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= 025423
         (253 letters)

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

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



>pdb|2KJK|A Chain A, Solution Structure Of The Second Domain Of The Listeria
           Protein Lin2157, Northeast Structural Genomics
           Consortium Target Lkr136b
          Length = 100

 Score = 30.0 bits (66), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 73  SWSEFIDYVVASIKSEDVKLILEGHSNADGAAYAKIVAQKSKGMPRISISLT 124
           S  EFIDY+ +    + VK+  + H N +  A  K+ A   KG P I I+L 
Sbjct: 40  SSQEFIDYIHSKKVGDTVKIKYK-HGNKNEEASIKLTAIDKKGTPGIGITLV 90


>pdb|4A18|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 1
 pdb|4A1B|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 3.
 pdb|4A1D|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 4.
 pdb|4A19|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
           Initiation Factor 6. This File Contains 26s Rrna And
           Proteins Of Molecule 2
          Length = 104

 Score = 29.6 bits (65), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 14/30 (46%), Positives = 21/30 (70%)

Query: 217 AAQSPVASKVANRVIPAHRRAKVRGALLQD 246
           A  S  A+K+A + +  HRRAKV+ ALL++
Sbjct: 67  AKDSKKATKIARKRLGTHRRAKVKKALLEE 96


>pdb|1IN4|A Chain A, Thermotoga Maritima Ruvb Holliday Junction Branch
           Migration Motor
          Length = 334

 Score = 28.9 bits (63), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/22 (50%), Positives = 19/22 (86%)

Query: 104 AYAKIVAQKSKGMPRISISLTR 125
           A A+++A++S+G PRI+I LT+
Sbjct: 203 AAAEMIAKRSRGTPRIAIRLTK 224


>pdb|1IN5|A Chain A, Thermogota Maritima Ruvb A156s Mutant
          Length = 334

 Score = 28.9 bits (63), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/22 (50%), Positives = 19/22 (86%)

Query: 104 AYAKIVAQKSKGMPRISISLTR 125
           A A+++A++S+G PRI+I LT+
Sbjct: 203 AAAEMIAKRSRGTPRIAIRLTK 224


>pdb|1IN6|A Chain A, Thermotoga Maritima Ruvb K64r Mutant
          Length = 334

 Score = 28.9 bits (63), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/22 (50%), Positives = 19/22 (86%)

Query: 104 AYAKIVAQKSKGMPRISISLTR 125
           A A+++A++S+G PRI+I LT+
Sbjct: 203 AAAEMIAKRSRGTPRIAIRLTK 224


>pdb|1IN7|A Chain A, Thermotoga Maritima Ruvb R170a
          Length = 334

 Score = 28.9 bits (63), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/22 (50%), Positives = 19/22 (86%)

Query: 104 AYAKIVAQKSKGMPRISISLTR 125
           A A+++A++S+G PRI+I LT+
Sbjct: 203 AAAEMIAKRSRGTPRIAIRLTK 224


>pdb|1IN8|A Chain A, Thermotoga Maritima Ruvb T158v
          Length = 334

 Score = 28.9 bits (63), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 11/22 (50%), Positives = 19/22 (86%)

Query: 104 AYAKIVAQKSKGMPRISISLTR 125
           A A+++A++S+G PRI+I LT+
Sbjct: 203 AAAEMIAKRSRGTPRIAIRLTK 224


>pdb|3I1E|A Chain A, Crystal Structure Of The Pdz Domain Of The Sdrc-Like
           Protein (Lin2157) From Listeria Innocua, Northeast
           Structural Genomics Consortium Target Lkr136c
 pdb|3I1E|B Chain B, Crystal Structure Of The Pdz Domain Of The Sdrc-Like
           Protein (Lin2157) From Listeria Innocua, Northeast
           Structural Genomics Consortium Target Lkr136c
          Length = 90

 Score = 27.7 bits (60), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 73  SWSEFIDYVVASIKSEDVKLILEGHSNADGAAYAKIVAQKSKGMPRISI 121
           S  EFIDY+ +    + VK+  + H N +  A  K+ A   KG P I I
Sbjct: 35  SSQEFIDYIHSKKVGDTVKIKYK-HGNKNEEASIKLTAIDKKGTPGIGI 82


  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
   0.314    0.128    0.355 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,416,612
Number of Sequences: 62578
Number of extensions: 217272
Number of successful extensions: 701
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 692
Number of HSP's gapped (non-prelim): 11
length of query: 253
length of database: 14,973,337
effective HSP length: 97
effective length of query: 156
effective length of database: 8,903,271
effective search space: 1388910276
effective search space used: 1388910276
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)