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= 043604
         (268 letters)

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

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



>pdb|2CT7|A Chain A, Solution Structure Of The Ibr Domain Of The Ring Finger
           Protein 31 Protein
          Length = 86

 Score = 30.4 bits (67), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 13/40 (32%), Positives = 20/40 (50%)

Query: 151 KARCPNCTQWFCFQCKLAWHAGYRCEESGNLRDWNDIAFG 190
           +A CP C Q FC +CK  W   +R     + ++W  +  G
Sbjct: 43  EATCPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWKRMNSG 82


>pdb|1WIM|A Chain A, Solution Structure Of The Ring Finger Domain Of The Human
           Ubcm4-Interacting Protein 4
          Length = 94

 Score = 28.5 bits (62), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 17/87 (19%), Positives = 38/87 (43%), Gaps = 3/87 (3%)

Query: 34  TNGIFTCEICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQ 93
           ++G   C++C+      ++      C   FC  C+ +Y+E  +++     I CP   C +
Sbjct: 2   SSGSSGCKLCLGEYPV-EQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAACPK 60

Query: 94  --FLDPFSCKLMIPSNLFSKWCDVLFE 118
              L     + M+ + +  ++  + FE
Sbjct: 61  QGHLQENEIECMVAAEIMQRYKKLQFE 87


>pdb|1Z6U|A Chain A, Np95-Like Ring Finger Protein Isoform B [homo Sapiens]
 pdb|1Z6U|B Chain B, Np95-Like Ring Finger Protein Isoform B [homo Sapiens]
          Length = 150

 Score = 27.7 bits (60), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 19/83 (22%), Positives = 34/83 (40%), Gaps = 19/83 (22%)

Query: 41  EICIEPISANDKFRNKDLCSHHFCQDCIAKYIEAKVQDNNTAKIECPGVHCDQFLDPFSC 100
           E+  +P++          C H+ C+DC+ +  +A+V         CP    D   +    
Sbjct: 86  ELVYQPVTTE--------CFHNVCKDCLQRSFKAQV-------FSCPACRHDLGQN---- 126

Query: 101 KLMIPSNLFSKWCDVLFEDYVLG 123
            +MIP+ +     D+ F  Y  G
Sbjct: 127 YIMIPNEILQTLLDLFFPGYSKG 149


>pdb|2OWO|A Chain A, Last Stop On The Road To Repair: Structure Of E.Coli Dna
           Ligase Bound To Nicked Dna-Adenylate
          Length = 671

 Score = 27.7 bits (60), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 12/20 (60%), Positives = 13/20 (65%)

Query: 201 CPACGSCVERKEGCRVMYCS 220
           CP CGS VER EG  V  C+
Sbjct: 408 CPVCGSDVERVEGEAVARCT 427


>pdb|4GLX|A Chain A, Dna Ligase A In Complex With Inhibitor
          Length = 586

 Score = 27.7 bits (60), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 12/20 (60%), Positives = 13/20 (65%)

Query: 201 CPACGSCVERKEGCRVMYCS 220
           CP CGS VER EG  V  C+
Sbjct: 408 CPVCGSDVERVEGEAVARCT 427


  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
   0.325    0.137    0.473 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,542,227
Number of Sequences: 62578
Number of extensions: 345664
Number of successful extensions: 759
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 750
Number of HSP's gapped (non-prelim): 30
length of query: 268
length of database: 14,973,337
effective HSP length: 97
effective length of query: 171
effective length of database: 8,903,271
effective search space: 1522459341
effective search space used: 1522459341
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)