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= 005060
         (716 letters)

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

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



>pdb|1WID|A Chain A, Solution Structure Of The B3 Dna-Binding Domain Of Rav1
          Length = 130

 Score = 66.6 bits (161), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 41/102 (40%), Positives = 56/102 (54%), Gaps = 6/102 (5%)

Query: 149 FSKKLTPSDTSTHGGFSVPKRHADEC--LPPLDMSKDPPLQELVAKDLHGLEWRFRHIYR 206
           F K +TPSD        +PK HA++   LP  ++S    L  L  +D++G  WRFR+ Y 
Sbjct: 14  FEKAVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVL--LNFEDVNGKVWRFRYSYW 71

Query: 207 GQPKRHLLTSGWSVFVTSKKLVAGDVCIFLR--GGDGELRVG 246
              + ++LT GWS FV  K L AGDV  F R  G D +L +G
Sbjct: 72  NSSQSYVLTKGWSRFVKEKNLRAGDVVSFSRSNGQDQQLYIG 113


>pdb|1RKY|A Chain A, Pplo + Xe
 pdb|1W7C|A Chain A, Pplo At 1.23 Angstroms
          Length = 747

 Score = 33.5 bits (75), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 78/318 (24%), Positives = 118/318 (37%), Gaps = 58/318 (18%)

Query: 96  KILCEVVYAQLKAEPGTDEVFAQITLLPRPEIDELSLEVGNSPPLPPKLNVCSFSKKLTP 155
           +I+ E+   +L AE G+D+ F Q T        ++S  VGN   L P  +  S +   T 
Sbjct: 330 RIVYELSLQELIAEYGSDDPFNQHTFYS-----DISYGVGNRFSLVPGYDCPSTAGYFT- 383

Query: 156 SDTSTHGGFSVPKRHADECLPPLDMSKDPPLQELVAKDLHGLEWRFRHIYRGQPKRHLLT 215
           +DT  +  F    R    C+   +  +D  L               RH          +T
Sbjct: 384 TDTFEYDEFY--NRTLSYCV--FENQEDYSL--------------LRHT---GASYSAIT 422

Query: 216 SGWSVFVTSKKLVAGDVCIFLRGG--DGELRVGVRRAMKLQN---NASTSVISSLSMQHG 270
              ++ V     +      FL     DG L V VR A  +Q    N  TS    L + H 
Sbjct: 423 QNPTLNVRFISTIGNXDYNFLYKFFLDGTLEVSVRAAGYIQAGYWNPETSAPYGLKI-HD 481

Query: 271 ILAGAFHAISTGTRFTVYYHPWTRPAEFLVPFSQY-MKSAEIDY--SIGTRFRMVFEGEE 327
           +L+G+FH      +  +        A      SQY MK  +++Y  + GT +        
Sbjct: 482 VLSGSFHDHVLNYKVDLDVGGTKNRA------SQYVMKDVDVEYPWAPGTVYNT------ 529

Query: 328 CADQRIAGTVVGTEDVDHIRWPASEWRCLKVKWDATTDSITRPARVSPWNIEP----IER 383
              ++IA  V   ED + I WP +    L ++    T+S   P     +NI P    + R
Sbjct: 530 ---KQIAREVFENEDFNGINWPENGQGILLIESAEETNSFGNP---RAYNIMPGGGGVHR 583

Query: 384 THKRPASVQHQQKRLRPN 401
             K   S    Q   R N
Sbjct: 584 IVKNSRSGPETQNWARSN 601


>pdb|4I1K|A Chain A, Crystal Structure Of Vrn1 (residues 208-341)
 pdb|4I1K|B Chain B, Crystal Structure Of Vrn1 (residues 208-341)
          Length = 146

 Score = 32.0 bits (71), Expect = 1.4,   Method: Composition-based stats.
 Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 198 EWRFRHIYRGQPKRHLLTSGWSVFVTSKKLVAGDVCIF--LRGGDGELRVGVRR 249
           +W  R +Y+    R   + GW  F     L  GDVC+F  LR  D  L+V   R
Sbjct: 90  QWPVRCLYKA--GRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFR 141


>pdb|1SFN|A Chain A, Crystal Structure Of Protein Dr1152 From Deinococcus
           Radiodurans R1, Pfam Duf861
 pdb|1SFN|B Chain B, Crystal Structure Of Protein Dr1152 From Deinococcus
           Radiodurans R1, Pfam Duf861
          Length = 246

 Score = 30.0 bits (66), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 29/73 (39%), Gaps = 3/73 (4%)

Query: 299 LVPFSQYM-KSAEIDYSIGTRFRMVFEGEECADQRIAGTVVGTEDVDHIRWPASEWRCLK 357
            V F+  M   A+   S+  RF  V  GE   D  + G      + D++  PA E   L 
Sbjct: 50  FVQFTAEMPAGAQATESVYQRFAFVLSGE--VDVAVGGETRTLREYDYVYLPAGEKHMLT 107

Query: 358 VKWDATTDSITRP 370
            K DA      +P
Sbjct: 108 AKTDARVSVFEKP 120


  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
   0.317    0.133    0.413 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,812,284
Number of Sequences: 62578
Number of extensions: 969691
Number of successful extensions: 2005
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: 2003
Number of HSP's gapped (non-prelim): 7
length of query: 716
length of database: 14,973,337
effective HSP length: 106
effective length of query: 610
effective length of database: 8,340,069
effective search space: 5087442090
effective search space used: 5087442090
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)