RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2802
         (74 letters)



>gnl|CDD|215685 pfam00060, Lig_chan, Ligand-gated ion channel.  This family
           includes the four transmembrane regions of the
           ionotropic glutamate receptors and NMDA receptors.
          Length = 268

 Score = 96.6 bits (241), Expect = 2e-26
 Identities = 35/74 (47%), Positives = 45/74 (60%)

Query: 1   MYYFMQMHKDKVFVSSETEGVNKVRSSHGKYAFLIESPRNDYENARQPCDTMKVGNNLDV 60
           M+ +M   K +V V S  EGV +VR  +G YAFL+ES   +YE AR PC    VG     
Sbjct: 137 MWEYMISFKGEVNVESYEEGVQRVRKGNGLYAFLMESAYLEYEVARDPCKLTTVGEVFGT 196

Query: 61  KGFGVATPIGSPLK 74
           KG+G+A P GSPL+
Sbjct: 197 KGYGIAFPKGSPLR 210


>gnl|CDD|197504 smart00079, PBPe, Eukaryotic homologues of bacterial periplasmic
           substrate binding proteins.  Prokaryotic homologues are
           represented by a separate alignment: PBPb.
          Length = 133

 Score = 82.0 bits (203), Expect = 5e-22
 Identities = 34/69 (49%), Positives = 43/69 (62%), Gaps = 3/69 (4%)

Query: 6   QMHKDKVFVSSETEGVNKVRSSHGKYAFLIESPRNDYENARQPCDTMKVGNNLDVKGFGV 65
            M   +VFV S  EGV +VR S   YAF++ESP  DYE + + CD M VG     KG+G+
Sbjct: 42  YMKSPEVFVKSYAEGVQRVRVS--NYAFIMESPYLDYELS-RNCDLMTVGEEFGRKGYGI 98

Query: 66  ATPIGSPLK 74
           A P GSPL+
Sbjct: 99  AFPKGSPLR 107


>gnl|CDD|187844 cd09713, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c.
           CRISPR (Clustered Regularly Interspaced Short
           Palindromic Repeats) and associated Cas proteins
           comprise a system for heritable host defense by
           prokaryotic cells against phage and other foreign DNA;
           Large proteins, some contain Zn-finger domain; signature
           gene for I-C subtype; also known as Csx13_N family.
          Length = 316

 Score = 26.3 bits (58), Expect = 1.4
 Identities = 15/52 (28%), Positives = 21/52 (40%), Gaps = 4/52 (7%)

Query: 23  KVRSSHGKYAFLIESPRNDYENARQPCDTMKVGNNLDVKGFGVATPIGSPLK 74
           ++RSS G YA +I    +    AR   D       L+     V  P  + LK
Sbjct: 203 ELRSSRGTYAIVIPELTDLETFARFRRDL----TELNYINMFVGGPGDAGLK 250


>gnl|CDD|183718 PRK12746, PRK12746, short chain dehydrogenase; Provisional.
          Length = 254

 Score = 25.4 bits (55), Expect = 3.1
 Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 11/65 (16%)

Query: 5  MQMHKDKVFVS--------SETEGVNKVRSSHGKYAFLIESPRNDYENARQPCDTMKVGN 56
          M++  D   V+        +  E + ++ S+ GK AFLIE+  N  +  ++  + +K  N
Sbjct: 24 MRLANDGALVAIHYGRNKQAADETIREIESNGGK-AFLIEADLNSIDGVKKLVEQLK--N 80

Query: 57 NLDVK 61
           L ++
Sbjct: 81 ELQIR 85


>gnl|CDD|181766 PRK09295, PRK09295, bifunctional cysteine
           desulfurase/selenocysteine lyase; Validated.
          Length = 406

 Score = 25.1 bits (55), Expect = 4.3
 Identities = 10/25 (40%), Positives = 15/25 (60%)

Query: 6   QMHKDKVFVSSETEGVNKVRSSHGK 30
           +  ++ VFV   TEG+N V +S G 
Sbjct: 83  RSAEELVFVRGTTEGINLVANSWGN 107


>gnl|CDD|226200 COG3675, COG3675, Predicted lipase [Lipid metabolism].
          Length = 332

 Score = 24.9 bits (54), Expect = 4.4
 Identities = 6/38 (15%), Positives = 12/38 (31%), Gaps = 6/38 (15%)

Query: 13  FVSSETEGVNKVRSSHGKYAFLIESPRNDYENARQPCD 50
            ++ + +  N      G+ A+ IE             D
Sbjct: 109 LLNFDVDERNCRHLCVGELAYRIE------AGFYHLLD 140


>gnl|CDD|233581 TIGR01810, betA, choline dehydrogenase.  Choline dehydrogenase
           catalyzes the conversion of exogenously supplied choline
           into the intermediate glycine betaine aldehyde, as part
           of a two-step oxidative reaction leading to the
           formation of osmoprotectant betaine. This enzymatic
           system can be found in both gram-positive and
           gram-negative bacteria. As in Escherichia coli ,
           Staphylococcus xylosus , and Sinorhizobium meliloti,
           this enzyme is found associated in a transciptionally
           co-induced gene cluster with betaine aldehyde
           dehydrogenase, the second catalytic enzyme in this
           reaction. Other gram-positive organisms have been shown
           to employ a different enzymatic system, utlizing a
           soluable choline oxidase or type III alcohol
           dehydrogenase instead of choline dehydrogenase. This
           enzyme is a member of the GMC oxidoreductase family
           (pfam00732 and pfam05199), sharing a common
           evoluntionary origin and enzymatic reaction with alcohol
           dehydrogenase. Outgrouping from this model, Caulobacter
           crescentus shares sequence homology with choline
           dehydrogenase, yet other genes participating in this
           enzymatic reaction have not currently been identified
           [Cellular processes, Adaptations to atypical
           conditions].
          Length = 532

 Score = 24.1 bits (52), Expect = 8.5
 Identities = 10/26 (38%), Positives = 12/26 (46%)

Query: 34  LIESPRNDYENARQPCDTMKVGNNLD 59
           + E  R   E A  PC T K+G   D
Sbjct: 453 IDEFVRRHGETALHPCGTCKMGPASD 478


  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
   0.316    0.134    0.394 

Gapped
Lambda     K      H
   0.267   0.0740    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,497,343
Number of extensions: 245348
Number of successful extensions: 164
Number of sequences better than 10.0: 1
Number of HSP's gapped: 162
Number of HSP's successfully gapped: 7
Length of query: 74
Length of database: 10,937,602
Length adjustment: 44
Effective length of query: 30
Effective length of database: 8,986,026
Effective search space: 269580780
Effective search space used: 269580780
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 (21.6 bits)
S2: 53 (24.2 bits)