memb, Neurotransmitter-gated ion-channel
          transmembrane region.  This family includes the four
          transmembrane helices that form the ion channel.
          Length = 228

 Score = 61.5 bits (150), Expect = 3e-13
 Identities = 16/46 (34%), Positives = 26/46 (56%)

Query: 14 YLPTILIVIISWVSFWMDVDSVPGRTTLGVTTLLAVSSQSSGYANI 59
           +P +LI  +SW+ FW+  D+ P + TLG+TTLL ++         
Sbjct: 2  IIPCVLISFLSWLVFWLPADAGPEKVTLGITTLLTMTVFLLLIRES 47


>gnl|CDD|133464 cd06854, GT_WbpL_WbcO_like, The members of this subfamily
          catalyze the formation of a phosphodiester bond between
          a membrane-associated undecaprenyl-phosphate (Und-P)
          molecule and N-acetylhexosamine 1-phosphate, which is
          usually donated by a soluble UDP-N-acetylhexosamine
          precursor. The WbcO/WbpL substrate specificity has not
          yet been determined, but the structure of their
          biosynthetic end products implies that
          UDP-N-acetyl-D-fucosamine (UDP-FucNAc) and/or
          UDPN-acetyl-D-quinosamine (UDP-QuiNAc) are used. The
          subgroup of bacterial UDP-HexNAc:polyprenol-P
          HexNAc-1-P transferases includes the WbcO protein from
          Yersinia enterocolitica and the WbpL protein from
          Pseudomonas aeruginosa. These transferases initiate LPS
          O-antigen biosynthesis. Similar to other
          GlcNAc/MurNAc-1-P transferase family members, WbpL is a
          highly hydrophobic protein possessing 11 predicted
          transmembrane segments.
          Length = 253

 Score = 27.6 bits (62), Expect = 0.78
 Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 1/44 (2%)

Query: 7  GLTGRLSYLP-TILIVIISWVSFWMDVDSVPGRTTLGVTTLLAV 49
          G    LSYL   I +++++ V F  D+ S+  +  L V  L A 
Sbjct: 38 GPLNDLSYLLLLIGLLLLAAVGFIDDLRSLSPKIRLLVQLLAAA 81


>gnl|CDD|234327 TIGR03718, R_switched_Alx, integral membrane protein, TerC family. 
           Rfam model RF00080 describes a structured RNA element
           called the yybP-ykoY leader, or SraF, which may precede
           one or several genes in a genome. Members of this highly
           hydrophobic protein family often are preceded by a
           yybP-ykoY leader, which may serve as a riboswitch. From
           the larger group of TerC homologs (pfam03741), this
           subfamily contains TerC itself from Alcaligenes sp.
           plasmid IncHI2 pMER610 and from Proteus mirabilis. It
           also contains the alkaline-inducible E. coli protein
           Alx, which unlike the two TerC examples is preceded by a
           yybP-ykoY leader.
          Length = 302

 Score = 27.1 bits (61), Expect = 1.00
 Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 6/50 (12%)

Query: 7   GLTGRLSYLPTILIVIISWVSFWM-----DVDSVPGRTTLGVT-TLLAVS 50
           GL  R  YL   L VI+ ++   M     DV  +P   +LGV    LAVS
Sbjct: 243 GLLERFHYLKYGLAVILVFIGVKMLLHATDVYHIPIGVSLGVIVGTLAVS 292


>gnl|CDD|217447 pfam03239, FTR1, Iron permease FTR1 family. 
          Length = 284

 Score = 25.8 bits (57), Expect = 3.3
 Identities = 13/51 (25%), Positives = 20/51 (39%), Gaps = 3/51 (5%)

Query: 5   KRGLTGRLSYLPTILIVIISWVSFWMDVDSVPGRTTLGVTTLLAVSSQSSG 55
           K    G LSY+     V+ISW+ FWM       +  +      A++     
Sbjct: 72  KELFEGVLSYIAV---VVISWMIFWMRRVGKKLKGEIEQKLAKALAMIGGL 119


>gnl|CDD|183355 PRK11877, psaI, photosystem I reaction center subunit VIII;
          Reviewed.
          Length = 38

 Score = 24.3 bits (53), Expect = 3.3
 Identities = 6/14 (42%), Positives = 10/14 (71%)

Query: 13 SYLPTILIVIISWV 26
          S+LP I + ++ WV
Sbjct: 8  SWLPWIFVPLVGWV 21


>gnl|CDD|239657 cd03685, ClC_6_like, ClC-6-like chloride channel proteins. This CD
           includes ClC-6, ClC-7 and ClC-B, C, D in plants.
           Proteins in this family are ubiquitous in eukarotes and
           their functions are unclear. They are expressed in
           intracellular organelles membranes.  This family belongs
           to the ClC superfamily of chloride ion channels, which
           share the unique double-barreled architecture and
           voltage-dependent gating mechanism. The gating is
           conferred by the permeating anion itself, acting as the
           gating charge. ClC chloride ion channel superfamily
           perform a variety of functions including cellular
           excitability regulation, cell volume regulation,
           membrane potential stabilization, acidification of
           intracellular organelles, signal transduction, and
           transepithelial transport in animals.
          Length = 466

 Score = 25.3 bits (56), Expect = 5.6
 Identities = 10/21 (47%), Positives = 16/21 (76%), Gaps = 2/21 (9%)

Query: 8   LTGRLSYL-PTILIVIIS-WV 26
           LT  L+YL P +L+++I+ WV
Sbjct: 418 LTNNLTYLPPIMLVLMIAKWV 438


>gnl|CDD|215415 PLN02776, PLN02776, prenyltransferase.
          Length = 341

 Score = 24.7 bits (54), Expect = 7.3
 Identities = 9/31 (29%), Positives = 15/31 (48%)

Query: 37  GRTTLGVTTLLAVSSQSSGYANIASQTEPTT 67
           GR ++      AV   ++G A +A +T   T
Sbjct: 71  GRISVPHAVAWAVVVGAAGVALLAYKTNMLT 101


>gnl|CDD|200218 TIGR02901, QoxD, cytochrome aa3 quinol oxidase, subunit IV.  This
          family (QoxD) encodes subunit IV of the aa3-type
          quinone oxidase, one of several bacterial terminal
          oxidases. This complex couples oxidation of reduced
          quinones with the reduction of molecular oxygen to
          water and the pumping of protons to form a proton
          gradient utilized for ATP production. aa3-type oxidases
          contain two heme a cofactors as well as copper atoms in
          the active site [Energy metabolism, Electron
          transport].
          Length = 94

 Score = 23.9 bits (52), Expect = 8.4
 Identities = 13/38 (34%), Positives = 20/38 (52%)

Query: 15 LPTILIVIISWVSFWMDVDSVPGRTTLGVTTLLAVSSQ 52
          L  IL ++  WV+F+ D+  V G T + V   +  S Q
Sbjct: 15 LSLILTLLALWVAFYSDLSLVVGLTIIIVFAFIQASLQ 52


>gnl|CDD|232845 TIGR00145, TIGR00145, FTR1 family protein.  A characterized
          member from yeast acts as oxidase-coupled high affinity
          iron transporter. Note that the apparent member from E.
          coli K12-MG1655 has a frameshift by homology with
          member sequences from other species [Unknown function,
          General].
          Length = 283

 Score = 24.7 bits (54), Expect = 8.9
 Identities = 7/29 (24%), Positives = 12/29 (41%), Gaps = 3/29 (10%)

Query: 2  GPNKRGLTGRLSYLPTILIVIISWVSFWM 30
             K  L G    +     V++S++  WM
Sbjct: 69 DEFKELLEGIFGVIAV---VMLSYMGLWM 94


>gnl|CDD|164584 MTH00008, COX2, cytochrome c oxidase subunit II; Validated.
          Length = 228

 Score = 24.4 bits (53), Expect = 8.9
 Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 3/28 (10%)

Query: 21  VIISWV--SFWMDVDSVPGR-TTLGVTT 45
           VI SW   S  + VD+VPGR   +G T 
Sbjct: 159 VIHSWTVPSLGVKVDAVPGRLNQIGFTI 186


>gnl|CDD|218018 pfam04306, DUF456, Protein of unknown function (DUF456).  This
          family is a putative membrane protein that contains
          glycine zipper motifs.
          Length = 140

 Score = 24.4 bits (54), Expect = 9.2
 Identities = 12/44 (27%), Positives = 17/44 (38%), Gaps = 1/44 (2%)

Query: 15 LP-TILIVIISWVSFWMDVDSVPGRTTLGVTTLLAVSSQSSGYA 57
          LP T+LI     +  W    +  G   L V  LL +    + Y 
Sbjct: 6  LPGTLLIFAGLLLYAWATGFTELGWVFLAVLALLTLLGLVADYL 49


  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
   0.313    0.129    0.366 

Gapped
Lambda     K      H
   0.267   0.0831    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,260,642
Number of extensions: 317751
Number of successful extensions: 294
Number of sequences better than 10.0: 1
Number of HSP's gapped: 294
Number of HSP's successfully gapped: 18
Length of query: 88
Length of database: 10,937,602
Length adjustment: 56
Effective length of query: 32
Effective length of database: 8,453,778
Effective search space: 270520896
Effective search space used: 270520896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.0 bits)