RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10647
         (92 letters)



>gnl|CDD|215866 pfam00339, Arrestin_N, Arrestin (or S-antigen), N-terminal
          domain.  Ig-like beta-sandwich fold. Scop reports
          duplication with C-terminal domain.
          Length = 148

 Score = 38.8 bits (91), Expect = 6e-05
 Identities = 14/35 (40%), Positives = 20/35 (57%)

Query: 56 FVILFDNTNLVYFPGQYLSGRVLIELKDDTPALAL 90
          F I  D  + VY PG+ +SG+VL+  K    A A+
Sbjct: 1  FTIYLDKPDPVYHPGEPVSGKVLLTTKKPIKARAV 35



 Score = 38.5 bits (90), Expect = 9e-05
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 8  FVILFDNTNLVYFPGQYLSGRVLIELKD 35
          F I  D  + VY PG+ +SG+VL+  K 
Sbjct: 1  FTIYLDKPDPVYHPGEPVSGKVLLTTKK 28


>gnl|CDD|183194 PRK11556, PRK11556, multidrug efflux system subunit MdtA;
           Provisional.
          Length = 415

 Score = 25.5 bits (56), Expect = 4.2
 Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 3/40 (7%)

Query: 54  IKFVILFDNTNLVYFPGQYLSGRVLIELKDDT---PALAL 90
           IK    F+N +   FP Q+++ R+L++   +    P  AL
Sbjct: 290 IKLKARFNNQDDALFPNQFVNARMLVDTLQNAVVIPTAAL 329


>gnl|CDD|177165 MTH00103, COX1, cytochrome c oxidase subunit I; Validated.
          Length = 513

 Score = 25.6 bits (56), Expect = 4.3
 Identities = 10/26 (38%), Positives = 14/26 (53%)

Query: 48  NMTRKLIKFVILFDNTNLVYFPGQYL 73
           N T   I F I+F   N+ +FP  +L
Sbjct: 406 NDTWAKIHFTIMFVGVNMTFFPQHFL 431



 Score = 25.2 bits (55), Expect = 6.9
 Identities = 8/20 (40%), Positives = 12/20 (60%)

Query: 6   IKFVILFDNTNLVYFPGQYL 25
           I F I+F   N+ +FP  +L
Sbjct: 412 IHFTIMFVGVNMTFFPQHFL 431


>gnl|CDD|226218 COG3694, COG3694, ABC-type uncharacterized transport system,
           permease component [General function prediction only].
          Length = 260

 Score = 25.4 bits (56), Expect = 4.6
 Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 2/45 (4%)

Query: 47  NNMTRKLIKFVILFDNTNLVYFPGQYLSGRVLIELKDDTPALALL 91
             + RK   F+I      L Y P  Y+ GR+  E    +   ALL
Sbjct: 197 PAILRKFFTFIIPV--AFLTYVPALYVLGRLDPEWAIGSLLAALL 239


>gnl|CDD|187810 cd09679, Cas10_III, CRISPR/Cas system-associated protein Cas10.
           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;
           Multidomain protein with permuted HD nuclease domain,
           palm domain and Zn-ribbon; MTH326-like has inactivated
           polymerase catalytic domain; alr1562 and slr7011 -
           predicted only on the basis of size, presence of HD
           domain, and location with RAMPs in one operon; signature
           gene for type III; also known as Crm2 family.
          Length = 475

 Score = 25.1 bits (55), Expect = 6.6
 Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 2/48 (4%)

Query: 22  GQYLSGRVLIELKDDTPAL--GFHRSKNNMTRKLIKFVILFDNTNLVY 67
           G++LSG  L E +  TP       R+ +N   K +K V+      LVY
Sbjct: 338 GKWLSGEKLPEKRLITPEYHRAISRALSNFALKAVKIVVEEHRGKLVY 385


>gnl|CDD|241162 cd12718, RRM_BRAP2, RNA recognition motif in BRCA1-associated
          protein (BRAP2).  This subgroup corresponds to the RRM
          of BRAP2, also termed impedes mitogenic signal
          propagation (IMP), or ring finger protein 52, or renal
          carcinoma antigen NY-REN-63, a novel cytoplasmic
          protein interacting with the two functional nuclear
          localisation signal (NLS) motifs of BRCA1, a nuclear
          protein linked to breast cancer. It also binds to the
          SV40 large T antigen NLS motif and the bipartite NLS
          motif found in mitosin. BRAP2 may serve as a
          cytoplasmic retention protein and play a role in the
          regulation of nuclear protein transport. It contains an
          N-terminal RNA recognition motif (RRM), also termed RBD
          (RNA binding domain) or RNP (ribonucleoprotein domain),
          followed by a C3HC4-type ring finger domain and a
          UBP-type zinc finger. .
          Length = 84

 Score = 24.1 bits (53), Expect = 7.3
 Identities = 9/30 (30%), Positives = 16/30 (53%), Gaps = 3/30 (10%)

Query: 21 PGQYLSGRVLIELKDDTPALGFHRSKNNMT 50
          P QY+   VL++ +  T A  F+++ N   
Sbjct: 40 PNQYM---VLLKFRSQTDADEFYKTYNGRP 66


  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
   0.327    0.146    0.420 

Gapped
Lambda     K      H
   0.267   0.0634    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,912,612
Number of extensions: 414616
Number of successful extensions: 413
Number of sequences better than 10.0: 1
Number of HSP's gapped: 413
Number of HSP's successfully gapped: 22
Length of query: 92
Length of database: 10,937,602
Length adjustment: 59
Effective length of query: 33
Effective length of database: 8,320,716
Effective search space: 274583628
Effective search space used: 274583628
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.4 bits)