BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= psy11719
         (657 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

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



>pdb|3J20|J Chain J, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
           Revealed By Cryo-em: Implications For Evolution Of
           Eukaryotic Ribosomes (30s Ribosomal Subunit)
          Length = 127

 Score = 39.3 bits (90), Expect = 0.007,   Method: Composition-based stats.
 Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 15/64 (23%)

Query: 526 IIGVKKNPNSPMYTNLGVITKGTVIEVNISELGLVTQAGKVVWGKYAQVTNNPENDGCIN 585
           II V +NP +  +    +ITKG +IE         T+ GK      A+VT+ P  DG +N
Sbjct: 77  IIRVIENPANRQFARRNIITKGAIIE---------TEIGK------AKVTSRPGQDGVVN 121

Query: 586 AVLL 589
           A+LL
Sbjct: 122 AILL 125


>pdb|2KCY|A Chain A, Solution Structure Of Ribosomal Protein S8e From
           Methanothermobacter Thermautotrophicus,
           Northeaststructural Genomics Consortium (Nesg) Target
           Tr71d
 pdb|2KCP|A Chain A, Solution Structure Of 30s Ribosomal Protein S8e; From
           Methanothermobacter Thermautotrophicus,
           Northeaststructural Genomics Consortium (Nesg) Target
           Tr71d
          Length = 98

 Score = 36.2 bits (82), Expect = 0.052,   Method: Composition-based stats.
 Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 15/80 (18%)

Query: 510 KAHVTHPELKATFYLPIIGVKKNPNSPMYTNLGVITKGTVIEVNISELGLVTQAGKVVWG 569
           + +V  PE        I  V +N  +P +    +IT+G V+E N+  +            
Sbjct: 24  RINVVDPETGKVEIAEIRNVVENTANPHFVRRNIITRGAVVETNLGNV------------ 71

Query: 570 KYAQVTNNPENDGCINAVLL 589
              +VT+ P  DG IN VL+
Sbjct: 72  ---RVTSRPGQDGVINGVLI 88


>pdb|2KCO|A Chain A, Solution Nmr Structure Of Ribosomal Protein Sso0164 From
           Sulfolobus Solfataricus. Northeast Structural Genomics
           Consortium (Nesg) Target Sst4
          Length = 133

 Score = 31.2 bits (69), Expect = 2.1,   Method: Composition-based stats.
 Identities = 24/79 (30%), Positives = 34/79 (43%), Gaps = 15/79 (18%)

Query: 511 AHVTHPELKATFYLPIIGVKKNPNSPMYTNLGVITKGTVIEVNISELGLVTQAGKVVWGK 570
           A+V  P       + I+ + + P +      G+I +G  I          T+AG  V   
Sbjct: 63  ANVLDPATNTAKKVKILEILETPANKELARRGIIIRGAKIR---------TEAGLAV--- 110

Query: 571 YAQVTNNPENDGCINAVLL 589
              VT+ P  DG INAVLL
Sbjct: 111 ---VTSRPGQDGVINAVLL 126


>pdb|3DNV|B Chain B, Mdt Protein
 pdb|2WIU|B Chain B, Mercury-Modified Bacterial Persistence Regulator Hipba
 pdb|2WIU|D Chain D, Mercury-Modified Bacterial Persistence Regulator Hipba
 pdb|3HZI|B Chain B, Structure Of Mdt Protein
          Length = 88

 Score = 28.9 bits (63), Expect = 9.2,   Method: Compositional matrix adjust.
 Identities = 19/76 (25%), Positives = 34/76 (44%), Gaps = 3/76 (3%)

Query: 223 LLRFLPIYLETGDNRLLLLTPMVSELNPWSIHEPSYRVGPMPQTVSNLPLQPSQSSGTLW 282
           ++ F  IY  T   +L     +V + N W+  E + ++G    T+SN    P  ++ T +
Sbjct: 1   MMSFQKIYSPT---QLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTF 57

Query: 283 LKAMCDALWLTAMCDA 298
            K +        +CDA
Sbjct: 58  FKILQSLELSMTLCDA 73


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.323    0.134    0.439 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,087,941
Number of Sequences: 62578
Number of extensions: 745754
Number of successful extensions: 1897
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1893
Number of HSP's gapped (non-prelim): 6
length of query: 657
length of database: 14,973,337
effective HSP length: 105
effective length of query: 552
effective length of database: 8,402,647
effective search space: 4638261144
effective search space used: 4638261144
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 55 (25.8 bits)