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= 008441
         (565 letters)

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

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



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

 Score = 37.4 bits (85), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 2/58 (3%)

Query: 304 GKTINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEP--TCPHEGC 359
           G + +  C +CL +  V  M +I  C   +C LC+K+++E  +++G+E   +CP   C
Sbjct: 1   GSSGSSGCKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLETAISCPDAAC 58


>pdb|1CHC|A Chain A, Structure Of The C3hc4 Domain By 1h-Nuclear Magnetic
           Resonance Spectroscopy; A New Structural Class Of Zinc-
           Finger
          Length = 68

 Score = 34.3 bits (77), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 10/59 (16%)

Query: 306 TINETCVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTCPHEGCKSKLE 364
           T+ E C ICLED     M     CLH +C++C+ + I +       PTCP   CK  +E
Sbjct: 3   TVAERCPICLEDPSNYSMAL--PCLHAFCYVCITRWIRQN------PTCP--LCKVPVE 51


>pdb|3HST|B Chain B, N-Terminal Rnase H Domain Of Rv2228c From Mycobacterium
           Tuberculosis As A Fusion Protein With Maltose Binding
           Protein
 pdb|3HST|D Chain D, N-Terminal Rnase H Domain Of Rv2228c From Mycobacterium
           Tuberculosis As A Fusion Protein With Maltose Binding
           Protein
          Length = 141

 Score = 33.5 bits (75), Expect = 0.36,   Method: Composition-based stats.
 Identities = 22/81 (27%), Positives = 34/81 (41%)

Query: 207 SAAETKALIEGLNAALSMELDRVRVFIDCFPLFQFVTGRWPAKQRKISVLVDQVSLLEKR 266
           + AE + LI GL+ A+ +      V +D   + + ++GRW  K   +  L  Q   L  +
Sbjct: 47  NVAEYRGLIAGLDDAVKLGATEAAVLMDSKLVVEQMSGRWKVKHPDLLKLYVQAQALASQ 106

Query: 267 FSYFKPRHVARNDMKYVYELA 287
           F       V R    Y   LA
Sbjct: 107 FRRINYEWVPRARNTYADRLA 127


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

 Score = 31.6 bits (70), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 6/40 (15%)

Query: 430 CTKCHRRFCIDCKVPW---HNNMTC---IYYKRLNPNPPT 463
           C +CH+ FC+ CK  W   H   +C     +KR+N  P +
Sbjct: 46  CPQCHQTFCVRCKRQWEEQHRGRSCEDFQNWKRMNSGPSS 85


>pdb|1WD2|A Chain A, Solution Structure Of The C-Terminal Ring From A Ring-Ibr-
           Ring (Triad) Motif
          Length = 60

 Score = 31.6 bits (70), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 17/39 (43%), Positives = 22/39 (56%), Gaps = 3/39 (7%)

Query: 478 RQCVKCNHLIELAEGCFHMTCR---CGHEFCYNCGAEWK 513
           ++C KC+  IE   GC HM CR   C  EFC+ C   W+
Sbjct: 7   KECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWE 45


>pdb|2Y43|A Chain A, Rad18 Ubiquitin Ligase Ring Domain Structure
 pdb|2Y43|B Chain B, Rad18 Ubiquitin Ligase Ring Domain Structure
          Length = 99

 Score = 31.2 bits (69), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 7/59 (11%)

Query: 298 PAEISRGKTINET--CVICLEDTDVGHMFSIDGCLHRYCFLCMKKHIEEKLRQGMEPTC 354
           P  ++  KTI++   C IC E  ++  +  I  C H YC LC++K +  K +    PTC
Sbjct: 10  PPGLAVMKTIDDLLRCGICFEYFNIAMI--IPQCSHNYCSLCIRKFLSYKTQC---PTC 63


  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
   0.322    0.135    0.420 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,678,548
Number of Sequences: 62578
Number of extensions: 526367
Number of successful extensions: 1318
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1305
Number of HSP's gapped (non-prelim): 16
length of query: 565
length of database: 14,973,337
effective HSP length: 104
effective length of query: 461
effective length of database: 8,465,225
effective search space: 3902468725
effective search space used: 3902468725
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)