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= 022691
         (293 letters)

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

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



>pdb|3NW0|A Chain A, Crystal Structure Of Mageg1 And Nse1 Complex
          Length = 238

 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/248 (23%), Positives = 98/248 (39%), Gaps = 47/248 (18%)

Query: 8   HHALVQALMTRGPLKEKDFHAIFSG-LTGKSPGAHQGLFNEYLLNINKELSSCQFELRAC 66
           H   +Q LMT G L+E D   + +         A      +++ NIN  L S   E++  
Sbjct: 7   HRRFLQLLMTHGVLEEWDVKRLQTHCYKVHDRNATVDKLEDFINNINSVLESLYIEIKRG 66

Query: 67  RDQYVGQVCYGVVNNVADEQSKLGTKYTVQQIAFFKGILEAIAQDVMAQGSISNIEALNI 126
             +  G+  Y +VN      SK+ T +   ++  F+  LE I        S +NI     
Sbjct: 67  VTEDDGRPIYALVNLATTSISKMATDFAENELDLFRKALELIIDSETGFASSTNI----- 121

Query: 127 RLENLVLSTQGSQLLNGPLPAAFRNFTMSQKEKTLDEFVQDQWLCCTPDGKIGLGVRSCL 186
              NLV   +G ++               + E+ L +FVQ++WL    +G+  L  R+ L
Sbjct: 122 --LNLVDQLKGKKMRK------------KEAEQVLQKFVQNKWL-IEKEGEFTLHGRAIL 166

Query: 187 DLRGWFRNL---DVPFCEVCNEAVVKG-----------------------EILCPRCGLR 220
           ++  + R      V  C +C+  +++G                       E  CP C   
Sbjct: 167 EMEQYIRETYPDAVKICNICHSLLIQGQSCETCGIRMHLPCVAKYFQSNAEPRCPHCNDY 226

Query: 221 WPNQVPKA 228
           WP+++PK 
Sbjct: 227 WPHEIPKV 234


>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome
           Complex Bound To Rna
          Length = 1003

 Score = 29.6 bits (65), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 41/143 (28%), Positives = 60/143 (41%), Gaps = 43/143 (30%)

Query: 51  NINKELSSCQFELRACRDQYVGQVCYGVVNNVADEQSKLGTKYTVQQIAFFKGILEAIAQ 110
           NIN++  + QF  RA  + YVGQV   + NN + E     T Y ++   F  GI+  + +
Sbjct: 885 NINRKHRNAQFAGRASIEYYVGQV---MRNNESTE-----TGYVIK--VFNNGIVVLVPK 934

Query: 111 DVMAQGSISNIEALNIRLENLVLSTQGSQLLNGPLPAAFR------NFTMSQKEKTLDEF 164
                     +E L IRL+NL            P  AAF        F  +  +K  D +
Sbjct: 935 --------FGVEGL-IRLDNLT---------EDPNSAAFDEVEYKLTFVPTNSDKPRDVY 976

Query: 165 VQDQWLCCTPDGKIGLGVRSCLD 187
           V D         K+ + VRS +D
Sbjct: 977 VFD---------KVEVQVRSVMD 990


>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease
          Length = 977

 Score = 29.6 bits (65), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 41/143 (28%), Positives = 60/143 (41%), Gaps = 43/143 (30%)

Query: 51  NINKELSSCQFELRACRDQYVGQVCYGVVNNVADEQSKLGTKYTVQQIAFFKGILEAIAQ 110
           NIN++  + QF  RA  + YVGQV   + NN + E     T Y ++   F  GI+  + +
Sbjct: 859 NINRKHRNAQFAGRASIEYYVGQV---MRNNESTE-----TGYVIK--VFNNGIVVLVPK 908

Query: 111 DVMAQGSISNIEALNIRLENLVLSTQGSQLLNGPLPAAFR------NFTMSQKEKTLDEF 164
                     +E L IRL+NL            P  AAF        F  +  +K  D +
Sbjct: 909 --------FGVEGL-IRLDNLT---------EDPNSAAFDEVEYKLTFVPTNSDKPRDVY 950

Query: 165 VQDQWLCCTPDGKIGLGVRSCLD 187
           V D         K+ + VRS +D
Sbjct: 951 VFD---------KVEVQVRSVMD 964


  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
   0.318    0.133    0.405 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,549,312
Number of Sequences: 62578
Number of extensions: 339109
Number of successful extensions: 648
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 645
Number of HSP's gapped (non-prelim): 4
length of query: 293
length of database: 14,973,337
effective HSP length: 98
effective length of query: 195
effective length of database: 8,840,693
effective search space: 1723935135
effective search space used: 1723935135
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)