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= 003011
         (857 letters)

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

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



>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
           Iii Effector Xcv3220 (Xopl)
          Length = 328

 Score = 46.2 bits (108), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 53/179 (29%), Positives = 83/179 (46%), Gaps = 19/179 (10%)

Query: 159 SIEGIFLDMSKIREIHLSSRAFACMTNLRMLKFYV-PKLSKLSDVKVHL-----HNGLDY 212
            +E + L  + +R +  S    A +  LR L     P+L++L +          H GL  
Sbjct: 128 GLETLTLARNPLRALPAS---IASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVN 184

Query: 213 LSDELRYLHWHGYPLKTLPSNFSP-ENLIELNLPYSKVEQMWEGKKESFKLKWIDLHHCQ 271
           L   LR L W G  +++LP++ +  +NL  L +  S +  +        KL+ +DL  C 
Sbjct: 185 LQS-LR-LEWTG--IRSLPASIANLQNLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCT 240

Query: 272 YLIRFPDPL---ETPNLERICLSDCIDLPCIPSSIENFNNLSILCLQGCESLRRFPSNI 327
            L  +P P+     P L+R+ L DC +L  +P  I     L  L L+GC +L R PS I
Sbjct: 241 ALRNYP-PIFGGRAP-LKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLI 297



 Score = 34.7 bits (78), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 43/187 (22%), Positives = 71/187 (37%), Gaps = 43/187 (22%)

Query: 226 PLKTLPSNFSPEN------------LIELNLPYSKVEQMWEGKK----ESFKLKWIDLHH 269
           PL+ LP++ +  N            L EL  P +  +   E +     +S +L+W  +  
Sbjct: 138 PLRALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRS 197

Query: 270 CQYLIRFPDPLETPNLERICLSDCIDLPCIPSSIENFNNLSILCLQGCESLRRFPSNIHF 329
               I         NL+ + + +   L  +  +I +   L  L L+GC +LR +P     
Sbjct: 198 LPASI-----ANLQNLKSLKIRNS-PLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGG 251

Query: 330 RSPIT-LDFSDCLNLTEFPQFSGNIKQLYLCGTAIEEVPSSVECLTELAELYMRQCTRLK 388
           R+P+  L   DC NL                       P  +  LT+L +L +R C  L 
Sbjct: 252 RAPLKRLILKDCSNLLTL--------------------PLDIHRLTQLEKLDLRGCVNLS 291

Query: 389 SISSRIC 395
            + S I 
Sbjct: 292 RLPSLIA 298



 Score = 33.5 bits (75), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 48/201 (23%), Positives = 72/201 (35%), Gaps = 39/201 (19%)

Query: 339 DCLNLTEFP----QFSGNIKQLYLCGTAIEEVPSSVECLTELAELYMRQCTRLKSISSRI 394
           D   L E P    QF+G ++ L L    +  +P+S+  L  L EL +R C  L  +   +
Sbjct: 112 DAAGLXELPDTXQQFAG-LETLTLARNPLRALPASIASLNRLRELSIRACPELTELPEPL 170

Query: 395 CXXXXXXXXXXXXXXXXERFPEITETMECLEYFSLASTTIQEQPSSNEDRILPSSIANW- 453
                                   + +  L+   L  T I         R LP+SIAN  
Sbjct: 171 ASTDASGEH---------------QGLVNLQSLRLEWTGI---------RSLPASIANLQ 206

Query: 454 ---SYGCRXXXXXXXXXXXXXXXXXXX--FRNITEI---PKDIGCLSSLRTLDLRG-NNF 504
              S   R                      R  T +   P   G  + L+ L L+  +N 
Sbjct: 207 NLKSLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPPIFGGRAPLKRLILKDCSNL 266

Query: 505 VSLPASIKQFTQMEELILSNC 525
           ++LP  I + TQ+E+L L  C
Sbjct: 267 LTLPLDIHRLTQLEKLDLRGC 287


>pdb|4B8C|D Chain D, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|J Chain J, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|K Chain K, Nuclease Module Of The Yeast Ccr4-Not Complex
 pdb|4B8C|L Chain L, Nuclease Module Of The Yeast Ccr4-Not Complex
          Length = 727

 Score = 35.0 bits (79), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 17/39 (43%), Positives = 25/39 (64%)

Query: 480 NITEIPKDIGCLSSLRTLDLRGNNFVSLPASIKQFTQME 518
           ++TE+P +I  LS+LR LDL  N   SLPA +    Q++
Sbjct: 258 SLTELPAEIKNLSNLRVLDLSHNRLTSLPAELGSCFQLK 296


>pdb|3E6J|A Chain A, Crystal Structure Of Variable Lymphocyte Receptor (Vlr)
           Rbc36 In Complex With H-Trisaccharide
          Length = 229

 Score = 30.4 bits (67), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 15/39 (38%), Positives = 25/39 (64%), Gaps = 1/39 (2%)

Query: 352 NIKQLYLCGTAIEEVPSSVECLTELAELYMRQCTRLKSI 390
           ++K+L++C   + E+P  +E LT L  L + Q  +LKSI
Sbjct: 113 HLKELFMCCNKLTELPRGIERLTHLTHLALDQ-NQLKSI 150


  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    0.137    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,828,898
Number of Sequences: 62578
Number of extensions: 957241
Number of successful extensions: 2538
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 2522
Number of HSP's gapped (non-prelim): 26
length of query: 857
length of database: 14,973,337
effective HSP length: 107
effective length of query: 750
effective length of database: 8,277,491
effective search space: 6208118250
effective search space used: 6208118250
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: 56 (26.2 bits)