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= psy11384
         (137 letters)

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

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



>pdb|3U5C|AA Chain a, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome A
 pdb|3U5G|AA Chain a, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 40s
           Subunit, Ribosome B
          Length = 119

 Score =  144 bits (363), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 67/100 (67%), Positives = 80/100 (80%)

Query: 1   MTCKRRNGGRSKHGRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQ 60
           M  KR + GR+K GRGHV PVRC NC++ +PKDKAIK+  IRNIVEAAAVRD++EAS Y 
Sbjct: 1   MPKKRASNGRNKKGRGHVKPVRCVNCSKSIPKDKAIKRMAIRNIVEAAAVRDLSEASVYP 60

Query: 61  SYQLPKLYAKLHYCVSCAIHSKVVRNRSKSDRRIRTPPQR 100
            Y LPK Y KLHYCVSCAIH+++VR RS+ DR+ R PPQR
Sbjct: 61  EYALPKTYNKLHYCVSCAIHARIVRVRSREDRKNRAPPQR 100


>pdb|3ZEY|V Chain V, High-resolution Cryo-electron Microscopy Structure Of
          The Trypanosoma Brucei Ribosome
          Length = 111

 Score =  101 bits (252), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 51/99 (51%), Positives = 68/99 (68%), Gaps = 4/99 (4%)

Query: 1  MTCKRRNGGRSKH--GRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEAS- 57
          MT KRRN GR+K    RG V PV C NC+R VPKDK++ +FV+R +++ A+ RD+ EAS 
Sbjct: 1  MTTKRRNHGRAKPPCSRGRVRPVHCFNCSRLVPKDKSVGRFVVRRMLDQASARDVAEASL 60

Query: 58 -YYQSYQLPKLYAKLHYCVSCAIHSKVVRNRSKSDRRIR 95
           Y   + +PKLY K  YC++CAIHS+ VR R   DR+ R
Sbjct: 61 IYGSGFPMPKLYMKQRYCIACAIHSRTVRARPVEDRKRR 99


>pdb|2XZM|5 Chain 5, Crystal Structure Of The Eukaryotic 40s Ribosomal
          Subunit In Complex With Initiation Factor 1. This File
          Contains The 40s Subunit And Initiation Factor For
          Molecule 1
 pdb|2XZN|5 Chain 5, Crystal Structure Of The Eukaryotic 40s Ribosomal
          Subunit In Complex With Initiation Factor 1. This File
          Contains The 40s Subunit And Initiation Factor For
          Molecule 2
          Length = 119

 Score = 99.0 bits (245), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 47/93 (50%), Positives = 65/93 (69%), Gaps = 2/93 (2%)

Query: 1  MTCKRRNGGRSKHGRGHVNPVRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDITEASYYQ 60
          M  KRRN GRS+  RGH   V CTNC R V KDKA+K++ +R++V+ ++ RDI +   ++
Sbjct: 1  MPVKRRNAGRSQKNRGHTRTVPCTNCGRQVAKDKAVKRYTVRDMVDPSSKRDIQQKLAFE 60

Query: 61 SYQ--LPKLYAKLHYCVSCAIHSKVVRNRSKSD 91
          + +  +PKLY KL YC+SCAIHS+VVR R   D
Sbjct: 61 NEKQGIPKLYVKLQYCISCAIHSRVVRVRCAED 93


>pdb|1KHT|A Chain A, Adenylate Kinase From Methanococcus Voltae
 pdb|1KHT|B Chain B, Adenylate Kinase From Methanococcus Voltae
 pdb|1KHT|C Chain C, Adenylate Kinase From Methanococcus Voltae
          Length = 192

 Score = 27.7 bits (60), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 14/51 (27%), Positives = 26/51 (50%)

Query: 38  KFVIRNIVEAAAVRDITEASYYQSYQLPKLYAKLHYCVSCAIHSKVVRNRS 88
           + ++R + +   VRD+  AS  + +Q     A + Y V      K+V+NR+
Sbjct: 127 EILMRRMSDETRVRDLDTASTIEQHQFMNRCAAMSYGVLTGATVKIVQNRN 177


>pdb|1W5S|A Chain A, Structure Of The Aeropyrum Pernix Orc2 Protein (Adp Form)
 pdb|1W5S|B Chain B, Structure Of The Aeropyrum Pernix Orc2 Protein (Adp Form)
 pdb|1W5T|A Chain A, Structure Of The Aeropyrum Pernix Orc2 Protein (Adpnp-Adp
           Complexes)
 pdb|1W5T|B Chain B, Structure Of The Aeropyrum Pernix Orc2 Protein (Adpnp-Adp
           Complexes)
 pdb|1W5T|C Chain C, Structure Of The Aeropyrum Pernix Orc2 Protein (Adpnp-Adp
           Complexes)
          Length = 412

 Score = 26.2 bits (56), Expect = 5.2,   Method: Composition-based stats.
 Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

Query: 36  IKKFVIRNIVEAAAVRDIT-EASYYQSYQLPKLYAKLHYCV 75
           + KF ++ + EAAA   +T + +Y  ++  P LY  L   V
Sbjct: 68  LAKFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIV 108


  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
   0.321    0.132    0.393 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,769,929
Number of Sequences: 62578
Number of extensions: 122704
Number of successful extensions: 251
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 240
Number of HSP's gapped (non-prelim): 9
length of query: 137
length of database: 14,973,337
effective HSP length: 89
effective length of query: 48
effective length of database: 9,403,895
effective search space: 451386960
effective search space used: 451386960
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: 46 (22.3 bits)