RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16244
         (86 letters)



>gnl|CDD|217293 pfam02931, Neur_chan_LBD, Neurotransmitter-gated ion-channel
          ligand binding domain.  This family is the
          extracellular ligand binding domain of these ion
          channels. This domain forms a pentameric arrangement in
          the known structure.
          Length = 215

 Score = 86.1 bits (214), Expect = 1e-22
 Identities = 30/52 (57%), Positives = 41/52 (78%)

Query: 30 NLKNQIMTTNLWVEQSWYDYKLRWEPKEYGGVHMLHVPSDHIWRPDIVLYNK 81
          + KNQ +TTN+W+ Q W D +L W+P++YGG+  L +PSD IW+PDIVLYNK
Sbjct: 41 DEKNQDLTTNVWLRQQWTDERLAWDPEDYGGITSLRLPSDKIWKPDIVLYNK 92


>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 = 66.3 bits (162), Expect = 1e-14
 Identities = 25/49 (51%), Positives = 32/49 (65%)

Query: 32  KNQIMTTNLWVEQSWYDYKLRWEPKEYGGVHMLHVPSDHIWRPDIVLYN 80
           KN   TTN+W+ Q W D +L+W P+EY GV ++  P D IW PDI  YN
Sbjct: 72  KNMDYTTNIWLRQEWTDERLQWNPEEYPGVTLVRTPDDSIWVPDIFFYN 120


>gnl|CDD|180319 PRK05945, sdhA, succinate dehydrogenase flavoprotein subunit;
           Reviewed.
          Length = 575

 Score = 27.4 bits (61), Expect = 0.80
 Identities = 11/43 (25%), Positives = 18/43 (41%)

Query: 29  HNLKNQIMTTNLWVEQSWYDYKLRWEPKEYGGVHMLHVPSDHI 71
           H L N +    + +   WY  +L  E  +  GV M H+    +
Sbjct: 139 HELVNNLRRYGVTIYDEWYVMRLILEDNQAKGVVMYHIADGRL 181


>gnl|CDD|173329 PTZ00031, PTZ00031, ribosomal protein L2; Provisional.
          Length = 317

 Score = 27.5 bits (61), Expect = 0.82
 Identities = 13/31 (41%), Positives = 19/31 (61%)

Query: 3  QNRVLKLLQNHETLLVELRTATLLSRHNLKN 33
          Q R+LKLL+N+  +L + R    LS   +KN
Sbjct: 41 QQRLLKLLENNPLVLYKGRVVKQLSCRRVKN 71


>gnl|CDD|240447 cd13432, LDT_IgD_like_2, IgD-like repeat domain of mycobacterial
          L,D-transpeptidases.  Immunoglobulin-like domain found
          in actinobacterial L,D-transpeptidases, including
          Mycobacterium tuberculosis LdtMt2, which is a
          non-classical transpeptidase that generates 3->3
          transpeptide linkages. LdtMt2 is associated with
          virulence and resistance to amoxicillin. This domain
          may occur in a tandem-repeat arrangement and is found
          N-terminal to the catalytic L,D-transpeptidase domain;
          this model represents the  repeat adjacent to the
          catalytic domain.
          Length = 99

 Score = 26.3 bits (59), Expect = 1.2
 Identities = 12/25 (48%), Positives = 16/25 (64%), Gaps = 3/25 (12%)

Query: 37 TTNLWVEQSWY---DYKLRWEPKEY 58
          TT+  VE +WY   D ++ W PKEY
Sbjct: 40 TTSPPVEGAWYWLSDREVHWRPKEY 64


>gnl|CDD|181592 PRK08947, fadA, 3-ketoacyl-CoA thiolase; Reviewed.
          Length = 387

 Score = 25.3 bits (56), Expect = 4.0
 Identities = 9/13 (69%), Positives = 10/13 (76%), Gaps = 1/13 (7%)

Query: 59  GGV-HMLHVPSDH 70
           GGV HM HVP +H
Sbjct: 116 GGVEHMGHVPMNH 128


  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
   0.322    0.136    0.451 

Gapped
Lambda     K      H
   0.267   0.0633    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,323,720
Number of extensions: 328262
Number of successful extensions: 267
Number of sequences better than 10.0: 1
Number of HSP's gapped: 267
Number of HSP's successfully gapped: 11
Length of query: 86
Length of database: 10,937,602
Length adjustment: 54
Effective length of query: 32
Effective length of database: 8,542,486
Effective search space: 273359552
Effective search space used: 273359552
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 (21.9 bits)
S2: 53 (24.4 bits)