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= 000444
         (1498 letters)

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

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



>pdb|4GMJ|A Chain A, Structure Of Human Not1 Mif4g Domain Co-Crystallized With
           Caf1
 pdb|4GMJ|C Chain C, Structure Of Human Not1 Mif4g Domain Co-Crystallized With
           Caf1
 pdb|4GMJ|E Chain E, Structure Of Human Not1 Mif4g Domain Co-Crystallized With
           Caf1
          Length = 229

 Score =  224 bits (570), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 104/214 (48%), Positives = 154/214 (71%), Gaps = 2/214 (0%)

Query: 47  VQDKISFIINNISALNVEAKAKEFTEILKEQYYPWFAQYMVMKRASIEPNFHDLYLKFLD 106
           +Q+KI+FI NN+S  N+  K +E  E +KE++ PW +QY+VMKR SIEPNFH LY  FLD
Sbjct: 7   IQEKIAFIFNNLSQSNMTQKVEELKETVKEEFMPWVSQYLVMKRVSIEPNFHSLYSNFLD 66

Query: 107 KVNSKALNREIVQATYENCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQVLRARE 166
            + +   N+ ++  TY N KVLL S+   ++  +RSLLKNLG WLG +T+ +N+ +   +
Sbjct: 67  TLKNPEFNKMVLNETYRNIKVLLTSDKAAANFSDRSLLKNLGHWLGMITLAKNKPILHTD 126

Query: 167 IDPKSLIIEAYEKGL--MIAVIPFTSKILEPCQSSLAYQPPNPWTMAILGLLAEIYSMPN 224
           +D KSL++EAY KG   ++ V+PF +K+LE    S+ ++PPNPWTMAI+ +LAE++   +
Sbjct: 127 LDVKSLLLEAYVKGQQELLYVVPFVAKVLESSIRSVVFRPPNPWTMAIMNVLAELHQEHD 186

Query: 225 LKMNLKFDIEVLFKNLGVDMKDITPTSLLKDRKR 258
           LK+NLKF+IEVL KNL +D+ ++ P +LLKD+ R
Sbjct: 187 LKLNLKFEIEVLCKNLALDINELKPGNLLKDKDR 220


>pdb|4GML|A Chain A, Crystal Structure Of Human Not1 Mif4g Domain
 pdb|4GML|B Chain B, Crystal Structure Of Human Not1 Mif4g Domain
 pdb|4GML|C Chain C, Crystal Structure Of Human Not1 Mif4g Domain
 pdb|4GML|D Chain D, Crystal Structure Of Human Not1 Mif4g Domain
 pdb|4GML|E Chain E, Crystal Structure Of Human Not1 Mif4g Domain
 pdb|4GML|F Chain F, Crystal Structure Of Human Not1 Mif4g Domain
          Length = 235

 Score =  223 bits (569), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 104/214 (48%), Positives = 154/214 (71%), Gaps = 2/214 (0%)

Query: 47  VQDKISFIINNISALNVEAKAKEFTEILKEQYYPWFAQYMVMKRASIEPNFHDLYLKFLD 106
           +Q+KI+FI NN+S  N+  K +E  E +KE++ PW +QY+VMKR SIEPNFH LY  FLD
Sbjct: 13  IQEKIAFIFNNLSQSNMTQKVEELKETVKEEFMPWVSQYLVMKRVSIEPNFHSLYSNFLD 72

Query: 107 KVNSKALNREIVQATYENCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQVLRARE 166
            + +   N+ ++  TY N KVLL S+   ++  +RSLLKNLG WLG +T+ +N+ +   +
Sbjct: 73  TLKNPEFNKMVLNETYRNIKVLLTSDKAAANFSDRSLLKNLGHWLGMITLAKNKPILHTD 132

Query: 167 IDPKSLIIEAYEKGL--MIAVIPFTSKILEPCQSSLAYQPPNPWTMAILGLLAEIYSMPN 224
           +D KSL++EAY KG   ++ V+PF +K+LE    S+ ++PPNPWTMAI+ +LAE++   +
Sbjct: 133 LDVKSLLLEAYVKGQQELLYVVPFVAKVLESSIRSVVFRPPNPWTMAIMNVLAELHQEHD 192

Query: 225 LKMNLKFDIEVLFKNLGVDMKDITPTSLLKDRKR 258
           LK+NLKF+IEVL KNL +D+ ++ P +LLKD+ R
Sbjct: 193 LKLNLKFEIEVLCKNLALDINELKPGNLLKDKDR 226


>pdb|4B89|A Chain A, Mif4g Domain Of The Yeast Not1
 pdb|4B8A|A Chain A, Structure Of Yeast Not1 Mif4g Domain Co-Crystallized With
           Caf1
 pdb|4B8C|B Chain B, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|G Chain G, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|H Chain H, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|I Chain I, Nuclease Module Of The Yeast Ccr4-Not Complex
          Length = 249

 Score =  153 bits (387), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 75/213 (35%), Positives = 128/213 (60%), Gaps = 2/213 (0%)

Query: 41  EAPASEVQDKISFIINNISALNVEAKAKEFTEILKEQYYPWFAQYMVMKRASIEPNFHDL 100
           E    +V +K+ F++NN++  N+  K  E  + L   Y+ WF+ Y+V +RA  EPN+HDL
Sbjct: 28  EGAPKDVVEKVLFVLNNVTLANLNNKVDELKKSLTPNYFSWFSTYLVTQRAKTEPNYHDL 87

Query: 101 YLKFLDKVNSKALNREIVQATYENCKVLLGSELIKSSSEERSLLKNLGSWLGKLTIGRNQ 160
           Y K +  + S  L++ +V  T     VLL ++     + ++  LKNL SWLG +T+  N+
Sbjct: 88  YSKVIVAMGSGLLHQFMVNVTLRQLFVLLSTK--DEQAIDKKHLKNLASWLGCITLALNK 145

Query: 161 VLRAREIDPKSLIIEAYEKGLMIAVIPFTSKILEPCQSSLAYQPPNPWTMAILGLLAEIY 220
            ++ + I  + ++IEAY++  +  V+PF +KIL+    S  ++PPNPWT+ IL LL E+ 
Sbjct: 146 PIKHKNIAFREMLIEAYKENRLEIVVPFVTKILQRASESKIFKPPNPWTVGILKLLIELN 205

Query: 221 SMPNLKMNLKFDIEVLFKNLGVDMKDITPTSLL 253
              N K++L F++EVL K+  +  K + P++ +
Sbjct: 206 EKANWKLSLTFEVEVLLKSFNLTTKSLKPSNFI 238


>pdb|3BBO|H Chain H, Homology Model For The Spinach Chloroplast 50s Subunit
           Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
          Length = 220

 Score = 32.7 bits (73), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 8/86 (9%)

Query: 256 RKREIEG-NPD----FSNKDVGASQPQLVPEVKPAIVSPLGHVDLPLDVASPPNSGGPTH 310
           R R+ +G NP+      N  VG  +  + PE+KP IV     +D+ +   +  +      
Sbjct: 125 RTRDFQGVNPNSFDGHGNYSVGFREQSVFPEIKPEIVGKARGMDVCITTTAKTDKEA-YK 183

Query: 311 LLSQYAAPLRLSSG--TLMEDEKLAA 334
           LLS    P R  SG  TL+  +KL +
Sbjct: 184 LLSLMGMPFREGSGPSTLVRKKKLKS 209


>pdb|2L7N|A Chain A, Nmr Structure Of The B Domain Of Talin
          Length = 168

 Score = 30.8 bits (68), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 13/44 (29%), Positives = 26/44 (59%)

Query: 864 LQTLVTDESRVVISELHNLVDALAKLAAKPGSPESLQQLIEIVR 907
           +Q +V D +  V+ +  +L++   K +  PG PES Q+L ++ +
Sbjct: 108 VQAIVLDTASDVLDKASSLIEEAKKASGHPGDPESQQRLAQVAK 151


>pdb|3IZS|J Chain J, Localization Of The Large Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
 pdb|3O5H|L Chain L, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
           Of The Second 80s In The Asymmetric Unit.
 pdb|3J16|H Chain H, Models Of Ribosome-Bound Dom34p And Rli1p And Their
           Ribosomal Binding Partners
          Length = 165

 Score = 30.4 bits (67), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 35/77 (45%), Gaps = 20/77 (25%)

Query: 536 FDPN----IYAQ---GSMGVPEALRPKPGHLSVSQQRVYEDF-------------VRLPW 575
           FDPN    +Y +   G +G   AL PK G L +S ++V ED              V+L  
Sbjct: 5   FDPNEVKYLYLRAVGGEVGASAALAPKIGPLGLSPKKVGEDIAKATKEFKGIKVTVQLKI 64

Query: 576 QNQSSQGSHAMSAGSLT 592
           QN+ +  S   SA SL 
Sbjct: 65  QNRQAAASVVPSASSLV 81


  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    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 40,889,080
Number of Sequences: 62578
Number of extensions: 1637492
Number of successful extensions: 3851
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 3826
Number of HSP's gapped (non-prelim): 26
length of query: 1498
length of database: 14,973,337
effective HSP length: 111
effective length of query: 1387
effective length of database: 8,027,179
effective search space: 11133697273
effective search space used: 11133697273
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: 58 (26.9 bits)