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= psy10418
         (389 letters)

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

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



>pdb|3EQV|A Chain A, Crystal Structure Of Penicillin-Binding Protein 2 From
           Neisseria Gonorrhoeae Containing Four Mutations
           Associated With Penicillin Resistance
 pdb|3EQV|B Chain B, Crystal Structure Of Penicillin-Binding Protein 2 From
           Neisseria Gonorrhoeae Containing Four Mutations
           Associated With Penicillin Resistance
          Length = 542

 Score = 32.7 bits (73), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 28/119 (23%), Positives = 49/119 (41%), Gaps = 12/119 (10%)

Query: 165 DVDNSDIPDLSNKAVYDLDDPNRPRFTTAELKEILHDRNTLKTRLNELEEERQCFKMVNR 224
           D    +I  L+N   YD   PNRP    +E +     RN   T + E     + F +   
Sbjct: 230 DARTGEILALANTPAYD---PNRPGRADSEQR-----RNRAVTDMIEPGSAIKPFVIAKA 281

Query: 225 LQEENKKLSKRLEHE----GSSPMKSQQLSPEIDISALQKLRGQVDSLRDQMRLKEKEL 279
           L      L++RL  +    G SP++   + P +D+  + +    V + +   R   +E+
Sbjct: 282 LDAGKTDLNERLNTQPYKIGPSPVRDTHVYPSLDVRGIMQKSSNVGTSKLSARFGAEEM 340


>pdb|3EQU|A Chain A, Crystal Structure Of Penicillin-Binding Protein 2 From
           Neisseria Gonorrhoeae
 pdb|3EQU|B Chain B, Crystal Structure Of Penicillin-Binding Protein 2 From
           Neisseria Gonorrhoeae
          Length = 542

 Score = 30.8 bits (68), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 28/118 (23%), Positives = 47/118 (39%), Gaps = 12/118 (10%)

Query: 165 DVDNSDIPDLSNKAVYDLDDPNRPRFTTAELKEILHDRNTLKTRLNELEEERQCFKMVNR 224
           D    +I  L+N   YD   PNRP    +E +     RN   T   E     + F +   
Sbjct: 230 DARTGEILALANTPAYD---PNRPGRADSEQR-----RNRAVTDXIEPGSAIKPFVIAKA 281

Query: 225 LQEENKKLSKRLEHE----GSSPMKSQQLSPEIDISALQKLRGQVDSLRDQMRLKEKE 278
           L      L++RL  +    G SP++   + P +D+  + +    V + +   R   +E
Sbjct: 282 LDAGKTDLNERLNTQPYKIGPSPVRDTHVYPSLDVRGIXQKSSNVGTSKLSARFGAEE 339


>pdb|2V71|A Chain A, Coiled-Coil Region Of Nudel
 pdb|2V71|B Chain B, Coiled-Coil Region Of Nudel
          Length = 189

 Score = 28.5 bits (62), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 35/133 (26%), Positives = 65/133 (48%), Gaps = 20/133 (15%)

Query: 224 RLQEENKKLSKRLEHEGSSPMKSQQLSPEIDISALQKLRGQVDSLRDQMRLKEKELGYRN 283
           RL+ E + L ++LEH+ +   K         +S L+    Q  ++++Q+    +EL   N
Sbjct: 67  RLKYEVEALKEKLEHQYAQSYKQ--------VSVLEDDLSQTRAIKEQLHKYVRELEQAN 118

Query: 284 SDVDNLKRQIDRLTSTVRELR-RKQRLSQVQVRGL-----IDERADFLAALQDHQREVAA 337
            D++  KR      +T+  L   +QRL+Q   R       +DE+   L ++Q  + E   
Sbjct: 119 DDLERAKR------ATIXSLEDFEQRLNQAIERNAFLESELDEKESLLVSVQRLKDEARD 172

Query: 338 LKQQLGLAEKENE 350
           L+Q+L + E++ E
Sbjct: 173 LRQELAVRERQQE 185


  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
   0.311    0.129    0.346 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,947,101
Number of Sequences: 62578
Number of extensions: 374261
Number of successful extensions: 1095
Number of sequences better than 100.0: 58
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 54
Number of HSP's that attempted gapping in prelim test: 1064
Number of HSP's gapped (non-prelim): 80
length of query: 389
length of database: 14,973,337
effective HSP length: 101
effective length of query: 288
effective length of database: 8,652,959
effective search space: 2492052192
effective search space used: 2492052192
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 52 (24.6 bits)