RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6970
         (148 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 = 85.9 bits (213), Expect = 2e-20
 Identities = 46/150 (30%), Positives = 64/150 (42%), Gaps = 9/150 (6%)

Query: 2   YEVEFLLQQQWHDPRLEYFNQTTYDFLNAIHHHSD-VWLPDTYFIMHGD-FKDPLIPVHF 59
           Y     L+Q+W D RL++ N   Y  +  +    D +W+PD +F    D     +   + 
Sbjct: 76  YTTNIWLRQEWTDERLQW-NPEEYPGVTLVRTPDDSIWVPDIFFYNEKDARFHGITMTNV 134

Query: 60  ALRIYRNGTVNYLMRRHLILSCQGSLHIFPFDDPTCSFAMESISYEQSAIEYVWKNDE-- 117
            +RI+ NG+V Y  R  L L+C   L  FPFD   CS   ES  Y  + I+  WK     
Sbjct: 135 LVRIHPNGSVLYSPRITLTLACPMDLRNFPFDVQNCSLKFESWGYTTNDIKLEWKEQGAV 194

Query: 118 ---DTLRKS-PSLTTLNAYLITNRTISCPT 143
              D+L  S P    L  Y     T    T
Sbjct: 195 QVDDSLFISLPEFELLGVYGTRYCTSETNT 224


>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 = 81.1 bits (201), Expect = 9e-20
 Identities = 33/121 (27%), Positives = 49/121 (40%), Gaps = 6/121 (4%)

Query: 2   YEVEFLLQQQWHDPRLEYFNQTTYDFLNAIHHHSD-VWLPDTYFI--MHGDFKDPLIPVH 58
                 L+QQW D RL  ++   Y  + ++   SD +W PD        G         +
Sbjct: 47  LTTNVWLRQQWTDERL-AWDPEDYGGITSLRLPSDKIWKPDIVLYNKADGIHDITTPNTN 105

Query: 59  FALRIYRNGTVNYLMRRHLILSCQGSLHIFPFDDPTCSFAMESISYEQSAIEYVWKNDED 118
             +R+Y +GTV +        SC   L  FPFD   CS    S +Y    ++  WK+D  
Sbjct: 106 --VRVYPDGTVLWSPPAIYKSSCPMDLTYFPFDQQNCSLKFGSWTYNGEEVDLRWKDDTP 163

Query: 119 T 119
            
Sbjct: 164 P 164


>gnl|CDD|165391 PHA03118, PHA03118, multifunctional expression regulator;
           Provisional.
          Length = 474

 Score = 29.3 bits (65), Expect = 0.84
 Identities = 11/38 (28%), Positives = 20/38 (52%)

Query: 81  CQGSLHIFPFDDPTCSFAMESISYEQSAIEYVWKNDED 118
           C   +H+ P DDP   FA+E   + + ++    + D+D
Sbjct: 17  CDDFMHLLPEDDPIDDFALEVQDWAEESVPNSVQIDDD 54


>gnl|CDD|204705 pfam11663, Toxin_YhaV, Toxin with endonuclease activity YhaV.  YhaV
           causes reversible bacteriostasis and is part of a
           toxin-antitoxin system in Escherichia coli along with
           PrlF. The toxicity of YhaV is counteracted by PrlF by
           the formation of a tight complex which binds to the
           promoter of the prlF-yhaV operon. In vitro, YhaV also
           has endonuclease activity.
          Length = 141

 Score = 27.3 bits (61), Expect = 2.4
 Identities = 13/25 (52%), Positives = 14/25 (56%), Gaps = 2/25 (8%)

Query: 108 AIEYVWKNDEDTLRKSPSLTTLNAY 132
            I Y W NDE TLR   S T  +AY
Sbjct: 93  IIVYAWVNDESTLRAYGSKT--DAY 115


>gnl|CDD|236172 PRK08173, PRK08173, DNA topoisomerase III; Validated.
          Length = 862

 Score = 27.7 bits (62), Expect = 2.5
 Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)

Query: 18 EYFNQTTYDFLNAIHHHSDVWLPDTYFIMHG--DFKD-PLIPVHFALR 62
          EYF    Y   +A+ H  ++  P+ Y +  G   F   P+IP HF L 
Sbjct: 29 EYFESDEYVLSSAVGHLLEIAAPEEYEVKRGKWSFAHLPVIPPHFDLN 76


>gnl|CDD|177356 PHA02256, PHA02256, hypothetical protein.
          Length = 113

 Score = 25.6 bits (56), Expect = 7.0
 Identities = 12/48 (25%), Positives = 24/48 (50%), Gaps = 2/48 (4%)

Query: 55  IPVHFALRIYRNGTVNYLMRRHLILSCQGSLHIFPFDDPTCSFAMESI 102
           I  +  L +++  T + L++  +I S + + H   F+DP   F +  I
Sbjct: 44  IGTYIVLTMFQ--TTSVLIKNDVIDSIENTEHYIGFNDPIIIFIISFI 89


  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
   0.324    0.138    0.452 

Gapped
Lambda     K      H
   0.267   0.0639    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,702,083
Number of extensions: 683215
Number of successful extensions: 699
Number of sequences better than 10.0: 1
Number of HSP's gapped: 694
Number of HSP's successfully gapped: 15
Length of query: 148
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 60
Effective length of database: 7,034,450
Effective search space: 422067000
Effective search space used: 422067000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.8 bits)