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= 043224
         (516 letters)

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

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



>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
           Tripartite Motif-containing Protein 31
          Length = 73

 Score = 29.6 bits (65), Expect = 3.8,   Method: Composition-based stats.
 Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 125 CNICCDDVSPQEVTTMDCGHCFCNNCWTE 153
           C IC D +  Q+  T+DCGH FC  C T+
Sbjct: 23  CPICLDIL--QKPVTIDCGHNFCLKCITQ 49


>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
          Length = 133

 Score = 29.6 bits (65), Expect = 4.7,   Method: Composition-based stats.
 Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 5/41 (12%)

Query: 115 PLSQCSSTFCCNICCDDVSP-----QEVTTMDCGHCFCNNC 150
           P+   S T  C IC D  S      + + + +CGH FC+ C
Sbjct: 65  PIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQC 105



 Score = 28.9 bits (63), Expect = 7.8,   Method: Composition-based stats.
 Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 5/36 (13%)

Query: 120 SSTFCCNICCDDVSP-----QEVTTMDCGHCFCNNC 150
           S T  C IC D  S      + + + +CGH FC+ C
Sbjct: 5   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQC 40


>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
           Tripartite Motif-containing Protein 31
          Length = 63

 Score = 29.6 bits (65), Expect = 4.8,   Method: Composition-based stats.
 Identities = 14/29 (48%), Positives = 18/29 (62%), Gaps = 2/29 (6%)

Query: 125 CNICCDDVSPQEVTTMDCGHCFCNNCWTE 153
           C IC D +  Q+  T+DCGH FC  C T+
Sbjct: 23  CPICLDIL--QKPVTIDCGHNFCLKCITQ 49


>pdb|3NG2|A Chain A, Crystal Structure Of The Rnf4 Ring Domain Dimer
 pdb|3NG2|B Chain B, Crystal Structure Of The Rnf4 Ring Domain Dimer
          Length = 71

 Score = 29.3 bits (64), Expect = 5.9,   Method: Composition-based stats.
 Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 5/36 (13%)

Query: 120 SSTFCCNICCDDVSP-----QEVTTMDCGHCFCNNC 150
           S T  C IC D  S      + + + +CGH FC+ C
Sbjct: 8   SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQC 43


  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
   0.321    0.135    0.428 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,118,990
Number of Sequences: 62578
Number of extensions: 599383
Number of successful extensions: 1357
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 20
Number of HSP's that attempted gapping in prelim test: 1346
Number of HSP's gapped (non-prelim): 31
length of query: 516
length of database: 14,973,337
effective HSP length: 103
effective length of query: 413
effective length of database: 8,527,803
effective search space: 3521982639
effective search space used: 3521982639
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)