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= 028049
         (214 letters)

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

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



>pdb|1GC5|A Chain A, Crystal Structure Of A Novel Adp-Dependent Glucokinase
           From Thermococcus Litoralis
          Length = 467

 Score = 30.0 bits (66), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 7/69 (10%)

Query: 139 CSNVKDLTWLVFAPNLKCLRILDCDDMEEIISVENFEKLIEVSEMMGEL-----NLFSG- 192
             NVK +  L +  N+  ++ LD DD+E+ ++ +  EK+ E+ E   E       L  G 
Sbjct: 27  IPNVKGVL-LAYNTNIDAIKYLDADDLEKRVTEKGKEKVFEIIENPPEKISSIEELLGGI 85

Query: 193 LESLSLGNA 201
           L S+ LG A
Sbjct: 86  LRSIKLGKA 94


>pdb|2W57|A Chain A, Crystal Structure Of The Vibrio Cholerae Ferric Uptake
           Regulator (Fur) Reveals Structural Rearrangement Of The
           Dna-Binding Domains
 pdb|2W57|B Chain B, Crystal Structure Of The Vibrio Cholerae Ferric Uptake
           Regulator (Fur) Reveals Structural Rearrangement Of The
           Dna-Binding Domains
          Length = 150

 Score = 27.3 bits (59), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 16/53 (30%), Positives = 28/53 (52%)

Query: 138 NCSNVKDLTWLVFAPNLKCLRILDCDDMEEIISVENFEKLIEVSEMMGELNLF 190
           N   +KD    V  P LK L +L   + + I + E ++KLI++ E +G   ++
Sbjct: 4   NNQALKDAGLKVTLPRLKILEVLQQPECQHISAEELYKKLIDLGEEIGLATVY 56


>pdb|1BKD|S Chain S, Complex Of Human H-Ras With Human Sos-1
          Length = 477

 Score = 27.3 bits (59), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 33/49 (67%), Gaps = 5/49 (10%)

Query: 155 KCLRILDCDDMEEIISVENFEKLIEVSEMMGELNLFSG-LESLSLGNAS 202
           KC  I++ +++EE ++V    ++IE+ ++  ELN F+G LE +S  N+S
Sbjct: 270 KC--IVETENLEERVAV--VSRIIEILQVFQELNNFNGVLEVVSAMNSS 314


>pdb|1NVU|S Chain S, Structural Evidence For Feedback Activation By Rasgtp Of
           The Ras-Specific Nucleotide Exchange Factor Sos
 pdb|1NVV|S Chain S, Structural Evidence For Feedback Activation By Rasgtp Of
           The Ras-specific Nucleotide Exchange Factor Sos
 pdb|1NVW|S Chain S, Structural Evidence For Feedback Activation By Rasgtp Of
           The Ras-specific Nucleotide Exchange Factor Sos
 pdb|1NVX|S Chain S, Structural Evidence For Feedback Activation By Rasgtp Of
           The Ras-Specific Nucleotide Exchange Factor Sos
          Length = 481

 Score = 27.3 bits (59), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 33/49 (67%), Gaps = 5/49 (10%)

Query: 155 KCLRILDCDDMEEIISVENFEKLIEVSEMMGELNLFSG-LESLSLGNAS 202
           KC  I++ +++EE ++V    ++IE+ ++  ELN F+G LE +S  N+S
Sbjct: 272 KC--IVETENLEERVAV--VSRIIEILQVFQELNNFNGVLEVVSAMNSS 316


>pdb|1XD2|C Chain C, Crystal Structure Of A Ternary Ras:sos:ras*gdp Complex
          Length = 484

 Score = 27.3 bits (59), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 33/49 (67%), Gaps = 5/49 (10%)

Query: 155 KCLRILDCDDMEEIISVENFEKLIEVSEMMGELNLFSG-LESLSLGNAS 202
           KC  I++ +++EE ++V    ++IE+ ++  ELN F+G LE +S  N+S
Sbjct: 272 KC--IVETENLEERVAV--VSRIIEILQVFQELNNFNGVLEVVSAMNSS 316


>pdb|2II0|A Chain A, Crystal Structure Of Catalytic Domain Of Son Of Sevenless
           (Rem-Cdc25) In The Absence Of Ras
          Length = 490

 Score = 27.3 bits (59), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 33/49 (67%), Gaps = 5/49 (10%)

Query: 155 KCLRILDCDDMEEIISVENFEKLIEVSEMMGELNLFSG-LESLSLGNAS 202
           KC  I++ +++EE ++V    ++IE+ ++  ELN F+G LE +S  N+S
Sbjct: 278 KC--IVETENLEERVAV--VSRIIEILQVFQELNNFNGVLEVVSAMNSS 322


  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
   0.320    0.135    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,872,087
Number of Sequences: 62578
Number of extensions: 220521
Number of successful extensions: 503
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 499
Number of HSP's gapped (non-prelim): 25
length of query: 214
length of database: 14,973,337
effective HSP length: 95
effective length of query: 119
effective length of database: 9,028,427
effective search space: 1074382813
effective search space used: 1074382813
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)