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= 025691
         (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 = 35.0 bits (79), Expect = 0.043,   Method: Compositional matrix adjust.
 Identities = 30/98 (30%), Positives = 46/98 (46%), 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---KKASLNVKDKKV 194
           E RV K  V+  VR  L  T Y+   ++  LN+ 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 = 34.7 bits (78), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 30/98 (30%), Positives = 46/98 (46%), 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---KKASLNVKDKKV 194
           E RV K  V+  VR  L  T Y+   ++  LN+ 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 = 29.3 bits (64), Expect = 2.4,   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|2IX0|A Chain A, Rnase Ii
          Length = 663

 Score = 28.1 bits (61), Expect = 4.5,   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|2IX1|A Chain A, Rnase Ii D209n Mutant
          Length = 664

 Score = 28.1 bits (61), Expect = 4.7,   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|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|1TZ7|A Chain A, Aquifex Aeolicus Amylomaltase
 pdb|1TZ7|B Chain B, Aquifex Aeolicus Amylomaltase
          Length = 505

 Score = 26.9 bits (58), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 9/80 (11%)

Query: 135 PPIPGFRREKGGKTTKVPRDFLIQILGEERVTKFVVQEIVRSTLTDYTKKASLNVKDKKV 194
           PPI G+    G ++ K   ++L + + EE+V     +E++R  L    K A + ++D   
Sbjct: 407 PPIRGWFENLGEESRKRLFEYLGREIKEEKVN----EELIRLVLISRAKFAIIQMQD--- 459

Query: 195 TTTQKAEELRKSFYPGNEFG 214
                  E R + YPG  FG
Sbjct: 460 -LLNLGNEARMN-YPGRPFG 477


  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    0.133    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,912,718
Number of Sequences: 62578
Number of extensions: 213562
Number of successful extensions: 581
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 581
Number of HSP's gapped (non-prelim): 9
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)