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= 000103
         (2224 letters)

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

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



>pdb|3S4W|A Chain A, Structure Of The Fanci-Fancd2 Complex
 pdb|3S4Z|A Chain A, Structure Of A Y Dna-Fanci Complex
 pdb|3S4Z|B Chain B, Structure Of A Y Dna-Fanci Complex
 pdb|3S4Z|C Chain C, Structure Of A Y Dna-Fanci Complex
 pdb|3S51|A Chain A, Structure Of Fanci
 pdb|3S51|B Chain B, Structure Of Fanci
 pdb|3S51|C Chain C, Structure Of Fanci
 pdb|3S51|D Chain D, Structure Of Fanci
          Length = 1308

 Score = 33.9 bits (76), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 14/30 (46%), Positives = 21/30 (70%)

Query: 1997 SSHGVPNQVEKVIELSFEHLSSIFGCWIEY 2026
            SS G+PN VEK+++LS  HL+ +   +I Y
Sbjct: 1187 SSRGIPNTVEKLVKLSGSHLTPVCYSFISY 1216


>pdb|3HA1|A Chain A, Alanine Racemase From Bacillus Anthracis (Ames)
 pdb|3HA1|B Chain B, Alanine Racemase From Bacillus Anthracis (Ames)
          Length = 397

 Score = 32.3 bits (72), Expect = 3.2,   Method: Composition-based stats.
 Identities = 24/71 (33%), Positives = 37/71 (52%), Gaps = 11/71 (15%)

Query: 51  VSLNSIYAQVNHAKKFASSFIELLS--SANAAADEWV-------LSKATRVYLEVMFLEN 101
           V L++IY  V H K+F  S +E+ +    NA   ++V        + ATR  L V FL+ 
Sbjct: 14  VDLDAIYNNVTHIKEFIPSDVEIFAVVXGNAYGHDYVPVAKIALEAGATR--LAVAFLDE 71

Query: 102 SLPLHRTLVSA 112
           +L L R  ++A
Sbjct: 72  ALVLRRAGITA 82


>pdb|4BD2|A Chain A, Bax Domain Swapped Dimer In Complex With Bidbh3
 pdb|4BD6|A Chain A, Bax Domain Swapped Dimer In Complex With Baxbh3
 pdb|4BD7|A Chain A, Bax Domain Swapped Dimer Induced By Octylmaltoside
 pdb|4BD7|B Chain B, Bax Domain Swapped Dimer Induced By Octylmaltoside
 pdb|4BD7|C Chain C, Bax Domain Swapped Dimer Induced By Octylmaltoside
 pdb|4BD7|D Chain D, Bax Domain Swapped Dimer Induced By Octylmaltoside
 pdb|4BD8|A Chain A, Bax Domain Swapped Dimer Induced By Bimbh3 With Chaps
 pdb|4BD8|D Chain D, Bax Domain Swapped Dimer Induced By Bimbh3 With Chaps
 pdb|4BD8|C Chain C, Bax Domain Swapped Dimer Induced By Bimbh3 With Chaps
 pdb|4BD8|B Chain B, Bax Domain Swapped Dimer Induced By Bimbh3 With Chaps
          Length = 174

 Score = 31.6 bits (70), Expect = 4.8,   Method: Composition-based stats.
 Identities = 24/107 (22%), Positives = 49/107 (45%), Gaps = 12/107 (11%)

Query: 422 DPIPEDMGTRILRIIWNNLEDPLSQTVKQVHLVFDLFLDIESSLRWDVGSERIKSFLQKI 481
           DP+P+D  T+            LS+++K++    D  ++++  +   V ++  +    ++
Sbjct: 48  DPVPQDASTK-----------KLSESLKRIGDELDSNMELQRMIA-AVDTDSPREVFFRV 95

Query: 482 ASDLLCLGPRCKGRYVPLALLTKRLGAKTLLGMSPDLLSEIVNAYID 528
           A+D+   G    GR V L     +L  K L    P+L+  I+   +D
Sbjct: 96  AADMFSDGNFNWGRVVALFYFASKLVLKALSTKVPELIRTIMGWTLD 142


>pdb|2XQY|A Chain A, Crystal Structure Of Pseudorabies Core Fragment Of
            Glycoprotein H In Complex With Fab D6.3
 pdb|2XQY|E Chain E, Crystal Structure Of Pseudorabies Core Fragment Of
            Glycoprotein H In Complex With Fab D6.3
          Length = 572

 Score = 31.6 bits (70), Expect = 4.8,   Method: Composition-based stats.
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 1906 VNMRKAATGSIVASGLLEQADLIGSYVS--NHQIPSENSSLHFEPQEAGNMYAHQVLVIW 1963
            V +R ++ G+I+ + L+E  D+    ++  N  IPS N +LH    +A  ++ +  +V  
Sbjct: 470  VFVRYSSAGTILETVLIESKDMEEQLMAGANSTIPSFNPTLHGGDVKALMLFPNGTVVDL 529

Query: 1964 FTCIKLLEDEDD 1975
             +     ED+DD
Sbjct: 530  LSFTSTFEDDDD 541


  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    0.136    0.408 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 60,523,516
Number of Sequences: 62578
Number of extensions: 2357155
Number of successful extensions: 5584
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 5581
Number of HSP's gapped (non-prelim): 8
length of query: 2224
length of database: 14,973,337
effective HSP length: 114
effective length of query: 2110
effective length of database: 7,839,445
effective search space: 16541228950
effective search space used: 16541228950
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: 59 (27.3 bits)