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= 028761
         (204 letters)

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

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



>pdb|3MCB|A Chain A, Crystal Structure Of Nac Domains Of Human Nascent
           Polypeptide- Associated Complex (Nac)
          Length = 54

 Score = 90.5 bits (223), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 39/54 (72%), Positives = 50/54 (92%)

Query: 72  AMLKLGMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFGEAKIEDLS 125
           AM KLG++ + GV+RVT++KSKNILFVI+KPDV+KSP +DTY++FGEAKIEDLS
Sbjct: 1   AMSKLGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLS 54


>pdb|3LKX|B Chain B, Human Nac Dimerization Domain
          Length = 54

 Score = 88.2 bits (217), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 37/53 (69%), Positives = 48/53 (90%)

Query: 77  GMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFGEAKIEDLSSQLQ 129
           G++ + GV+RVT++KSKNILFVI+KPDV+KSP +DTY++FGEAKIEDLS Q Q
Sbjct: 2   GLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLSQQAQ 54


>pdb|3MCE|A Chain A, Crystal Structure Of The Nac Domain Of Alpha Subunit Of
           Nascent Polypeptide-Associated Complex(Nac)
 pdb|3MCE|B Chain B, Crystal Structure Of The Nac Domain Of Alpha Subunit Of
           Nascent Polypeptide-Associated Complex(Nac)
 pdb|3MCE|C Chain C, Crystal Structure Of The Nac Domain Of Alpha Subunit Of
           Nascent Polypeptide-Associated Complex(Nac)
 pdb|3MCE|D Chain D, Crystal Structure Of The Nac Domain Of Alpha Subunit Of
           Nascent Polypeptide-Associated Complex(Nac)
          Length = 61

 Score = 86.3 bits (212), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 37/51 (72%), Positives = 48/51 (94%)

Query: 75  KLGMKPIPGVSRVTVKKSKNILFVISKPDVFKSPTTDTYVIFGEAKIEDLS 125
           KLG++ + GV+RVT++KSKNILFVI+KPDV+KSP +DTY++FGEAKIEDLS
Sbjct: 10  KLGLRQVTGVTRVTIRKSKNILFVITKPDVYKSPASDTYIVFGEAKIEDLS 60


>pdb|1TR8|A Chain A, Crystal Structure Of Archaeal Nascent
           Polypeptide-Associated Complex (Aenac)
 pdb|1TR8|B Chain B, Crystal Structure Of Archaeal Nascent
           Polypeptide-Associated Complex (Aenac)
          Length = 102

 Score = 36.2 bits (82), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 34/126 (26%), Positives = 49/126 (38%), Gaps = 36/126 (28%)

Query: 79  KPIPGVSRVTVK-KSKNILFVISKPDVFKSPTTDTYVIFGEAKIEDLSSQLQTQAAEQFK 137
           K + GV  V +K K K I+    K +V +     TY + G+A+   L ++ +        
Sbjct: 12  KDLRGVEEVVIKLKRKEIIIKNPKVNVXEFXGQKTYQVTGKARERSLEAEXEI------- 64

Query: 138 APDLSHVVSKPESSAMAQDDEEVDETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVS 197
                     PE                   DIELV  Q G SR  A +AL+   GD+  
Sbjct: 65  ----------PED------------------DIELVXNQTGASREDATRALQETGGDLAE 96

Query: 198 AIMELT 203
           AI  L+
Sbjct: 97  AIXRLS 102


>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
 pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
          Length = 854

 Score = 26.9 bits (58), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 3/61 (4%)

Query: 139 PDLSHVVSKPESSAMAQDDEEVDETGVEPKDIELVMTQAGVSRAKAVKALKAADGDIVSA 198
           PD ++ +  P SS         D     P+D    +   G SR +A+KAL+A +  +  A
Sbjct: 695 PDFANPLILPGSSGPGSTSAAADPP---PEDCVTTIVSMGFSRDQALKALRATNNSLERA 751

Query: 199 I 199
           +
Sbjct: 752 V 752


  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
   0.310    0.127    0.336 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,731,007
Number of Sequences: 62578
Number of extensions: 118119
Number of successful extensions: 263
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 246
Number of HSP's gapped (non-prelim): 21
length of query: 204
length of database: 14,973,337
effective HSP length: 94
effective length of query: 110
effective length of database: 9,091,005
effective search space: 1000010550
effective search space used: 1000010550
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: 49 (23.5 bits)