RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2313
         (62 letters)



>gnl|CDD|204533 pfam10613, Lig_chan-Glu_bd, Ligated ion channel L-glutamate- and
          glycine-binding site.  This region, sometimes called
          the S1 domain, is the luminal domain just upstream of
          the first, M1, transmembrane region of transmembrane
          ion-channel proteins, and it binds L-glutamate and
          glycine. It is found in association with Lig_chan,
          pfam00060.
          Length = 65

 Score = 55.7 bits (135), Expect = 1e-12
 Identities = 17/45 (37%), Positives = 33/45 (73%), Gaps = 3/45 (6%)

Query: 1  MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLV 45
          +DLL+ +A+ L F++ +Y+V DG YG++ +  +   WNG++G+L+
Sbjct: 23 IDLLDELAKILGFNYEIYLVPDGKYGSEDKTGE---WNGMIGELI 64


>gnl|CDD|214911 smart00918, Lig_chan-Glu_bd, Ligated ion channel L-glutamate- and
          glycine-binding site.  This region, sometimes called
          the S1 domain, is the luminal domain just upstream of
          the first, M1, transmembrane region of transmembrane
          ion-channel proteins, and it binds L-glutamate and
          glycine. It is found in association with Lig_chan.
          Length = 62

 Score = 49.9 bits (120), Expect = 2e-10
 Identities = 18/45 (40%), Positives = 30/45 (66%), Gaps = 3/45 (6%)

Query: 1  MDLLENIAQELEFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLV 45
          +DLL+ +A++L F + + +V DG YG ++       WNG+VG+LV
Sbjct: 21 IDLLKELAKKLGFTYEIILVPDGKYGARLPNGS---WNGMVGELV 62


>gnl|CDD|152641 pfam12206, DUF3599, Domain of unknown function (DUF3599).  This
          family of proteins is found in bacteria. Proteins in
          this family are approximately 120 amino acids in
          length. This domain is the phage-like element pbsx
          protein xkdh.
          Length = 116

 Score = 26.3 bits (58), Expect = 0.69
 Identities = 8/17 (47%), Positives = 10/17 (58%)

Query: 25 YGTKVRENQKDKWNGVV 41
           G  +R N K  W+GVV
Sbjct: 77 LGADIRVNDKVIWDGVV 93


>gnl|CDD|223461 COG0384, COG0384, Predicted epimerase, PhzC/PhzF homolog [General
           function prediction only].
          Length = 291

 Score = 25.4 bits (56), Expect = 1.9
 Identities = 9/17 (52%), Positives = 11/17 (64%)

Query: 39  GVVGDLVTGTAHMSFAA 55
           GVV D  TG+A  + AA
Sbjct: 218 GVVEDPATGSAAGALAA 234


>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily. 
          Length = 201

 Score = 25.1 bits (55), Expect = 2.0
 Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 1/47 (2%)

Query: 3   LLENIAQEL-EFDFHLYIVADGLYGTKVRENQKDKWNGVVGDLVTGT 48
           L E  A+EL +    L +   GLYG   +  Q  K      D++  T
Sbjct: 66  LAEQWAEELKKLGPSLGLKVVGLYGGDSKREQLRKLESGKTDILVTT 112


>gnl|CDD|168661 PRK06753, PRK06753, hypothetical protein; Provisional.
          Length = 373

 Score = 24.6 bits (54), Expect = 3.8
 Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 11/42 (26%)

Query: 12  EFDFHLYIVADGLYGTKVRE--NQKDK--------WNGVVGD 43
              F L I ADG++ +KVR+  N   K        + G++ D
Sbjct: 138 SEAFDLCIGADGIH-SKVRQSVNADSKVRYQGYTCFRGLIDD 178


>gnl|CDD|216406 pfam01275, Myelin_PLP, Myelin proteolipid protein (PLP or
           lipophilin). 
          Length = 244

 Score = 24.3 bits (53), Expect = 4.9
 Identities = 8/20 (40%), Positives = 12/20 (60%), Gaps = 2/20 (10%)

Query: 4   LENIAQELEFD--FHLYIVA 21
           L +I +  EF   +HL+I A
Sbjct: 188 LASICKTSEFQMTYHLFIAA 207


>gnl|CDD|185221 PRK15321, PRK15321, putative type III secretion system effector
           protein OrgC; Provisional.
          Length = 120

 Score = 23.9 bits (51), Expect = 6.5
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)

Query: 3   LLENIAQELEFDFHLYIVADG-LYGTKVRENQKDKW 37
           +L+N+  ++E   HLY   +G L GT   ++Q   W
Sbjct: 68  MLQNMLAKVEPGTHLYEALNGVLVGTMNAQSQMTSW 103


  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
   0.318    0.134    0.385 

Gapped
Lambda     K      H
   0.267   0.0761    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,046,265
Number of extensions: 210654
Number of successful extensions: 169
Number of sequences better than 10.0: 1
Number of HSP's gapped: 167
Number of HSP's successfully gapped: 8
Length of query: 62
Length of database: 10,937,602
Length adjustment: 33
Effective length of query: 29
Effective length of database: 9,473,920
Effective search space: 274743680
Effective search space used: 274743680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.1 bits)