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= 006986
         (622 letters)

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

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



>pdb|3C5H|A Chain A, Crystal Structure Of The Ras Homolog Domain Of Human Grlf1
           (P190rhogap)
          Length = 255

 Score = 35.0 bits (79), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 30/97 (30%), Positives = 44/97 (45%), Gaps = 8/97 (8%)

Query: 401 KSPAASLLATGDRLREFA-GSLSLNLEFEPILIPIRKLRASSFRVDPNEALVVNFMLQLN 459
           K  AA+ LA+ ++L  F    L L  +FE   +P  KL    F       L ++    +N
Sbjct: 124 KRAAATKLASAEKLMYFCTDQLGLEQDFEQKQMPDGKLLVDGF------LLGIDVSRGMN 177

Query: 460 SLLDDNRLAVENAL-QMAKSLNPIVVTLAEYEANLNR 495
              DD    V N   Q+AK+  PIVV L + +  + R
Sbjct: 178 RNFDDQLKFVSNLYNQLAKTKKPIVVVLTKCDEGVER 214


>pdb|4G0H|A Chain A, Crystal Structure Of The N-Terminal Domain Of Helicobacter
           Pylori Caga Protein
          Length = 916

 Score = 30.4 bits (67), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 31/63 (49%)

Query: 372 SFLLQALANRPTGKPVKVRISGIPAPALGKSPAASLLATGDRLREFAGSLSLNLEFEPIL 431
           S L Q++ N      V   +SGI A AL K+ +       ++ + F G L+  LE +PI 
Sbjct: 839 SELYQSVKNSVNKTLVGNGLSGIEATALAKNFSDIKKELNEKFKNFKGELNSKLEGKPIP 898

Query: 432 IPI 434
            P+
Sbjct: 899 NPL 901


>pdb|4GME|A Chain A, Crystal Structure Of Mannonate Dehydratase (Target
           Efi-502209) From Caulobacter Crescentus Cb15 Complexed
           With Magnesium And D-Mannonate
 pdb|4GME|C Chain C, Crystal Structure Of Mannonate Dehydratase (Target
           Efi-502209) From Caulobacter Crescentus Cb15 Complexed
           With Magnesium And D-Mannonate
          Length = 426

 Score = 30.0 bits (66), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 543 LAPEKQGAKRERVEDIENWRIFMENSDFEGIPFSHYALSQAEILLWN 589
           + P   G    ++EDI  W+ F   S + G P +  AL+  ++ LW+
Sbjct: 75  MVPSLIGRDAHQIEDI--WQFFYRGSYWRGGPVAMTALAAVDMALWD 119


>pdb|3VCN|A Chain A, Crystal Structure Of Mannonate Dehydratase (Target
           Efi-502209) From Caulobacter Crescentus Cb15
 pdb|3VCN|C Chain C, Crystal Structure Of Mannonate Dehydratase (Target
           Efi-502209) From Caulobacter Crescentus Cb15
          Length = 425

 Score = 30.0 bits (66), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 543 LAPEKQGAKRERVEDIENWRIFMENSDFEGIPFSHYALSQAEILLWN 589
           + P   G    ++EDI  W+ F   S + G P +  AL+  ++ LW+
Sbjct: 74  MVPSLIGRDAHQIEDI--WQFFYRGSYWRGGPVAMTALAAVDMALWD 118


  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
   0.318    0.133    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,157,192
Number of Sequences: 62578
Number of extensions: 550435
Number of successful extensions: 1188
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1187
Number of HSP's gapped (non-prelim): 6
length of query: 622
length of database: 14,973,337
effective HSP length: 105
effective length of query: 517
effective length of database: 8,402,647
effective search space: 4344168499
effective search space used: 4344168499
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)