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= 017670
         (368 letters)

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

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



>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
           Pspc1NONO
          Length = 261

 Score = 33.9 bits (76), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 37/149 (24%), Positives = 60/149 (40%), Gaps = 14/149 (9%)

Query: 195 RIRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKE-NCSAKMIPRVAFASPYFGQSFVI 253
           RIR A  HG  + ++NL P     V  +L+  AF +     K +  V       G+ FV 
Sbjct: 89  RIRFAT-HGAALTVKNLSP----VVSNELLEQAFSQFGPVEKAVVVVDDRGRATGKGFVE 143

Query: 254 FKTREVAELVVTKLEEGCLLLSNGRPLLGSIGTPCFTGKQSKFVGHLAL-DKLKFQMQRE 312
           F  +  A   + +  +G  LL+       +   P       +F     L +KL  + Q+ 
Sbjct: 144 FAAKPPARKALERCGDGAFLLT-------TTPRPVIVEPMEQFDDEDGLPEKLMQKTQQY 196

Query: 313 MREAVSTSHCSQPNSLEYDMAIEWSLLQE 341
            +E       +QP + E++ A  W  L E
Sbjct: 197 HKEREQPPRFAQPGTFEFEYASRWKALDE 225


>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
           Pspc1NONO
          Length = 261

 Score = 29.3 bits (64), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 37/148 (25%), Positives = 58/148 (39%), Gaps = 12/148 (8%)

Query: 195 RIRVAHEHGTLVVLENLDPSYTSTVVEDLVWHAFKENCSAKMIPRVAFASPYFGQSFVIF 254
           R+R A    +L V  NL P Y S  + +  +  F +   A +I  V       G+  V F
Sbjct: 89  RVRFACHSASLTV-RNL-PQYVSNELLEEAFSVFGQVERAVVI--VDDRGRPSGKGIVEF 144

Query: 255 KTREVAELVVTKLEEGCLLLSNGRPLLGSIGTPCFTGKQSKFVGHLAL-DKLKFQMQREM 313
             +  A   + +  EG  LL+       +   P       +      L +KL  + Q+  
Sbjct: 145 SGKPAARKALDRCSEGSFLLT-------TFPRPVTVEPMDQLDDEEGLPEKLVIKNQQFH 197

Query: 314 REAVSTSHCSQPNSLEYDMAIEWSLLQE 341
           +E       +QP S EY+ A+ W  L E
Sbjct: 198 KEREQPPRFAQPGSFEYEYAMRWKALIE 225


>pdb|2W9M|A Chain A, Structure Of Family X Dna Polymerase From Deinococcus
           Radiodurans
 pdb|2W9M|B Chain B, Structure Of Family X Dna Polymerase From Deinococcus
           Radiodurans
          Length = 578

 Score = 28.5 bits (62), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 23/43 (53%)

Query: 183 RSKWFKELPWEERIRVAHEHGTLVVLENLDPSYTSTVVEDLVW 225
           RS W   +   ER+R A E G L  L+       +T++E++V+
Sbjct: 111 RSLWLAGIDSLERLREAAESGELAGLKGFGAKSAATILENVVF 153


>pdb|3V4R|A Chain A, Crystal Structure Of A Uvrb Dimer-Dna Complex
 pdb|3V4R|B Chain B, Crystal Structure Of A Uvrb Dimer-Dna Complex
          Length = 667

 Score = 28.5 bits (62), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 7/86 (8%)

Query: 175 VTRRPSLDRSKWFKELPWEERIRVAHEHGTLVVLENLD--PSYTSTVVEDLVWHAFKENC 232
           VTR   ++++    E   EE+++V HE+G L+  + L+    Y   ++ ++ + +  EN 
Sbjct: 256 VTRAEKMEKAIQNIEKELEEQLKVMHENGKLLEAQRLEQRTRYDLEMMREMGFCSGIENY 315

Query: 233 SAKMIPRVAFASP-----YFGQSFVI 253
           S  +  R   ++P     YF   F+I
Sbjct: 316 SRHLTLRPPGSTPYTLLDYFPDDFMI 341


>pdb|2D7D|A Chain A, Structural Insights Into The Cryptic Dna Dependent Atp-Ase
           Activity Of Uvrb
 pdb|2NMV|A Chain A, Damage Detection By The Uvrabc Pathway: Crystal Structure
           Of Uvrb Bound To Fluorescein-Adducted Dna
          Length = 661

 Score = 28.5 bits (62), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 7/86 (8%)

Query: 175 VTRRPSLDRSKWFKELPWEERIRVAHEHGTLVVLENLD--PSYTSTVVEDLVWHAFKENC 232
           VTR   ++++    E   EE+++V HE+G L+  + L+    Y   ++ ++ + +  EN 
Sbjct: 250 VTRAEKMEKAIQNIEKELEEQLKVMHENGKLLEAQRLEQRTRYDLEMMREMGFCSGIENY 309

Query: 233 SAKMIPRVAFASP-----YFGQSFVI 253
           S  +  R   ++P     YF   F+I
Sbjct: 310 SRHLTLRPPGSTPYTLLDYFPDDFMI 335


  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
   0.315    0.132    0.385 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,187,046
Number of Sequences: 62578
Number of extensions: 329469
Number of successful extensions: 707
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 703
Number of HSP's gapped (non-prelim): 8
length of query: 368
length of database: 14,973,337
effective HSP length: 100
effective length of query: 268
effective length of database: 8,715,537
effective search space: 2335763916
effective search space used: 2335763916
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)