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= psy11495
         (81 letters)

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

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



>pdb|3QFW|A Chain A, Crystal Structure Of Rubisco-Like Protein From
           Rhodopseudomonas Palustris
 pdb|3QFW|B Chain B, Crystal Structure Of Rubisco-Like Protein From
           Rhodopseudomonas Palustris
          Length = 378

 Score = 27.7 bits (60), Expect = 1.9,   Method: Composition-based stats.
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 2   KALREKSAYATYRLCFEEAMSGLDEVFSREKGVNREDRIHGSLLVLNELLRVSN 55
           KA+RE +A    R  +   +SG  +   R+ GV R++ I G++LV   ++ VSN
Sbjct: 186 KAVREANAARGGRTLYAPNISGTLDDMRRQLGVIRDEGI-GAVLVAPMIVGVSN 238


>pdb|2RCN|A Chain A, Crystal Structure Of The Ribosomal Interacting Gtpase Yjeq
           From The Enterobacterial Species Salmonella Typhimurium
          Length = 358

 Score = 26.9 bits (58), Expect = 3.1,   Method: Composition-based stats.
 Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 2/43 (4%)

Query: 17  FEEAMSGLDEVFSREKGVNREDRIHGSLLVLNELLR--VSNVT 57
            EEA++G   +F+ + GV +   ++  L + NE+L   VSNV+
Sbjct: 209 LEEALTGRISIFAGQSGVGKSSLLNALLGLQNEILTNDVSNVS 251


>pdb|2WW9|M Chain M, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
          To The Yeast 80s Ribosome
 pdb|2WWA|M Chain M, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To
          The Yeast 80s Ribosome
 pdb|2WWB|M Chain M, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound
          To The Actively Translating Wheat Germ 80s Ribosome
 pdb|3IZS|GG Chain g, Localization Of The Large Subunit Ribosomal Proteins
          Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
          Translating 80s Ribosome
 pdb|3O58|AA Chain a, Yeast 80s Ribosome. This Entry Consists Of The 60s
          Subunit Of The First 80s In The Asymmetric Unit.
 pdb|3O5H|AA Chain a, Yeast 80s Ribosome. This Entry Consists Of The 60s
          Subunit Of The Second 80s In The Asymmetric Unit.
 pdb|3U5E|DD Chain d, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 60s
          Subunit, Ribosome A
 pdb|3U5I|DD Chain d, The Structure Of The Eukaryotic Ribosome At 3.0 A
          Resolution. This Entry Contains Proteins Of The 60s
          Subunit, Ribosome B
 pdb|4B6A|DD Chain d, Cryo-Em Structure Of The 60s Ribosomal Subunit In
          Complex With Arx1 And Rei1
          Length = 113

 Score = 26.6 bits (57), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 10/22 (45%), Positives = 15/22 (68%)

Query: 21 MSGLDEVFSREKGVNREDRIHG 42
          M+GL +V +RE  +N   R+HG
Sbjct: 1  MAGLKDVVTREYTINLHKRLHG 22


>pdb|4A2I|V Chain V, Cryo-Electron Microscopy Structure Of The 30s Subunit In
           Complex With The Yjeq Biogenesis Factor
          Length = 277

 Score = 25.0 bits (53), Expect = 10.0,   Method: Composition-based stats.
 Identities = 11/35 (31%), Positives = 21/35 (60%)

Query: 17  FEEAMSGLDEVFSREKGVNREDRIHGSLLVLNELL 51
            EEA++G   +F+ + GV +   ++  L + NE+L
Sbjct: 154 LEEALTGRISIFAGQSGVGKSSLLNALLGLQNEIL 188


  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
   0.318    0.132    0.377 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,145,759
Number of Sequences: 62578
Number of extensions: 63656
Number of successful extensions: 165
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 162
Number of HSP's gapped (non-prelim): 9
length of query: 81
length of database: 14,973,337
effective HSP length: 50
effective length of query: 31
effective length of database: 11,844,437
effective search space: 367177547
effective search space used: 367177547
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)