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= 023083
         (287 letters)

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

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



>pdb|3RFZ|B Chain B, Crystal Structure Of The Fimd Usher Bound To Its Cognate
           Fimc:fimh Substrate
 pdb|3RFZ|E Chain E, Crystal Structure Of The Fimd Usher Bound To Its Cognate
           Fimc:fimh Substrate
          Length = 843

 Score = 30.4 bits (67), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 39/156 (25%), Positives = 63/156 (40%), Gaps = 14/156 (8%)

Query: 4   LPYNSLMQLKIPSHSCAKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLP 63
           +PY+S+  L+   H+    T   +    R  N+QQE+ +   S L    G+P        
Sbjct: 315 VPYSSVPLLQREGHTRYSITAGEY----RSGNAQQEKPRFFQSTL--LHGLPA------- 361

Query: 64  RWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQK 123
            W  YG G+ +   + AF+  +         L + +   + TLP   +   Q    +  K
Sbjct: 362 GWTIYG-GTQLADRYRAFNFGIGKNMGALGALSVDMTQANSTLPDDSQHDGQSVRFLYNK 420

Query: 124 SLPESGEQIFVMSQNISDALKENLAWATYVLLRNTN 159
           SL ESG  I ++    S +   N A  TY  +   N
Sbjct: 421 SLNESGTNIQLVGYRYSTSGYFNFADTTYSRMNGYN 456


>pdb|3OHN|A Chain A, Crystal Structure Of The Fimd Translocation Domain
 pdb|3OHN|B Chain B, Crystal Structure Of The Fimd Translocation Domain
          Length = 558

 Score = 30.0 bits (66), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 39/156 (25%), Positives = 63/156 (40%), Gaps = 14/156 (8%)

Query: 4   LPYNSLMQLKIPSHSCAKTTRKSFSICARLDNSQQEEQQLNLSVLRFTFGIPGFDESYLP 63
           +PY+S+  L+   H+    T   +    R  N+QQE+ +   S L    G+P        
Sbjct: 192 VPYSSVPLLQREGHTRYSITAGEY----RSGNAQQEKPRFFQSTL--LHGLP-------A 238

Query: 64  RWIGYGFGSLIVLNHFAFSNSVTSAQLRSEVLGLSLAAFSVTLPYLGKFLKQGASPVSQK 123
            W  YG G+ +   + AF+  +         L + +   + TLP   +   Q    +  K
Sbjct: 239 GWTIYG-GTQLADRYRAFNFGIGKNMGALGALSVDMTQANSTLPDDSQHDGQSVRFLYNK 297

Query: 124 SLPESGEQIFVMSQNISDALKENLAWATYVLLRNTN 159
           SL ESG  I ++    S +   N A  TY  +   N
Sbjct: 298 SLNESGTNIQLVGYRYSTSGYFNFADTTYSRMNGYN 333


>pdb|1J9A|A Chain A, Oligoribonuclease
          Length = 184

 Score = 28.9 bits (63), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 26/109 (23%), Positives = 51/109 (46%), Gaps = 24/109 (22%)

Query: 100 AAFSVTLPYLGKFLKQGASPVSQKSLPESGEQIFVMSQNISDALKENLAWATYVLLRNTN 159
           AA   TL +L K++ +GASP+   S+ +    +     +++D          Y   R+ +
Sbjct: 86  AAELQTLDFLKKWVPKGASPICGNSIAQDKRFLVKYXPDLAD----------YFHYRHLD 135

Query: 160 SISVLISIRGELCVRGYWQTPDGASKTQLLEWFERQIENIGLSDLKDSL 208
                +S   EL  R  W       K ++LE F+++  ++ L D+++S+
Sbjct: 136 -----VSTLKELAAR--W-------KPEILEGFKKENTHLALDDIRESI 170


  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
   0.319    0.133    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,287,566
Number of Sequences: 62578
Number of extensions: 318350
Number of successful extensions: 710
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 709
Number of HSP's gapped (non-prelim): 8
length of query: 287
length of database: 14,973,337
effective HSP length: 98
effective length of query: 189
effective length of database: 8,840,693
effective search space: 1670890977
effective search space used: 1670890977
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: 51 (24.3 bits)