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= psy13345
         (276 letters)

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

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



>pdb|2I7T|A Chain A, Structure Of Human Cpsf-73
 pdb|2I7V|A Chain A, Structure Of Human Cpsf-73
          Length = 459

 Score = 58.2 bits (139), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 44/83 (53%), Gaps = 3/83 (3%)

Query: 37  MSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDLFFQWC 96
           M+DK+ K      NNPF FKH+    S+     +  P VV+ S   M+ G SR+LF  WC
Sbjct: 289 MNDKIRKQIN--INNPFVFKHISNLKSMDHFDDI-GPSVVMASPGMMQSGLSRELFESWC 345

Query: 97  SSPENSIIITNRTSPGTLARDLI 119
           +   N +II      GTLA+ ++
Sbjct: 346 TDKRNGVIIAGYCVEGTLAKHIM 368



 Score = 34.7 bits (78), Expect = 0.052,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 19/33 (57%)

Query: 208 VVLVSTPDMECGFSRDLFFQWCSSPENSIIITN 240
           VV+ S   M+ G SR+LF  WC+   N +II  
Sbjct: 324 VVMASPGMMQSGLSRELFESWCTDKRNGVIIAG 356


>pdb|3AF5|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
           From Pyrococcus Horikoshii
 pdb|3AF6|A Chain A, The Crystal Structure Of An Archaeal Cpsf Subunit, Ph1404
           From Pyrococcus Horikoshii Complexed With Rna-Analog
          Length = 651

 Score = 35.0 bits (79), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 3/87 (3%)

Query: 35  EWMSDKLMKSFEGARNNPFH---FKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDL 91
           E++S +L +       NPF    F  V       ++     P +++ S+  +  G S + 
Sbjct: 474 EYLSRRLREQIFKEGYNPFLSEIFHPVANSRERQDIIDSNEPAIIIASSGMLVGGPSVEY 533

Query: 92  FFQWCSSPENSIIITNRTSPGTLARDL 118
           F Q    P+NSII  +  + GTL R +
Sbjct: 534 FKQLAPDPKNSIIFVSYQAEGTLGRQV 560


>pdb|2XR1|A Chain A, Dimeric Archaeal Cleavage And Polyadenylation Specificity
           Factor With N-Terminal Kh Domains (Kh-Cpsf) From
           Methanosarcina Mazei
 pdb|2XR1|B Chain B, Dimeric Archaeal Cleavage And Polyadenylation Specificity
           Factor With N-Terminal Kh Domains (Kh-Cpsf) From
           Methanosarcina Mazei
          Length = 640

 Score = 34.7 bits (78), Expect = 0.067,   Method: Compositional matrix adjust.
 Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 3/87 (3%)

Query: 35  EWMSDKLMKSFEGARNNPFH---FKHVKLCHSLAELAKVPSPKVVLVSTPDMECGFSRDL 91
           E++++ L K       NPF    FK V    +  ++ + P P V+L ++  M  G   + 
Sbjct: 463 EYLNNDLRKLIFQKGQNPFLSECFKPVDSHEARQKIIQNPQPCVILATSGMMNGGPVMEY 522

Query: 92  FFQWCSSPENSIIITNRTSPGTLARDL 118
           F  +   P N+++     + GT+ R +
Sbjct: 523 FKAFAEDPRNTLVFVGYQADGTIGRRI 549


>pdb|2YCB|A Chain A, Structure Of The Archaeal Beta-Casp Protein With
           N-Terminal Kh Domains From Methanothermobacter
           Thermautotrophicus
 pdb|2YCB|B Chain B, Structure Of The Archaeal Beta-Casp Protein With
           N-Terminal Kh Domains From Methanothermobacter
           Thermautotrophicus
          Length = 636

 Score = 33.5 bits (75), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 4/88 (4%)

Query: 32  AKIEWMSDKLMKSFEGARNNPFHFKHVKLCHSLAELAKV--PSPKVVLVSTPDMECGFSR 89
           A+ E++S  L        +NPF        + + E  ++    P ++L ST  M  G + 
Sbjct: 457 ARPEYLSKDLRDQIFHMGHNPFISDIFHKVNGMDERREIVEGEPSIIL-STSGMLTGGNS 515

Query: 90  DLFFQW-CSSPENSIIITNRTSPGTLAR 116
             +F+W C  P+NS++     + G+L R
Sbjct: 516 LEYFKWLCEDPDNSLVFVGYQAEGSLGR 543


>pdb|2I7X|A Chain A, Structure Of Yeast Cpsf-100 (Ydh1p)
          Length = 717

 Score = 29.3 bits (64), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 3/48 (6%)

Query: 34  IEWMSDKLMKSFEGARNN--PFHFKHVKLCHSLAELAKVPSPKVVLVS 79
           +EW+S  L+K++E  RNN  PF         +  EL+K P  K+  VS
Sbjct: 297 LEWLSPSLLKTWEN-RNNTSPFEIGSRIKIIAPNELSKYPGSKICFVS 343


>pdb|3BRE|A Chain A, Crystal Structure Of P.Aeruginosa Pa3702
 pdb|3BRE|B Chain B, Crystal Structure Of P.Aeruginosa Pa3702
          Length = 358

 Score = 29.3 bits (64), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 1/42 (2%)

Query: 93  FQWCSSPENSIIITNRTSPGTLARDLIELGGNRTLTLQVKKR 134
           F +CS P+ ++ + N+  P  + +DL+ + G   LTL    R
Sbjct: 46  FHFCSDPQQAVAVANQIKPTVILQDLV-MPGVDGLTLLAAYR 86


  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
   0.323    0.137    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,507,609
Number of Sequences: 62578
Number of extensions: 271298
Number of successful extensions: 492
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 483
Number of HSP's gapped (non-prelim): 9
length of query: 276
length of database: 14,973,337
effective HSP length: 97
effective length of query: 179
effective length of database: 8,903,271
effective search space: 1593685509
effective search space used: 1593685509
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (24.3 bits)