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= 025721
         (249 letters)

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

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



>pdb|2D3O|1 Chain 1, Structure Of Ribosome Binding Domain Of The Trigger Factor
           On The 50s Ribosomal Subunit From D. Radiodurans
          Length = 112

 Score = 36.2 bits (82), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 17/98 (17%)

Query: 102 SQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILG 161
           S++ +K++ +V +      R +D+V   LAR    +PGFR        K PR  +     
Sbjct: 6   SKEGNKVEFKVSVPAAEVNRAYDQVWAGLARDV-RVPGFR------PGKAPRKVI----- 53

Query: 162 EERVTKFVVQEIVRSTL--TDYT---KKEGLNVKDKKV 194
           E RV K  V+  VR  L  T Y+   ++ GLN+ D  V
Sbjct: 54  ENRVGKGYVESQVRDRLLETHYSQGLRELGLNLVDATV 91


>pdb|2AAR|7 Chain 7, Structure Of Trigger Factor Binding Domain In Biologically
           Homologous Complex With Eubacterial Ribosome
          Length = 113

 Score = 36.2 bits (82), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 17/98 (17%)

Query: 102 SQDEDKIQVRVDLTGDATQRVFDKVLTNLARSAPPIPGFRREKGGKTTKVPRDFLIQILG 161
           S++ +K++ +V +      R +D+V   LAR    +PGFR        K PR  +     
Sbjct: 5   SKEGNKVEFKVSVPAAEVNRAYDQVWAGLARDV-RVPGFR------PGKAPRKVI----- 52

Query: 162 EERVTKFVVQEIVRSTL--TDYT---KKEGLNVKDKKV 194
           E RV K  V+  VR  L  T Y+   ++ GLN+ D  V
Sbjct: 53  ENRVGKGYVESQVRDRLLETHYSQGLRELGLNLVDATV 90


>pdb|2VE3|A Chain A, Retinoic Acid Bound Cyanobacterial Cyp120a1
 pdb|2VE3|B Chain B, Retinoic Acid Bound Cyanobacterial Cyp120a1
 pdb|2VE4|A Chain A, Substrate Free Cyanobacterial Cyp120a1
 pdb|2VE4|B Chain B, Substrate Free Cyanobacterial Cyp120a1
          Length = 444

 Score = 28.9 bits (63), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 27/43 (62%), Gaps = 2/43 (4%)

Query: 103 QDEDKIQVRVDLTGDATQRV--FDKVLTNLARSAPPIPGFRRE 143
           Q+++K+Q+  +LT +  +++   D+VL  + R  PP+ G  RE
Sbjct: 282 QEQNKLQLSQELTAETLKKMPYLDQVLQEVLRLIPPVGGGFRE 324


>pdb|2IX1|A Chain A, Rnase Ii D209n Mutant
          Length = 664

 Score = 28.1 bits (61), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 5/54 (9%)

Query: 38 KSVNFFHFQNSSCFFVRPSLYCNPLMRRVQHVLKTVSAVDSGVEVSITEPEDLI 91
          K   F        +F+ P     P M++V H  + ++ + S  E    EPE+L+
Sbjct: 51 KGFGFLEVDAQKSYFIPP-----PQMKKVMHGDRIIAVIHSEKERESAEPEELV 99


>pdb|2IX0|A Chain A, Rnase Ii
          Length = 663

 Score = 28.1 bits (61), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 5/54 (9%)

Query: 38 KSVNFFHFQNSSCFFVRPSLYCNPLMRRVQHVLKTVSAVDSGVEVSITEPEDLI 91
          K   F        +F+ P     P M++V H  + ++ + S  E    EPE+L+
Sbjct: 50 KGFGFLEVDAQKSYFIPP-----PQMKKVMHGDRIIAVIHSEKERESAEPEELV 98


>pdb|1R8S|E Chain E, Arf1[delta1-17]-Gdp In Complex With A Sec7 Domain Carrying
           The Mutation Of The Catalytic Glutamate To Lysine
          Length = 203

 Score = 27.7 bits (60), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 11  IPSKFQNIELFSPRSCRNYTLCHPNAPKSVNFFHFQNSSCFFVRPSLYCNPLMRRVQHVL 70
           +P K Q I+       + Y LC+P   +S +  +  + S   +   L+ NP +R  +  L
Sbjct: 104 LPGKAQKIDRMMEAFAQRYCLCNPGVFQSTDTCYVLSYSVIMLNTDLH-NPNVRD-KMGL 161

Query: 71  KTVSAVDSGVEVSITEPEDLI 91
           +   A++ G+      PE+L+
Sbjct: 162 ERFVAMNRGINEGGDLPEELL 182


>pdb|2HQM|A Chain A, Crystal Structure Of Glutathione Reductase Glr1 From The
           Yeast Saccharomyces Cerevisiae
 pdb|2HQM|B Chain B, Crystal Structure Of Glutathione Reductase Glr1 From The
           Yeast Saccharomyces Cerevisiae
          Length = 479

 Score = 27.3 bits (59), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 19/48 (39%), Positives = 28/48 (58%), Gaps = 3/48 (6%)

Query: 159 ILGEERVTKFVVQEIVRSTLTDYTKKEGLNV-KDKKVTTTQKAEELRK 205
           I GE  + KF   E +++T+TD+  KEG+NV K  K+   +K  E  K
Sbjct: 215 IRGETVLRKF--DECIQNTITDHYVKEGINVHKLSKIVKVEKNVETDK 260


  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
   0.319    0.134    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,008,124
Number of Sequences: 62578
Number of extensions: 221803
Number of successful extensions: 615
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 611
Number of HSP's gapped (non-prelim): 21
length of query: 249
length of database: 14,973,337
effective HSP length: 96
effective length of query: 153
effective length of database: 8,965,849
effective search space: 1371774897
effective search space used: 1371774897
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)