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= 036876
         (234 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 = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 43/152 (28%), Positives = 73/152 (48%), Gaps = 17/152 (11%)

Query: 58  FTKMPKLRFLKFYSSSFNGENKCKVSYLQDLGFVEVKYLHWHGYPLKSLPSNLSA-EKLV 116
            T++P+       S+  +GE++  V+ LQ L       L W G  ++SLP++++  + L 
Sbjct: 163 LTELPE----PLASTDASGEHQGLVN-LQSL------RLEWTG--IRSLPASIANLQNLK 209

Query: 117 LLEVPGSSIEQLWDGVKHYSKLNQIIHVACKKLIAKTPNPTLMPHLNKLVILILRGSKSL 176
            L++  S +  L   + H  KL ++    C  L    P   +      L  LIL+   +L
Sbjct: 210 SLKIRNSPLSALGPAIHHLPKLEELDLRGCTALRNYPP---IFGGRAPLKRLILKDCSNL 266

Query: 177 KSLPAEIFNLECLTELDLSDCSKLKRLPEILS 208
            +LP +I  L  L +LDL  C  L RLP +++
Sbjct: 267 LTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIA 298



 Score = 32.0 bits (71), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 31/56 (55%), Gaps = 10/56 (17%)

Query: 176 LKSLPAEIFNLECLTELDLSDCSKLKRLPEILS---------GIVN-DALRIQHIG 221
           L++LPA I +L  L EL +  C +L  LPE L+         G+VN  +LR++  G
Sbjct: 139 LRALPASIASLNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTG 194


>pdb|1CP9|B Chain B, Crystal Structure Of Penicillin G Acylase From The Bro1
           Mutant Strain Of Providencia Rettgeri
          Length = 553

 Score = 28.5 bits (62), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 37/144 (25%), Positives = 64/144 (44%), Gaps = 27/144 (18%)

Query: 104 KSLPSNLSAEKLVLLEVPGSSIEQLWDGV-------KHY-SKLNQIIHVACKKLIAKTPN 155
           + LPSN ++ KLV       S+ Q WDG+       KHY    + I+ +  K+++  T  
Sbjct: 308 QGLPSNDNSVKLV-------SMLQQWDGINQLSSDGKHYIHPGSAILDIWLKEMLKATLG 360

Query: 156 PTLMPHLNKLVILILRGSKSLKSLPAEIFNLEC----LTELDLSDCSKLKRLPEILSG-I 210
            T+    +K    +  G ++ +  P    N+      L E  L D S + +  ++ SG  
Sbjct: 361 QTVPAPFDKW--YLASGYETTQEGPTGSLNISTGAKLLYESLLEDKSPISQSIDLFSGQP 418

Query: 211 VNDALRIQHIGHLLAVRWKEMLEK 234
            ND +R       L   +++M+EK
Sbjct: 419 QNDVIR-----KTLNTTYQKMIEK 437


>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 = 27.3 bits (59), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 22/45 (48%), Positives = 25/45 (55%), Gaps = 2/45 (4%)

Query: 165 LVILILRGSKSLKSLPAEIFNLECLTELDLSDCSKLKRLPEILSG 209
           L  L L G+ SL  LPAEI NL  L  LDLS  ++L  LP  L  
Sbjct: 249 LTRLYLNGN-SLTELPAEIKNLSNLRVLDLSH-NRLTSLPAELGS 291


  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
   0.320    0.138    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,992,130
Number of Sequences: 62578
Number of extensions: 275569
Number of successful extensions: 629
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 625
Number of HSP's gapped (non-prelim): 5
length of query: 234
length of database: 14,973,337
effective HSP length: 96
effective length of query: 138
effective length of database: 8,965,849
effective search space: 1237287162
effective search space used: 1237287162
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)