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= 016409
         (390 letters)

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

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



>pdb|2RBC|A Chain A, Crystal Structure Of A Putative Ribokinase From
           Agrobacterium Tumefaciens
          Length = 343

 Score = 30.8 bits (68), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 2/46 (4%)

Query: 313 PDQMRVVDAVIRDMHSPAYLLDITMLSELRKDGHPSIYSGDLNPKQ 358
           P+ + + DAV+ D+  P   LD+  L+  R  G P+I  GD+ P +
Sbjct: 152 PEDIALFDAVLVDVRWPELALDV--LTVARALGKPAILDGDVAPVE 195


>pdb|2QHK|A Chain A, Crystal Structure Of Methyl-Accepting Chemotaxis Protein
           From Vibrio Parahaemolyticus Rimd 2210633
          Length = 174

 Score = 30.4 bits (67), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 13/29 (44%), Positives = 19/29 (65%)

Query: 225 LQGWDYMESMGTYYQDMDRLVALEKGLRT 253
           LQ WD++   G Y  D+D+ VA ++ LRT
Sbjct: 138 LQKWDWVLGTGIYIDDIDQQVAXQRELRT 166


>pdb|2PNT|A Chain A, Crystal Structure Of The Pdz Domain Of Human Grasp (Grp1)
           In Complex With The C-Terminal Peptide Of The
           Metabotropic Glutamate Receptor Type 1
 pdb|2PNT|B Chain B, Crystal Structure Of The Pdz Domain Of Human Grasp (Grp1)
           In Complex With The C-Terminal Peptide Of The
           Metabotropic Glutamate Receptor Type 1
          Length = 98

 Score = 28.9 bits (63), Expect = 5.5,   Method: Composition-based stats.
 Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 12/89 (13%)

Query: 117 LVKMKGKTVMFVGDSLGLNQWE-------SLICMIHAAAPRTRTHMTRGDPLSTFKFLDY 169
           L K   +T  F   + GL+  E       + +C +H ++P     +T GD +++      
Sbjct: 10  LEKEDNQTFGFEIQTYGLHHREEQRVEMVTFVCRVHESSPAQLAGLTPGDTIASVN---- 65

Query: 170 GISVSFYRAPYLVDIDVVHGKRVLKLEDI 198
           G++V   R   +VDI    G  VL+LE +
Sbjct: 66  GLNVEGIRHREIVDIIKASGN-VLRLETL 93


>pdb|3F1S|B Chain B, Crystal Structure Of Protein Z Complexed With Protein
           Z-Dependent Inhibitor
          Length = 283

 Score = 28.9 bits (63), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 9/19 (47%), Positives = 14/19 (73%)

Query: 357 KQKANPDRSADCSHWCLPG 375
           K + +P+R+  C H+CLPG
Sbjct: 2   KNECHPERTDGCQHFCLPG 20


>pdb|3H5C|B Chain B, X-Ray Structure Of Protein Z-Protein Z Inhibitor Complex
          Length = 317

 Score = 28.5 bits (62), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 9/19 (47%), Positives = 14/19 (73%)

Query: 357 KQKANPDRSADCSHWCLPG 375
           K + +P+R+  C H+CLPG
Sbjct: 43  KNECHPERTDGCQHFCLPG 61


>pdb|2HZL|A Chain A, Crystal Structures Of A Sodium-Alpha-Keto Acid Binding
           Subunit From A Trap Transporter In Its Closed Forms
 pdb|2HZL|B Chain B, Crystal Structures Of A Sodium-Alpha-Keto Acid Binding
           Subunit From A Trap Transporter In Its Closed Forms
          Length = 365

 Score = 28.1 bits (61), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 6/62 (9%)

Query: 231 MESMGTYYQDM---DRLVALEKGLRTWANWVDNNIDRSKTRVFFQSISPTHYNPSEWSAG 287
           ME +G   Q +   D   ALEKG      WV    D    ++ F  ++P +Y P  W  G
Sbjct: 186 MERLGVVPQQIAGGDIYPALEKGTIDATEWVGPYDDE---KLGFFKVAPYYYYPGWWEGG 242

Query: 288 ST 289
            T
Sbjct: 243 PT 244


  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
   0.321    0.136    0.441 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,642,036
Number of Sequences: 62578
Number of extensions: 549117
Number of successful extensions: 1110
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1106
Number of HSP's gapped (non-prelim): 8
length of query: 390
length of database: 14,973,337
effective HSP length: 101
effective length of query: 289
effective length of database: 8,652,959
effective search space: 2500705151
effective search space used: 2500705151
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)