RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16309
         (271 letters)



>gnl|CDD|183397 PRK12277, PRK12277, 50S ribosomal protein L13e; Provisional.
          Length = 83

 Score = 31.7 bits (72), Expect = 0.071
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 4/50 (8%)

Query: 86  HFDFPPSSPDLRMRARTKGYDSKTELEKVGMGIEFSRFVKAELKISLKTV 135
            F++     D R     +G+ S  ELE  G+ I+ +R +   +    KTV
Sbjct: 18  RFEYGGKRKDKR---IGRGF-SIGELEAAGLDIKNARKLGIRVDKRRKTV 63


>gnl|CDD|239315 cd03017, PRX_BCP, Peroxiredoxin (PRX) family, Bacterioferritin
           comigratory protein (BCP) subfamily; composed of
           thioredoxin-dependent thiol peroxidases, widely
           expressed in pathogenic bacteria, that protect cells
           against toxicity from reactive oxygen species by
           reducing and detoxifying hydroperoxides. The protein was
           named BCP based on its electrophoretic mobility before
           its function was known. BCP shows substrate selectivity
           toward fatty acid hydroperoxides rather than hydrogen
           peroxide or alkyl hydroperoxides. BCP contains the
           peroxidatic cysteine but appears not to possess a
           resolving cysteine (some sequences, not all, contain a
           second cysteine but its role is still unknown). Unlike
           other PRXs, BCP exists as a monomer. The plant homolog
           of BCP is PRX Q, which is expressed only in leaves and
           is cellularly localized in the chloroplasts and the
           guard cells of stomata. Also included in this subfamily
           is the fungal nuclear protein,  Dot5p (for disrupter of
           telomere silencing protein 5), which functions as an
           alkyl-hydroperoxide reductase during post-diauxic
           growth.
          Length = 140

 Score = 27.1 bits (61), Expect = 5.7
 Identities = 21/67 (31%), Positives = 28/67 (41%), Gaps = 7/67 (10%)

Query: 79  AQRKFCTHFDFP-P--SSPDLRMRARTKGYDSKTELEKVGMGIEFSRFV-KAELKISLKT 134
           +  KF   +  P P  S PD ++    K Y    E +K  MGIE S F+   + KI    
Sbjct: 70  SHAKFAEKYGLPFPLLSDPDGKLA---KAYGVWGEKKKKYMGIERSTFLIDPDGKIVKVW 126

Query: 135 VNFKAAG 141
              K  G
Sbjct: 127 RKVKPKG 133


>gnl|CDD|238555 cd01135, V_A-ATPase_B, V/A-type ATP synthase (non-catalytic)
           subunit B. These ATPases couple ATP hydrolysis to the
           build up of a H+ gradient, but V-type ATPases do not
           catalyze the reverse reaction. The Vacuolar (V-type)
           ATPase is found in the membranes of vacuoles, the golgi
           apparatus and in other coated vesicles in eukaryotes.
           Archaea have a protein which is similar in sequence to
           V-ATPases, but functions like an F-ATPase (called
           A-ATPase).  A similar protein is also found in a few
           bacteria. This subfamily consists of the non-catalytic
           beta subunit.
          Length = 276

 Score = 27.6 bits (62), Expect = 5.8
 Identities = 10/33 (30%), Positives = 17/33 (51%)

Query: 224 LKYETINFFQEKFNKKLSMEGRLEFLNLWYDAV 256
           +  E   FF++ F +  ++E  + FLNL  D  
Sbjct: 111 ITMEDARFFKDDFEETGALERVVLFLNLANDPT 143


>gnl|CDD|220778 pfam10487, Nup188, Nucleoporin subcomplex protein binding to Pom34.
            This is one of the many peptides that make up the
           nucleoporin complex (NPC), and is found across
           eukaryotes. The Nup188 subcomplex
           (Nic96p-Nup188p-Nup192p-Pom152p) is one of at least six
           that make up the NPC, and as such is symmetrically
           localised on both faces of the NPC at the nuclear end,
           being integrally bound to the C-terminus of Pom34p.
          Length = 931

 Score = 27.9 bits (62), Expect = 6.6
 Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 3/49 (6%)

Query: 157 LDNSDMDGQVLISLDTEPTRLACKGDVK---YYDNNRLDFILRSLLNLL 202
           L+       +L +L T+P +     D+K   YY  +RL  ILR +L++L
Sbjct: 72  LERYRGTRDILKTLLTDPRQSQALMDLKLADYYYEDRLCKILRCVLHIL 120


>gnl|CDD|173199 PRK14737, gmk, guanylate kinase; Provisional.
          Length = 186

 Score = 27.3 bits (60), Expect = 7.1
 Identities = 11/29 (37%), Positives = 15/29 (51%)

Query: 85  THFDFPPSSPDLRMRARTKGYDSKTELEK 113
           T F  PPS  +   R   +G DS+  +EK
Sbjct: 119 TIFIEPPSEEEWEERLIHRGTDSEESIEK 147


  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
   0.325    0.139    0.435 

Gapped
Lambda     K      H
   0.267   0.0607    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,528,461
Number of extensions: 1253182
Number of successful extensions: 1126
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1126
Number of HSP's successfully gapped: 11
Length of query: 271
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 176
Effective length of database: 6,723,972
Effective search space: 1183419072
Effective search space used: 1183419072
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.4 bits)