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= 006647
         (637 letters)

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

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



>pdb|2YUD|A Chain A, Solution Structure Of The Yth Domain In Yth Domain-
           Containing Protein 1 (Putative Splicing Factor Yt521)
          Length = 180

 Score = 79.7 bits (195), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 48/145 (33%), Positives = 76/145 (52%), Gaps = 12/145 (8%)

Query: 382 DAKFFVIKSYSEDDVHKSIKYSVWASTPNGNKKLDAAYQEAQQKSRSCPVFLLFSVNTSG 441
           DA+FF+IKS + ++V  +    VW++ P   KKL+ A++ A+       V L+FSV  SG
Sbjct: 25  DARFFLIKSNNHENVSLAKAKGVWSTLPVNEKKLNLAFRSARS------VILIFSVRESG 78

Query: 442 QFVGLAEMAGPVDFNKNVEYW------QQDKWTGCFPVKWHIVKDVPNSLLKHITLENNE 495
           +F G A ++       +  +W            G F + W   +++P +   H+T   NE
Sbjct: 79  KFQGFARLSSESHHGGSPIHWVLPAGMSAKMLGGVFKIDWICRRELPFTKSAHLTNPWNE 138

Query: 496 NKPVTNSRDTQEIKLEQGLKLIKIF 520
           +KPV   RD QEI+LE G +L  +F
Sbjct: 139 HKPVKIGRDGQEIELECGTQLCLLF 163


>pdb|2YU6|A Chain A, Solution Structure Of The Yth Domain In Yth Domain-
           Containing Protein 2
          Length = 141

 Score = 71.2 bits (173), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 41/141 (29%), Positives = 78/141 (55%), Gaps = 7/141 (4%)

Query: 381 TDAKFFVIKSYSEDDVHKSIKYSVWASTPNGNKKLDAAYQEAQQKSRSCPVFLLFSVNTS 440
           +  ++F++KS +  ++  S +  +W++TP+  +KL+ A+ E      S  V+L+FSV  S
Sbjct: 6   SGVRYFIMKSSNLRNLEISQQKGIWSTTPSNERKLNRAFWE------SSIVYLVFSVQGS 59

Query: 441 GQFVGLAEMAGPVDFNKNVEYWQQDKWTGCFPVKWHIVKDVPNSLLKHITLENNENKPVT 500
           G F G + M+  +   K+ + W      G F V+W   + +P     H+    N+NK V 
Sbjct: 60  GHFQGFSRMSSEIGREKSQD-WGSAGLGGVFKVEWIRKESLPFQFAHHLLNPWNDNKKVQ 118

Query: 501 NSRDTQEIKLEQGLKLIKIFK 521
            SRD QE++ + G +L+++++
Sbjct: 119 ISRDGQELEPQVGEQLLQLWE 139


>pdb|3H4L|A Chain A, Crystal Structure Of N Terminal Domain Of A Dna Repair
           Prote
 pdb|3H4L|B Chain B, Crystal Structure Of N Terminal Domain Of A Dna Repair
           Prote
          Length = 367

 Score = 30.4 bits (67), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 25/91 (27%), Positives = 40/91 (43%), Gaps = 8/91 (8%)

Query: 366 PDRDEYNKADFPEEYTDAKFFVIKSYSEDDVHKSIKYSVWASTPNGNKKLDAAYQEAQQK 425
           P R +     F  ++T     VI+ Y+   ++ +IK+SVW  TP G K L  +       
Sbjct: 157 PVRQKEFSKTFKRQFTKC-LTVIQGYAI--INAAIKFSVWNITPKGKKNLILSTMRNSSM 213

Query: 426 SRSCPVFLLFSVNTSGQFVGLAEMAGPVDFN 456
            ++       SV  +G   GL E+   +D N
Sbjct: 214 RKNIS-----SVFGAGGMRGLEEVDLVLDLN 239


>pdb|4EE2|A Chain A, Crystal Structure Of Anthrax Protective Antigen K446m
           Mutant To 1.91-A Resolution
          Length = 736

 Score = 28.9 bits (63), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 43/82 (52%), Gaps = 5/82 (6%)

Query: 460 EYWQQDKWTGCFPVKWHIVKDVPNSLLKHITLENNENKPVTNSRDTQEIKLEQG-LKLIK 518
           +Y+Q   W+G   VK         S   H+T+  ++ + +  + ++ +I+LE+G L  IK
Sbjct: 59  QYFQSAIWSGFIKVKKSDEYTFATSADNHVTMWVDDQEVINKASNSNKIRLEKGRLYQIK 118

Query: 519 I--FKDHPSKTCILDDFGFYET 538
           I   +++P++  +  DF  Y T
Sbjct: 119 IQYQRENPTEKGL--DFKLYWT 138


  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
   0.313    0.133    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,838,214
Number of Sequences: 62578
Number of extensions: 755467
Number of successful extensions: 991
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 985
Number of HSP's gapped (non-prelim): 10
length of query: 637
length of database: 14,973,337
effective HSP length: 105
effective length of query: 532
effective length of database: 8,402,647
effective search space: 4470208204
effective search space used: 4470208204
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (25.8 bits)