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= 027482
         (223 letters)

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

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



>pdb|3JRU|B Chain B, Crystal Structure Of Leucyl Aminopeptidase (Pepa) From
           Xoo0834, Xanthomonas Oryzae Pv. Oryzae Kacc10331
 pdb|3JRU|A Chain A, Crystal Structure Of Leucyl Aminopeptidase (Pepa) From
           Xoo0834, Xanthomonas Oryzae Pv. Oryzae Kacc10331
          Length = 490

 Score = 29.6 bits (65), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 88  GFGSLLSENSARSTFPNLINFRVAKLRGFRRVFAHVA-PIFFERGIAKPETKE-ISSLSV 145
           G GSLLS     +  P LI  +     G  R +  V   I F+ G    +T+  I  +  
Sbjct: 226 GMGSLLSVARGSANRPRLIVLKW-NGGGDARPYVLVGKGITFDTGGVNLKTQGGIEEMKY 284

Query: 146 EPCEGETLIVTVFEIKKSEIP 166
           + C G T+I T     K+E+P
Sbjct: 285 DMCGGATVIGTFVATVKAELP 305


>pdb|2A91|A Chain A, Crystal Structure Of Erbb2 Domains 1-3
          Length = 517

 Score = 29.3 bits (64), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 35/80 (43%), Gaps = 7/80 (8%)

Query: 123 VAPIFFERGIAKPETKEISSLSVEPCE------GETLIVTVFEIKKSEIPAFIKREHEFR 176
           V P+  +   A+  T++    S +PC       G   +  V  +  + I  F   +  F 
Sbjct: 293 VCPLHNQEVTAEDGTQKCEKCS-KPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFG 351

Query: 177 FLAVLPETLDGKPFTNRAVL 196
            LA LPE+ DG P +N A L
Sbjct: 352 SLAFLPESFDGDPASNTAPL 371


>pdb|1S78|A Chain A, Insights Into Erbb Signaling From The Structure Of The
           Erbb2- Pertuzumab Complex
 pdb|1S78|B Chain B, Insights Into Erbb Signaling From The Structure Of The
           Erbb2- Pertuzumab Complex
 pdb|3BE1|A Chain A, Dual Specific Bh1 Fab In Complex With The Extracellular
           Domain Of Her2ERBB-2
 pdb|3MZW|A Chain A, Her2 Extracelluar Region With Affinity Matured 3-Helix
           Affibody Zher2:342
 pdb|3N85|A Chain A, Crystallographic Trimer Of Her2 Extracellular Regions In
           Complex With Tryptophan-Rich Antibody Fragment
          Length = 624

 Score = 28.9 bits (63), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 123 VAPIFFERGIAKPETKEISSLSVEPCE------GETLIVTVFEIKKSEIPAFIKREHEFR 176
           V P+  +   A+  T+     S +PC       G   +  V  +  + I  F   +  F 
Sbjct: 292 VCPLHNQEVTAEDGTQRCEKCS-KPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFG 350

Query: 177 FLAVLPETLDGKPFTNRAVL 196
            LA LPE+ DG P +N A L
Sbjct: 351 SLAFLPESFDGDPASNTAPL 370


>pdb|1QKL|A Chain A, Hrpabc14.4, Essential Subunit Of Human Rna Polymerases I,
           Ii And Iii
          Length = 127

 Score = 28.9 bits (63), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 22/79 (27%), Positives = 34/79 (43%), Gaps = 21/79 (26%)

Query: 96  NSARSTFPNLINFRVAKLRGFRRV-FAHVAPIFFERGIAKPETKEISSLSVEPCEGET-- 152
           N  R T P +  +  A++ G R +  A  AP+  E                   EGET  
Sbjct: 48  NQKRITTPYMTKYERARVLGTRALQIAMCAPVMVE------------------LEGETDP 89

Query: 153 LIVTVFEIKKSEIPAFIKR 171
           L++ + E+K  +IP  I+R
Sbjct: 90  LLIAMKELKARKIPIIIRR 108


>pdb|1N8Z|C Chain C, Crystal Structure Of Extracellular Domain Of Human Her2
           Complexed With Herceptin Fab
          Length = 607

 Score = 28.9 bits (63), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 23/80 (28%), Positives = 34/80 (42%), Gaps = 7/80 (8%)

Query: 123 VAPIFFERGIAKPETKEISSLSVEPCE------GETLIVTVFEIKKSEIPAFIKREHEFR 176
           V P+  +   A+  T+     S +PC       G   +  V  +  + I  F   +  F 
Sbjct: 292 VCPLHNQEVTAEDGTQRCEKCS-KPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFG 350

Query: 177 FLAVLPETLDGKPFTNRAVL 196
            LA LPE+ DG P +N A L
Sbjct: 351 SLAFLPESFDGDPASNTAPL 370


  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
   0.323    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: 6,247,352
Number of Sequences: 62578
Number of extensions: 241127
Number of successful extensions: 623
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 623
Number of HSP's gapped (non-prelim): 5
length of query: 223
length of database: 14,973,337
effective HSP length: 95
effective length of query: 128
effective length of database: 9,028,427
effective search space: 1155638656
effective search space used: 1155638656
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 49 (23.5 bits)