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= 028945
         (201 letters)

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

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



>pdb|3VKW|A Chain A, Crystal Structure Of The Superfamily 1 Helicase From
           Tomato Mosaic Virus
          Length = 446

 Score = 30.4 bits (67), Expect = 0.60,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 70  KLQVDRLALEQPSAECVADILHMVDQESLGLQNHLLNEDYSLAQEALVQSKLDITPTQER 129
           KL+VD +   + +  C AD+ H ++Q   G      +E  S++QE +V     I P  + 
Sbjct: 289 KLEVDEVETRRTTLRCPADVTHFLNQRYEGHVMCTSSEKKSVSQE-MVSGAASINPVSKP 347

Query: 130 SFFR-MGLSYGDAFASRMRGYMD 151
              + +  +  D  A   RGY D
Sbjct: 348 LKGKILTFTQSDKEALLSRGYAD 370


>pdb|3IPL|A Chain A, Crystal Structure Of O-Succinylbenzoic Acid-Coa Ligase
           From Staphylococcus Aureus Subsp. Aureus Mu50
 pdb|3IPL|B Chain B, Crystal Structure Of O-Succinylbenzoic Acid-Coa Ligase
           From Staphylococcus Aureus Subsp. Aureus Mu50
 pdb|3IPL|C Chain C, Crystal Structure Of O-Succinylbenzoic Acid-Coa Ligase
           From Staphylococcus Aureus Subsp. Aureus Mu50
          Length = 501

 Score = 28.5 bits (62), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 16/36 (44%), Positives = 19/36 (52%), Gaps = 3/36 (8%)

Query: 143 ASRMRGYMDPTELMGFAARGLFMNGRTTDIAAIVRE 178
           A+ M GY+ PT+L G    G F  G   DIA I  E
Sbjct: 356 ANVMNGYLYPTDLTGTFENGYFNTG---DIAEIDHE 388


>pdb|1OEN|A Chain A, Phosphoenolpyruvate Carboxykinase
          Length = 540

 Score = 28.5 bits (62), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 33/131 (25%), Positives = 48/131 (36%), Gaps = 19/131 (14%)

Query: 25  KTVTVLIGDPIEFDDLVDEEQTKYLSRGKLYDAV---ASRIGHRLKKLKLQVDRLALEQP 81
           + VTV  G  I+FDD    E T+        D +    S+ GH  K + L  D   +  P
Sbjct: 311 ENVTVRAGGTIDFDDGSKTENTRVSYPIYHIDNIVKPVSKAGHATKVIFLTADAFGVLPP 370

Query: 82  SAECVADILHMVDQESLGLQNHLLNEDYSLAQEALVQSKLDITPTQERSFFRMGLS---- 137
            +   AD            Q H L+  ++ A     +   + TPT    F    LS    
Sbjct: 371 VSRLTAD----------QTQYHFLS-GFTAAAAGTERGITEPTPTFSACFGAAFLSLHPT 419

Query: 138 -YGDAFASRMR 147
            Y +    RM+
Sbjct: 420 QYAEVLVKRMQ 430


>pdb|2GRY|A Chain A, Crystal Structure Of The Human Kif2 Motor Domain In
           Complex With Adp
          Length = 420

 Score = 27.3 bits (59), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 14/44 (31%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 52  GKLYDAVASRIGHR-LKKLKLQVDRLALEQPSAECVADILHMVD 94
           GK++D +  +   R L+  K QV  + L++   +CV D+L ++D
Sbjct: 239 GKVFDLLNRKTKLRVLEDGKQQVQVVGLQEREVKCVEDVLKLID 282


>pdb|3MR7|A Chain A, Crystal Structure Of AdenylateGUANYLATE CYCLASEHYDROLASE
           FROM Silicibacter Pomeroyi
 pdb|3MR7|B Chain B, Crystal Structure Of AdenylateGUANYLATE CYCLASEHYDROLASE
           FROM Silicibacter Pomeroyi
 pdb|3MR7|C Chain C, Crystal Structure Of AdenylateGUANYLATE CYCLASEHYDROLASE
           FROM Silicibacter Pomeroyi
          Length = 189

 Score = 27.3 bits (59), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 13/32 (40%), Positives = 19/32 (59%), Gaps = 7/32 (21%)

Query: 77  ALEQPSAECVADILHMVDQE-------SLGLQ 101
           A+ +P A CV+DI+H + Q+        LGLQ
Sbjct: 125 AISEPGAICVSDIVHQITQDRVSEPFTDLGLQ 156


>pdb|1X9X|A Chain A, Solution Structure Of Dimeric Sam Domain From Mapkkk
          Ste11
 pdb|1X9X|B Chain B, Solution Structure Of Dimeric Sam Domain From Mapkkk
          Ste11
          Length = 68

 Score = 26.9 bits (58), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 14/32 (43%), Positives = 20/32 (62%)

Query: 39 DLVDEEQTKYLSRGKLYDAVASRIGHRLKKLK 70
          +LV EE+ KYL +  L     ++IG RLK L+
Sbjct: 30 NLVTEEEIKYLDKDILIALGVNKIGDRLKILR 61


  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
   0.322    0.137    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,740,116
Number of Sequences: 62578
Number of extensions: 213619
Number of successful extensions: 552
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 542
Number of HSP's gapped (non-prelim): 15
length of query: 201
length of database: 14,973,337
effective HSP length: 94
effective length of query: 107
effective length of database: 9,091,005
effective search space: 972737535
effective search space used: 972737535
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: 49 (23.5 bits)