RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4842
         (95 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 = 98.1 bits (245), Expect = 4e-27
 Identities = 37/96 (38%), Positives = 51/96 (53%), Gaps = 5/96 (5%)

Query: 1   MRYRWVDPRLAHNAKENYLGEINLR---DRVWTPHLYLVNEHDSRIMGSGRQDILISVQP 57
           +R +W D RLA +  E+Y G  +LR   D++W P + L N+ D  I      +  + V P
Sbjct: 53  LRQQWTDERLAWD-PEDYGGITSLRLPSDKIWKPDIVLYNKADG-IHDITTPNTNVRVYP 110

Query: 58  DGTVLYSTRLKVTLLCLMNLKKFPFDEQECPLVLES 93
           DGTVL+S        C M+L  FPFD+Q C L   S
Sbjct: 111 DGTVLWSPPAIYKSSCPMDLTYFPFDQQNCSLKFGS 146


>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 = 79.8 bits (197), Expect = 4e-19
 Identities = 40/95 (42%), Positives = 55/95 (57%), Gaps = 4/95 (4%)

Query: 2   RYRWVDPRLAHNAKENYLGEINLR---DRVWTPHLYLVNEHDSRIMGSGRQDILISVQPD 58
           R  W D RL  N  E Y G   +R   D +W P ++  NE D+R  G    ++L+ + P+
Sbjct: 83  RQEWTDERLQWN-PEEYPGVTLVRTPDDSIWVPDIFFYNEKDARFHGITMTNVLVRIHPN 141

Query: 59  GTVLYSTRLKVTLLCLMNLKKFPFDEQECPLVLES 93
           G+VLYS R+ +TL C M+L+ FPFD Q C L  ES
Sbjct: 142 GSVLYSPRITLTLACPMDLRNFPFDVQNCSLKFES 176


>gnl|CDD|183640 PRK12636, flgG, flagellar basal body rod protein FlgG; Provisional.
          Length = 263

 Score = 27.8 bits (62), Expect = 0.67
 Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 7/38 (18%)

Query: 34  YLVNEHDSRIMGSGRQDILI-------SVQPDGTVLYS 64
            +VN     ++G     I I       S+  DGTV Y 
Sbjct: 125 NIVNADGLYLLGMNGGRIQIPTDAQSFSIGADGTVSYV 162


>gnl|CDD|199906 cd10318, RGL11, Rhamnogalacturonan lyase of the polysaccharide
           lyase family 11.  The rhamnogalacturonan lyase of the
           polysaccharide lyase family 11 (RGL11) cleaves glycoside
           bonds in polygalacturonan as well as RG
           (rhamnogalacturonan) type-I through a beta-elimination
           reaction. Functionally characterized members of this
           family, YesW and YesX from Bacillus subtilis, cleave
           glycoside bonds between rhamnose and galacturonic acid
           residues in the RG-I region of plant cell wall pectin.
           YesW and YesX work synergistically, with YesW cleaving
           the glycoside bond of the RG chain endolytically, and
           YesX converting the resultant oligosaccharides through
           an exotype reaction. This domain is sometimes found in
           architectures with non-catalytic carbohydrate-binding
           modules (CBMs). There are two types of RG lyases, which
           both cleave the alpha-1,4 bonds of the RG-I main chain
           through a beta-elimination reaction, but belong to two
           structurally unrelated polysaccharide lyase (PL)
           families, 4 and 11.
          Length = 564

 Score = 25.7 bits (57), Expect = 4.6
 Identities = 11/26 (42%), Positives = 16/26 (61%), Gaps = 3/26 (11%)

Query: 45  GSGRQDIL---ISVQPDGTVLYSTRL 67
           G G+ +I+    ++  DGT LYST L
Sbjct: 332 GDGKDEIIYGSATIDHDGTGLYSTGL 357


>gnl|CDD|183222 PRK11596, PRK11596, cyclic-di-GMP phosphodiesterase; Provisional.
          Length = 255

 Score = 25.3 bits (56), Expect = 6.1
 Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 5/64 (7%)

Query: 14  AKENYLGEINLRDR--VWTPHLYLVNEHDSRIMGSGRQDILISVQPDGTVLYSTRLKVTL 71
           + E Y  EI +  R  V    L L+ +     +   R  +L SV  DG  L + R +  +
Sbjct: 64  SPERYFAEITVSHRLDVVKEQLDLLAQWADFFV---RHGLLASVNIDGPTLIALRQQPAI 120

Query: 72  LCLM 75
           L L+
Sbjct: 121 LRLI 124


>gnl|CDD|217294 pfam02934, GatB_N, GatB/GatE catalytic domain.  This domain is
           found in the GatB and GatE proteins.
          Length = 288

 Score = 24.7 bits (55), Expect = 8.6
 Identities = 10/22 (45%), Positives = 14/22 (63%)

Query: 45  GSGRQDILISVQPDGTVLYSTR 66
           GS R D  +SV+P G+  + TR
Sbjct: 187 GSLRCDANVSVRPKGSEEFGTR 208


>gnl|CDD|217366 pfam03098, An_peroxidase, Animal haem peroxidase. 
          Length = 521

 Score = 24.6 bits (54), Expect = 9.2
 Identities = 12/48 (25%), Positives = 17/48 (35%), Gaps = 5/48 (10%)

Query: 3   YRW----VDPRLA-HNAKENYLGEINLRDRVWTPHLYLVNEHDSRIMG 45
           YR+    + P L   +       EI L D  + P   L    D  + G
Sbjct: 305 YRFGHSLIPPGLERLDEFRTIAPEIPLHDTFFNPSRILEEGIDPLLRG 352


  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
   0.323    0.140    0.442 

Gapped
Lambda     K      H
   0.267   0.0778    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,835,735
Number of extensions: 385084
Number of successful extensions: 276
Number of sequences better than 10.0: 1
Number of HSP's gapped: 273
Number of HSP's successfully gapped: 10
Length of query: 95
Length of database: 10,937,602
Length adjustment: 62
Effective length of query: 33
Effective length of database: 8,187,654
Effective search space: 270192582
Effective search space used: 270192582
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.1 bits)