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= 032904
         (130 letters)

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

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



>pdb|2QAI|A Chain A, Crystal Structure Of The V-Type Atp Synthase Subunit F
           From Pyrococcus Furiosus. Nesg Target Pfr7.
 pdb|2QAI|B Chain B, Crystal Structure Of The V-Type Atp Synthase Subunit F
           From Pyrococcus Furiosus. Nesg Target Pfr7
          Length = 111

 Score = 46.6 bits (109), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 30/87 (34%), Positives = 46/87 (52%), Gaps = 10/87 (11%)

Query: 15  IAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS 74
           I +  D DTVVGF LAGV          Y   +S  ++++  +  +E   R+D+ I+LI+
Sbjct: 3   IVVXGDSDTVVGFRLAGV-------HEAYEYDESLESVERARNKLRELLERDDVGIILIT 55

Query: 75  QYVANRIRFLVDSHNKPIPAILEIPSK 101
           + +A RI  L +      P IL+IP K
Sbjct: 56  ERLAQRIGSLPEVK---FPIILQIPDK 79


>pdb|2I4R|A Chain A, Crystal Structure Of The V-Type Atp Synthase Subunit F
           From Archaeoglobus Fulgidus. Nesg Target Gr52a.
 pdb|2I4R|B Chain B, Crystal Structure Of The V-Type Atp Synthase Subunit F
           From Archaeoglobus Fulgidus. Nesg Target Gr52a
          Length = 102

 Score = 33.5 bits (75), Expect = 0.037,   Method: Compositional matrix adjust.
 Identities = 24/92 (26%), Positives = 42/92 (45%), Gaps = 24/92 (26%)

Query: 15  IAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAFKEFTSREDIAIVLIS 74
           +A++ D D  +GF LAG+ ++       Y +   +  +K +ED  K    R+D+ +V+  
Sbjct: 12  LAVVGDPDFTIGFXLAGISDI-------YEVTSDEEIVKAVEDVLK----RDDVGVVIXK 60

Query: 75  QYVANRIRFLVDSHNKPIPAIL--EIPSKDHP 104
           Q            + K +P +L  EI  K  P
Sbjct: 61  Q-----------EYLKKLPPVLRREIDEKVEP 81


>pdb|3D8U|A Chain A, The Crystal Structure Of A Purr Family Transcriptional
           Regulator From Vibrio Parahaemolyticus Rimd 2210633
 pdb|3D8U|B Chain B, The Crystal Structure Of A Purr Family Transcriptional
           Regulator From Vibrio Parahaemolyticus Rimd 2210633
          Length = 275

 Score = 27.3 bits (59), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 18/64 (28%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 40  KTNY--LIVDSKTTIKQIEDAFKEFTSREDIAIVLISQYVANRIRFLVDSHNKPIPAILE 97
           K  Y  L+  S  +I+Q E     F       +VL     + R   L+++ N P+  I E
Sbjct: 31  KAGYQLLLGYSDYSIEQEEKLLSTFLESRPAGVVLFGSEHSQRTHQLLEASNTPVLEIAE 90

Query: 98  IPSK 101
           + SK
Sbjct: 91  LSSK 94


>pdb|3DYJ|A Chain A, Crystal Structure A Talin Rod Fragment
 pdb|3DYJ|B Chain B, Crystal Structure A Talin Rod Fragment
          Length = 332

 Score = 26.9 bits (58), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 14/26 (53%), Positives = 17/26 (65%)

Query: 9  TAASALIAMIADEDTVVGFLLAGVGN 34
          TAASA+  +IAD DT + F  AG  N
Sbjct: 19 TAASAVSGIIADLDTTIXFATAGTLN 44


>pdb|3CMM|A Chain A, Crystal Structure Of The Uba1-Ubiquitin Complex
 pdb|3CMM|C Chain C, Crystal Structure Of The Uba1-Ubiquitin Complex
          Length = 1015

 Score = 25.4 bits (54), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 9/58 (15%)

Query: 2   ANRPQIRTAASALIAMIADEDTVVGFLLAGVGNVDLRRKTNYLIVDSKTTIKQIEDAF 59
           A+R + +  A  +I  IA   ++V     G+ N++L     Y ++D+KT I+Q ++ F
Sbjct: 841 ADRQKTKFIAGRIIPAIATTTSLV----TGLVNLEL-----YKLIDNKTDIEQYKNGF 889


  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    0.360 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,120,129
Number of Sequences: 62578
Number of extensions: 103982
Number of successful extensions: 282
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 276
Number of HSP's gapped (non-prelim): 8
length of query: 130
length of database: 14,973,337
effective HSP length: 88
effective length of query: 42
effective length of database: 9,466,473
effective search space: 397591866
effective search space used: 397591866
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: 45 (21.9 bits)