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= 005158
         (711 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 = 79.3 bits (194), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 48/145 (33%), Positives = 76/145 (52%), Gaps = 12/145 (8%)

Query: 456 DAKFFVIKSYSEDDVHKSIKYSVWASTPNGNKKLDAAYQEAQQKSRSCPVFLLFSVNTSG 515
           DA+FF+IKS + ++V  +    VW++ P   KKL+ A++ A+       V L+FSV  SG
Sbjct: 25  DARFFLIKSNNHENVSLAKAKGVWSTLPVNEKKLNLAFRSARS------VILIFSVRESG 78

Query: 516 QFVGLAEMAGPVDFNKNVEYW------QQDKWTGCFPVKWHIVKDVPNSLLKHITLENNE 569
           +F G A ++       +  +W            G F + W   +++P +   H+T   NE
Sbjct: 79  KFQGFARLSSESHHGGSPIHWVLPAGMSAKMLGGVFKIDWICRRELPFTKSAHLTNPWNE 138

Query: 570 NKPVTNSRDTQEIKLEQGLKLIKIF 594
           +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 = 69.7 bits (169), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 41/138 (29%), Positives = 77/138 (55%), Gaps = 7/138 (5%)

Query: 458 KFFVIKSYSEDDVHKSIKYSVWASTPNGNKKLDAAYQEAQQKSRSCPVFLLFSVNTSGQF 517
           ++F++KS +  ++  S +  +W++TP+  +KL+ A+ E      S  V+L+FSV  SG F
Sbjct: 9   RYFIMKSSNLRNLEISQQKGIWSTTPSNERKLNRAFWE------SSIVYLVFSVQGSGHF 62

Query: 518 VGLAEMAGPVDFNKNVEYWQQDKWTGCFPVKWHIVKDVPNSLLKHITLENNENKPVTNSR 577
            G + M+  +   K+ + W      G F V+W   + +P     H+    N+NK V  SR
Sbjct: 63  QGFSRMSSEIGREKSQD-WGSAGLGGVFKVEWIRKESLPFQFAHHLLNPWNDNKKVQISR 121

Query: 578 DTQEIKLEQGLKLIKIFK 595
           D QE++ + G +L+++++
Sbjct: 122 DGQELEPQVGEQLLQLWE 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 = 31.2 bits (69), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 25/91 (27%), Positives = 40/91 (43%), Gaps = 8/91 (8%)

Query: 440 PDRDEYNKADFPEEYTDAKFFVIKSYSEDDVHKSIKYSVWASTPNGNKKLDAAYQEAQQK 499
           P R +     F  ++T     VI+ Y+   ++ +IK+SVW  TP G K L  +       
Sbjct: 157 PVRQKEFSKTFKRQFTKC-LTVIQGYAI--INAAIKFSVWNITPKGKKNLILSTMRNSSM 213

Query: 500 SRSCPVFLLFSVNTSGQFVGLAEMAGPVDFN 530
            ++       SV  +G   GL E+   +D N
Sbjct: 214 RKNIS-----SVFGAGGMRGLEEVDLVLDLN 239


  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
   0.312    0.131    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 20,912,210
Number of Sequences: 62578
Number of extensions: 876679
Number of successful extensions: 1132
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: 1126
Number of HSP's gapped (non-prelim): 10
length of query: 711
length of database: 14,973,337
effective HSP length: 106
effective length of query: 605
effective length of database: 8,340,069
effective search space: 5045741745
effective search space used: 5045741745
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (25.8 bits)