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= 009415
         (535 letters)

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

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



>pdb|3DZD|A Chain A, Crystal Structure Of Sigma54 Activator Ntrc4 In The
           Inactive State
 pdb|3DZD|B Chain B, Crystal Structure Of Sigma54 Activator Ntrc4 In The
           Inactive State
          Length = 368

 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/90 (33%), Positives = 46/90 (51%), Gaps = 7/90 (7%)

Query: 60  FPGRRVQILELLRLLGTLNSSMPPLFVYGSASTGKTSIIIQVFRHLSR--PFVYTSCLSC 117
           F G   +ILE+ RL+  +  S  P+ + G + TGK  +   + R+  R   FV  +C S 
Sbjct: 131 FVGEHPKILEIKRLIPKIAKSKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASI 190

Query: 118 YSPRILFESILNQLLLHKKNAFNGYSSAKR 147
             P+ L ES   +L  H+K AF G  + K+
Sbjct: 191 --PQELAES---ELFGHEKGAFTGALTRKK 215


>pdb|2QBY|A Chain A, Crystal Structure Of A Heterodimer Of Cdc6ORC1 INITIATORS
           Bound To Origin Dna (From S. Solfataricus)
          Length = 386

 Score = 33.9 bits (76), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 27/95 (28%), Positives = 42/95 (44%), Gaps = 10/95 (10%)

Query: 60  FPGRRVQILELLRLLGTLNSSMPP--LFVYGSASTGKTSIIIQVFRHLSRPF------VY 111
            P R  QI ++  +L  L     P  +F+YG   TGKT+++  V   L + F      VY
Sbjct: 22  LPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVY 81

Query: 112 TSCLSCYSPRILFESILNQLLLHKKNAFNGYSSAK 146
            +     +P  +   +L  L +  K  F G S A+
Sbjct: 82  INTRQIDTPYRVLADLLESLDV--KVPFTGLSIAE 114


>pdb|1L8Q|A Chain A, Crystal Structure Of Dna Replication Initiation Factor
          Length = 324

 Score = 30.0 bits (66), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 12/25 (48%), Positives = 16/25 (64%)

Query: 74 LGTLNSSMPPLFVYGSASTGKTSII 98
          L  L S   P+F+YGS  TGKT ++
Sbjct: 30 LENLGSLYNPIFIYGSVGTGKTHLL 54


>pdb|3R8F|A Chain A, Protein-Dna Complex
 pdb|3R8F|B Chain B, Protein-Dna Complex
 pdb|3R8F|C Chain C, Protein-Dna Complex
 pdb|3R8F|D Chain D, Protein-Dna Complex
          Length = 324

 Score = 30.0 bits (66), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 12/25 (48%), Positives = 16/25 (64%)

Query: 74 LGTLNSSMPPLFVYGSASTGKTSII 98
          L  L S   P+F+YGS  TGKT ++
Sbjct: 30 LENLGSLYNPIFIYGSVGTGKTHLL 54


>pdb|2HCB|A Chain A, Structure Of Amppcp-Bound Dnaa From Aquifex Aeolicus
 pdb|2HCB|B Chain B, Structure Of Amppcp-Bound Dnaa From Aquifex Aeolicus
 pdb|2HCB|C Chain C, Structure Of Amppcp-Bound Dnaa From Aquifex Aeolicus
 pdb|2HCB|D Chain D, Structure Of Amppcp-Bound Dnaa From Aquifex Aeolicus
          Length = 323

 Score = 30.0 bits (66), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 12/25 (48%), Positives = 16/25 (64%)

Query: 74 LGTLNSSMPPLFVYGSASTGKTSII 98
          L  L S   P+F+YGS  TGKT ++
Sbjct: 29 LENLGSLYNPIFIYGSVGTGKTHLL 53


>pdb|1U89|A Chain A, Solution Structure Of Vbs2 Fragment Of Talin
          Length = 139

 Score = 30.0 bits (66), Expect = 3.1,   Method: Composition-based stats.
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 3/83 (3%)

Query: 128 LNQLLLHKKNAFNGYSSAKRCEKPSDFVIFVREALINVIDSLKENAEKTSTSKLKGQVNG 187
           LN+LL H K    G   A R ++ +D ++ V E   N+  S+ +  E    +++  Q   
Sbjct: 28  LNELLQHVKAHATGAGPAGRYDQATDTILTVTE---NIFSSMGDAGEMVRQARILAQATS 84

Query: 188 KMIYLIFDNFELVREWDKSSSIL 210
            ++  I  + E   + + S  +L
Sbjct: 85  DLVNAIKADAEGESDLENSRKLL 107


>pdb|1S0U|A Chain A, Eif2gamma Apo
          Length = 408

 Score = 30.0 bits (66), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 15/46 (32%), Positives = 24/46 (52%)

Query: 450 AIFQCITSVGEEEEGNDGLRVDEGSNALMSDILLQLTSLCNSNFIV 495
           AI Q +  VG+E E   G++V EG+      +  ++ SL   N I+
Sbjct: 235 AIIQGVFKVGDEIEIRPGIKVTEGNKTFWKPLTTKIVSLAAGNTIL 280


  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    0.137    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,801,858
Number of Sequences: 62578
Number of extensions: 522359
Number of successful extensions: 1155
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1150
Number of HSP's gapped (non-prelim): 7
length of query: 535
length of database: 14,973,337
effective HSP length: 103
effective length of query: 432
effective length of database: 8,527,803
effective search space: 3684010896
effective search space used: 3684010896
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: 54 (25.4 bits)