RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5853
         (217 letters)



>gnl|CDD|216928 pfam02204, VPS9, Vacuolar sorting protein 9 (VPS9) domain. 
          Length = 104

 Score =  110 bits (277), Expect = 2e-31
 Identities = 39/103 (37%), Positives = 64/103 (62%), Gaps = 3/103 (2%)

Query: 115 WPAAQAEISSISSYKTAHDKVQCVYRTLNTILNLLSLTS--AVPAADDLIPVLVYVLIKA 172
           W  AQ E+  ++  K+  +K++C+ RT   I   LS ++      ADDL+P+L+YVLIKA
Sbjct: 1   WEKAQEELKKLNEAKSPREKLKCLLRTCKLITEALSKSNPGEPLGADDLLPILIYVLIKA 60

Query: 173 NPPSLLSTVQYVNSF-YANKMEGEIQYWWVQFCSAIEFIKTMD 214
           NPP+L S +Q+++ F   + + GE  Y+     +A+EFI+ +D
Sbjct: 61  NPPNLYSNLQFISLFRDPDLLSGEEGYYLTTLEAALEFIENLD 103


>gnl|CDD|128469 smart00167, VPS9, Domain present in VPS9.  Domain present in yeast
           vacuolar sorting protein 9 and other proteins.
          Length = 117

 Score = 87.9 bits (218), Expect = 2e-22
 Identities = 34/102 (33%), Positives = 52/102 (50%), Gaps = 2/102 (1%)

Query: 114 PWPAAQAEISSISSYKTAHDKVQCVYRTLNTILNLLSLTS-AVPAADDLIPVLVYVLIKA 172
                Q E+  +  YK+  DK++C+ R    I  LL   S  V  ADD +PVL+YV+IK 
Sbjct: 1   FVEIEQIELKFLQLYKSPSDKIKCLLRACKLIYTLLETQSGEVAGADDFLPVLIYVIIKC 60

Query: 173 NPPSLLSTVQYVNSF-YANKMEGEIQYWWVQFCSAIEFIKTM 213
           +P  LL   +Y+  F   + + GE  Y+     +A+  IK +
Sbjct: 61  DPRDLLLNAEYMEEFLEPSLLTGEGGYYLTSLSAALALIKGL 102


>gnl|CDD|218131 pfam04530, Viral_Beta_CD, Viral Beta C/D like family.  Family of
           ssRNA positive-strand viral proteins. Conserved region
           found in the Beta C and Beta D transcripts.
          Length = 122

 Score = 27.1 bits (60), Expect = 4.0
 Identities = 13/33 (39%), Positives = 18/33 (54%)

Query: 43  YSDSNSVQLSLAKIAIDRAVISRCYMYAMYPNG 75
           Y D NSV++ L    ID  VI+  + +  YP G
Sbjct: 85  YQDLNSVEIKLGPGPIDPEVIAAIHHWQKYPFG 117


>gnl|CDD|183097 PRK11359, PRK11359, cyclic-di-GMP phosphodiesterase; Provisional.
          Length = 799

 Score = 27.0 bits (60), Expect = 8.3
 Identities = 11/30 (36%), Positives = 19/30 (63%), Gaps = 1/30 (3%)

Query: 38  DYRSGYSD-SNSVQLSLAKIAIDRAVISRC 66
           D+ +G+S  S  V L + +I ID++ + RC
Sbjct: 698 DFGTGFSGLSRLVSLPVTEIKIDKSFVDRC 727


>gnl|CDD|237403 PRK13505, PRK13505, formate--tetrahydrofolate ligase; Provisional.
          Length = 557

 Score = 27.1 bits (61), Expect = 9.5
 Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 11  ISNVTGQGG-GTAEYRRRTYEFVDNNRRDYRSGYSDSNSVQLSLAKIA 57
           +S V  +GG G  E   +  E ++    +++  Y D +S++  + KIA
Sbjct: 406 LSEVWAKGGEGGVELAEKVVELIEEGESNFKPLYDDEDSLEEKIEKIA 453


  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
   0.319    0.134    0.404 

Gapped
Lambda     K      H
   0.267   0.0660    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,822,242
Number of extensions: 961691
Number of successful extensions: 668
Number of sequences better than 10.0: 1
Number of HSP's gapped: 664
Number of HSP's successfully gapped: 17
Length of query: 217
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 124
Effective length of database: 6,812,680
Effective search space: 844772320
Effective search space used: 844772320
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 (21.8 bits)
S2: 57 (25.9 bits)