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= 037395
         (121 letters)

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

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



>pdb|3IZR|MM Chain m, Localization Of The Large Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
          Length = 92

 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/25 (80%), Positives = 22/25 (88%)

Query: 97  KYAIKRKVVGIWSCKYCGKVKAGGA 121
           K+A+KRK VGIW CK CGKVKAGGA
Sbjct: 44  KFAVKRKAVGIWGCKDCGKVKAGGA 68


>pdb|1YSH|D Chain D, Localization And Dynamic Behavior Of Ribosomal Protein
           L30e
          Length = 73

 Score = 43.9 bits (102), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/25 (80%), Positives = 22/25 (88%)

Query: 97  KYAIKRKVVGIWSCKYCGKVKAGGA 121
           K+A+KRK VGIW CK CGKVKAGGA
Sbjct: 35  KFAVKRKAVGIWGCKDCGKVKAGGA 59


>pdb|4A17|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 5s Rrna, 5.8s
           Rrna And Proteins Of Molecule 2.
 pdb|4A1A|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 5s Rrna, 5.8s
           Rrna And Proteins Of Molecule 3.
 pdb|4A1C|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 5s Rrna, 5.8s
           Rrna And Proteins Of Molecule 4.
 pdb|4A1E|Y Chain Y, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 5s Rrna, 5.8s
           Rrna And Proteins Of Molecule 1
          Length = 103

 Score = 34.3 bits (77), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 16/25 (64%), Positives = 18/25 (72%)

Query: 97  KYAIKRKVVGIWSCKYCGKVKAGGA 121
           K A+KR  VGIW CK C K+ AGGA
Sbjct: 44  KVAVKRAAVGIWKCKPCKKIIAGGA 68


>pdb|3ZF7|OO Chain o, High-resolution Cryo-electron Microscopy Structure Of The
           Trypanosoma Brucei Ribosome
          Length = 93

 Score = 34.3 bits (77), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 15/25 (60%), Positives = 17/25 (68%)

Query: 97  KYAIKRKVVGIWSCKYCGKVKAGGA 121
           K+A +RK VGIW C  C K  AGGA
Sbjct: 44  KFAFRRKAVGIWRCDGCSKTVAGGA 68


>pdb|2ZKR|ZZ Chain z, Structure Of A Mammalian Ribosomal 60s Subunit Within An
           80s Complex Obtained By Docking Homology Models Of The
           Rna And Proteins Into An 8.7 A Cryo-Em Map
          Length = 92

 Score = 29.6 bits (65), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 14/25 (56%), Positives = 16/25 (64%)

Query: 97  KYAIKRKVVGIWSCKYCGKVKAGGA 121
           K  +KR+ VGIW C  C K  AGGA
Sbjct: 44  KTKMKRRAVGIWHCGSCMKTVAGGA 68


>pdb|3G9K|S Chain S, Crystal Structure Of Bacillus Anthracis Transpeptidase
          Enzyme Capd
 pdb|3G9K|F Chain F, Crystal Structure Of Bacillus Anthracis Transpeptidase
          Enzyme Capd
 pdb|3GA9|S Chain S, Crystal Structure Of Bacillus Anthracis Transpeptidase
          Enzyme Capd, Crystal Form Ii
          Length = 177

 Score = 29.6 bits (65), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 14/51 (27%), Positives = 24/51 (47%)

Query: 24 SEVVSVDRDESRVPSICSCANRITPHAFDHGFILSGFAEKDDQEGMNCWKP 74
          +  V +DRD + V S  + +N      +  GF L+   +    EG N ++P
Sbjct: 2  THFVIIDRDGTVVSSTNTLSNFFGTGKYTAGFFLNNQLQNFGSEGFNSYEP 52


>pdb|3J21|II Chain i, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
           Revealed By Cryo-em: Implications For Evolution Of
           Eukaryotic Ribosomes (50s Ribosomal Proteins)
          Length = 83

 Score = 29.3 bits (64), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 16/25 (64%)

Query: 97  KYAIKRKVVGIWSCKYCGKVKAGGA 121
           + A+KR   GIW C+ CG   AGGA
Sbjct: 43  RKAVKRISTGIWQCQKCGATFAGGA 67


>pdb|3JYW|9 Chain 9, Structure Of The 60s Proteins For Eukaryotic Ribosome
           Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
           At 8.9a Resolution
          Length = 72

 Score = 28.9 bits (63), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 15/25 (60%)

Query: 97  KYAIKRKVVGIWSCKYCGKVKAGGA 121
           K  +KR   GIW+C  C K  AGGA
Sbjct: 34  KKTVKRGAAGIWTCSCCKKTVAGGA 58


>pdb|1S1I|9 Chain 9, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
           Yeast Obtained By Docking Atomic Models For Rna And
           Protein Components Into A 11.7 A Cryo-Em Map. This File,
           1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
           In File 1s1h
          Length = 91

 Score = 28.9 bits (63), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 15/25 (60%)

Query: 97  KYAIKRKVVGIWSCKYCGKVKAGGA 121
           K  +KR   GIW+C  C K  AGGA
Sbjct: 43  KKTVKRGAAGIWTCSCCKKTVAGGA 67


>pdb|3IZS|MM Chain m, Localization Of The Large Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
 pdb|3O58|GG Chain g, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
           Of The First 80s In The Asymmetric Unit.
 pdb|3O5H|GG Chain g, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
           Of The Second 80s In The Asymmetric Unit.
 pdb|3U5E|PP Chain p, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome A
 pdb|3U5I|PP Chain p, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome B
 pdb|4B6A|PP Chain p, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
           With Arx1 And Rei1
          Length = 92

 Score = 28.9 bits (63), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 13/25 (52%), Positives = 15/25 (60%)

Query: 97  KYAIKRKVVGIWSCKYCGKVKAGGA 121
           K  +KR   GIW+C  C K  AGGA
Sbjct: 44  KKTVKRGAAGIWTCSCCKKTVAGGA 68


>pdb|1PXV|A Chain A, The Staphostatin-Staphopain Complex: A Forward Binding
           Inhibitor In Complex With Its Target Cysteine Protease
 pdb|1PXV|B Chain B, The Staphostatin-Staphopain Complex: A Forward Binding
           Inhibitor In Complex With Its Target Cysteine Protease
          Length = 183

 Score = 26.2 bits (56), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 18  EGIDSRSEVVSVDRDESRVPSICSCA--NRITPHAFDHGFILSGFAEKDDQEGMNCWKP 74
           EG+ S ++V  + +D   +  +      N   PH   H   + G A+ +DQE +  W P
Sbjct: 94  EGVPSYNQVDQLTKDNVGIMILAQSVSQNPNDPH-LGHALAVVGNAKINDQEKLIYWNP 151


>pdb|1Y4H|A Chain A, Wild Type Staphopain-staphostatin Complex
 pdb|1Y4H|B Chain B, Wild Type Staphopain-staphostatin Complex
          Length = 188

 Score = 26.2 bits (56), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 18  EGIDSRSEVVSVDRDESRVPSICSCA--NRITPHAFDHGFILSGFAEKDDQEGMNCWKP 74
           EG+ S ++V  + +D   +  +      N   PH   H   + G A+ +DQE +  W P
Sbjct: 99  EGVPSYNQVDQLTKDNVGIMILAQSVSQNPNDPH-LGHALAVVGNAKINDQEKLIYWNP 156


>pdb|1X9Y|A Chain A, The Prostaphopain B Structure
 pdb|1X9Y|B Chain B, The Prostaphopain B Structure
 pdb|1X9Y|C Chain C, The Prostaphopain B Structure
 pdb|1X9Y|D Chain D, The Prostaphopain B Structure
          Length = 367

 Score = 25.4 bits (54), Expect = 8.7,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 3/60 (5%)

Query: 18  EGIDSRSEVVSVDRDESRVPSICSCA--NRITPHAFDHGFILSGFAEKDDQEGMNCWKPF 75
           EG+ S ++V  + +D   +  +      N   PH   H   + G A+ +DQE +  W P+
Sbjct: 270 EGVPSYNQVDQLTKDNVGIMILAQSVSQNPNDPH-LGHALAVVGNAKINDQEKLIYWNPW 328


  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
   0.322    0.137    0.456 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,941,074
Number of Sequences: 62578
Number of extensions: 144868
Number of successful extensions: 143
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 125
Number of HSP's gapped (non-prelim): 21
length of query: 121
length of database: 14,973,337
effective HSP length: 83
effective length of query: 38
effective length of database: 9,779,363
effective search space: 371615794
effective search space used: 371615794
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)