RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6028
         (141 letters)



>gnl|CDD|201967 pfam01778, Ribosomal_L28e, Ribosomal L28e protein family. 
          Length = 114

 Score =  107 bits (269), Expect = 4e-31
 Identities = 50/119 (42%), Positives = 71/119 (59%), Gaps = 5/119 (4%)

Query: 6   LIWNIVKNNNAYLMKADNIKKWFSKEPGNLPNLASFKYSGLIHSKTIHIQPTADNKGFAC 65
           LIW I++ NN +L+K +   K FS+EP NL  L S KYSGL +SK + + PTA   G   
Sbjct: 1   LIWEIIRKNNCFLVKRN--GKTFSREPYNLTGLCSRKYSGLANSKYVTVVPTA-KGGVVL 57

Query: 66  VTKRATKKYKPGKAVIKQEWKSGPRRSLLKLRKYIVGNKYRKELTKAALRRASAVLQSQ 124
           VTK+  + +KP K   K       R++L +++K +    YR +L K A RRAS +L+SQ
Sbjct: 58  VTKKPKRAHKPAKLWEKVTLSKNYRKALKQIKKAL--AYYRPDLIKKAKRRASKLLRSQ 114


>gnl|CDD|188267 TIGR03001, Sig-70_gmx1, RNA polymerase sigma-70 factor,
           Myxococcales family 1.  This group of sigma factors are
           members of the sigma-70 family (TIGR02937) and are found
           in multiple copies in the order Myxococcales. This model
           supercedes TIGR02233, which has now been retired.
          Length = 244

 Score = 28.5 bits (64), Expect = 0.91
 Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 8/41 (19%)

Query: 87  SGPRRSLLKLRKYIVGNKYRKELTKAALRRASAVLQSQKRA 127
           S P   LL+ R       YR++  + ALR A A L  ++R 
Sbjct: 136 SDPELDLLRER-------YRQDF-RQALREALAALSERERH 168


>gnl|CDD|140328 PTZ00307, PTZ00307, ethanolamine phosphotransferase; Provisional.
          Length = 417

 Score = 27.1 bits (60), Expect = 3.3
 Identities = 8/14 (57%), Positives = 9/14 (64%)

Query: 32 PGNLPNLASFKYSG 45
          P  LPNL  +KYS 
Sbjct: 22 PAYLPNLKKYKYSS 35


>gnl|CDD|187827 cd09696, Cas3_I, CRISPR/Cas system-associated protein Cas3;
           Distinct Cas3 family with HD domain fused to C-termus of
           Helicase domain.  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; DNA helicase Cas3; This protein includes
           both DEAH and HD motifs; signature gene for Type I.
          Length = 843

 Score = 26.9 bits (59), Expect = 5.1
 Identities = 7/32 (21%), Positives = 12/32 (37%)

Query: 50  KTIHIQPTADNKGFACVTKRATKKYKPGKAVI 81
           K + + P +D K  + + K      K     I
Sbjct: 243 KIVKLVPPSDEKFLSTMVKELNLLMKDSGGAI 274


>gnl|CDD|226702 COG4251, COG4251, Bacteriophytochrome (light-regulated signal
           transduction histidine kinase) [Signal transduction
           mechanisms].
          Length = 750

 Score = 26.2 bits (58), Expect = 6.9
 Identities = 14/35 (40%), Positives = 16/35 (45%)

Query: 83  QEWKSGPRRSLLKLRKYIVGNKYRKELTKAALRRA 117
           Q W      + L+LRK IVG   R     A LRR 
Sbjct: 482 QPWSEVEIEAALELRKAIVGIVLRHAEELAQLRRE 516


>gnl|CDD|226988 COG4641, COG4641, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 373

 Score = 26.3 bits (58), Expect = 7.5
 Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 3/61 (4%)

Query: 67  TKRATKKYKPGKAVIKQEWKSGPRRSLLKLRKYIVGNKYRKELTKAALRRASAVLQSQKR 126
            K   K +KPGK +I        +    KL+  +     RKE+ + A  R  A    ++R
Sbjct: 295 WKDLEKFFKPGKDII---VYQDSKDLKEKLKYLLNHPDERKEIAECAYERVLARHTYEER 351

Query: 127 A 127
            
Sbjct: 352 I 352


>gnl|CDD|237952 PRK15362, PRK15362, pathogenicity island 2 effector protein SseC;
           Provisional.
          Length = 473

 Score = 25.9 bits (57), Expect = 9.1
 Identities = 12/51 (23%), Positives = 25/51 (49%), Gaps = 3/51 (5%)

Query: 67  TKRATKKY--KPGKAVIKQEWKSGPRRSLLKLRKYIVGNKYRKELTKAALR 115
           TK A +    +  +  +K+  + G +  L +  K +V  +  K++ KA +R
Sbjct: 327 TKEAIEAMVTEAVEEALKKAVQEGVKFLLKEFTKQVV-KEVFKKVIKALIR 376


>gnl|CDD|218545 pfam05300, DUF737, Protein of unknown function (DUF737).  This
           family consists of several uncharacterized mammalian
           proteins of unknown function.
          Length = 187

 Score = 25.5 bits (56), Expect = 9.4
 Identities = 17/86 (19%), Positives = 44/86 (51%), Gaps = 9/86 (10%)

Query: 55  QPTADNKGFACVTKRATKKYKPGKAVIKQEWKSGPRRSLLKLRKYIVGNKYRKELTKAAL 114
           + TA     + V +   K+Y+  +A++++E        + K  +        ++L++A L
Sbjct: 69  EETAGGLQSSEVKEDLLKRYEQEQAIVQEELAR-----IAKRER----EAAEEQLSRAVL 119

Query: 115 RRASAVLQSQKRAQIPAKKSNKKKAD 140
           R  ++  Q +++A+  A++  +K+A+
Sbjct: 120 REKASAEQERQKAKHLARQLEEKEAE 145


  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
   0.314    0.128    0.370 

Gapped
Lambda     K      H
   0.267   0.0618    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,721,902
Number of extensions: 563115
Number of successful extensions: 542
Number of sequences better than 10.0: 1
Number of HSP's gapped: 535
Number of HSP's successfully gapped: 19
Length of query: 141
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 54
Effective length of database: 7,078,804
Effective search space: 382255416
Effective search space used: 382255416
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: 54 (24.8 bits)