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= psy16971
         (383 letters)

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

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



>pdb|2C5W|B Chain B, Penicillin-Binding Protein 1a (Pbp-1a) Acyl-Enzyme Complex
           (Cefotaxime) From Streptococcus Pneumoniae
          Length = 385

 Score = 30.8 bits (68), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 33/141 (23%), Positives = 58/141 (41%), Gaps = 11/141 (7%)

Query: 35  LNGYAVDYYLTDKSQCAGGRGSCPDYRIQDNTESVRLLNAALVNGYSIVTYQRPLRSHDI 94
           LNG  +DY     S       +  D +   ++E +    AA  NG    TY +P+  H +
Sbjct: 184 LNGLGIDYPSIHYSNAISSNTTESDKKYGASSEKMAAAYAAFANG---GTYYKPMYIHKV 240

Query: 95  LDHDIYTNQSQAIIWAIGPLNSKQEVSFHSVFPKKNIL-FNFGRTPYWNCPIPEGETGTP 153
               ++++ S+     +G    K+  ++      K +L +  GR  Y       G+TGT 
Sbjct: 241 ----VFSDGSEKEFSNVGTRAMKETTAYMMTDMMKTVLTYGTGRNAYLAWLPQAGKTGTS 296

Query: 154 NHGEYSDESSGANTKVQEVLG 174
           N   Y+DE    + K  + + 
Sbjct: 297 N---YTDEEIENHIKTSQFVA 314


>pdb|2C6W|B Chain B, Penicillin-Binding Protein 1a (Pbp-1a) From Streptococcus
           Pneumoniae
          Length = 384

 Score = 30.8 bits (68), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 33/141 (23%), Positives = 58/141 (41%), Gaps = 11/141 (7%)

Query: 35  LNGYAVDYYLTDKSQCAGGRGSCPDYRIQDNTESVRLLNAALVNGYSIVTYQRPLRSHDI 94
           LNG  +DY     S       +  D +   ++E +    AA  NG    TY +P+  H +
Sbjct: 183 LNGLGIDYPSIHYSNAISSNTTESDKKYGASSEKMAAAYAAFANG---GTYYKPMYIHKV 239

Query: 95  LDHDIYTNQSQAIIWAIGPLNSKQEVSFHSVFPKKNIL-FNFGRTPYWNCPIPEGETGTP 153
               ++++ S+     +G    K+  ++      K +L +  GR  Y       G+TGT 
Sbjct: 240 ----VFSDGSEKEFSNVGTRAMKETTAYMMTDMMKTVLTYGTGRNAYLAWLPQAGKTGTS 295

Query: 154 NHGEYSDESSGANTKVQEVLG 174
           N   Y+DE    + K  + + 
Sbjct: 296 N---YTDEEIENHIKTSQFVA 313


>pdb|2ZC5|B Chain B, Penicillin-Binding Protein 1a (Pbp 1a) Acyl-Enzyme Complex
           (Biapenem) From Streptococcus Pneumoniae
 pdb|2ZC5|D Chain D, Penicillin-Binding Protein 1a (Pbp 1a) Acyl-Enzyme Complex
           (Biapenem) From Streptococcus Pneumoniae
 pdb|2ZC6|B Chain B, Penicillin-Binding Protein 1a (Pbp 1a) Acyl-Enzyme Complex
           (Tebipenem) From Streptococcus Pneumoniae
 pdb|2ZC6|D Chain D, Penicillin-Binding Protein 1a (Pbp 1a) Acyl-Enzyme Complex
           (Tebipenem) From Streptococcus Pneumoniae
          Length = 390

 Score = 28.5 bits (62), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 32/141 (22%), Positives = 58/141 (41%), Gaps = 11/141 (7%)

Query: 35  LNGYAVDYYLTDKSQCAGGRGSCPDYRIQDNTESVRLLNAALVNGYSIVTYQRPLRSHDI 94
           LNG  +DY     S       +  D +   ++E +    AA  NG    TY +P+  H +
Sbjct: 186 LNGLGIDYPSIHYSNAISSNTTESDKKYGASSEKMAAAYAAFANG---GTYYKPMYIHKV 242

Query: 95  LDHDIYTNQSQAIIWAIGPLNSKQEVSFHSVFPKKNIL-FNFGRTPYWNCPIPEGETGTP 153
               ++++ S+     +G    K+  ++      K +L +  G+  Y       G+TGT 
Sbjct: 243 ----VFSDGSEKEFSNVGTRAMKETTAYMMTDMMKTVLSYGTGQNAYLAWLPQAGKTGTS 298

Query: 154 NHGEYSDESSGANTKVQEVLG 174
           N   Y+DE    + K  + + 
Sbjct: 299 N---YTDEEIENHIKTSQFVA 316


  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
   0.316    0.137    0.440 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,064,322
Number of Sequences: 62578
Number of extensions: 669139
Number of successful extensions: 1209
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 1209
Number of HSP's gapped (non-prelim): 12
length of query: 383
length of database: 14,973,337
effective HSP length: 101
effective length of query: 282
effective length of database: 8,652,959
effective search space: 2440134438
effective search space used: 2440134438
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)