BLASTP 2.2.18 [Mar-02-2008]


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= 0490.0063.p
         (677 letters)

Database: COG 
           115,334 sequences; 38,378,431 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

STM0363 [K] COG2207 AraC-type DNA-binding domain-containing prot...   124   5e-28

>STM0363 [K] COG2207 AraC-type DNA-binding domain-containing proteins
          Length = 334

 Score =  124 bits (311), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 0/353 (0%), Positives = 0/353 (0%), Gaps = 21/353 (5%)

Query: 322 EMASLWQAFDT-----VLEPVRKCRFSPMSGANAKGK-PV-FSAIPLTLPDDHVKHYSSI 374
              +L           +       R   +     +                         
Sbjct: 202 LGYALNLCQPATQKRGLPVTGEYQRLELIRRLLEQTPEKAYTLNELARRAAMSPSSLRCK 261

Query: 375 SSCLEDYYGDKAERDTVKQRVSDLIRFLSNERSKNVKKLA-NLQKDLDEAQDADQFRIWG 433
                        RD    R    +    +   +           +   A         G
Sbjct: 262 FRHAYGCTVFDYLRDCRLARARRYLMEGYS-VQQAAWMSGYQHATNFATAFRRRYGCSPG 320

Query: 434 ELLFASLHAVSKGDKQARLVNYYDEDQAEITIPLDPLLSPSDNAQRYFKKYNKYKNSLLV 493
                                                                       
Sbjct: 321 ----                                                         376

Query: 494 INEQLLKTHEEIAYIETLLQQLAHASLNDIEEIRDELVSQ-GYLRDRSXXXXXXXXAARP 552
                                                                       
Sbjct: 377 --                                                           434

Query: 553 TLQVFTSSEGIDIYVGKNNLQNEYVTNRLASANDTWLHTKDIPGSHVVIRSE--TFGDAT 610
                                                                       
Sbjct: 435 ---                                                          491

Query: 611 LEEAAQLAAYFSQAKQSSSVPVDCTLIRHVRKPSGAKPGFVIYDHQKTLFVTP 663
                                                                
Sbjct: 492                                                       544



 Score = 70.5 bits (171), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 10/165 (6%), Positives = 29/165 (17%), Gaps = 9/165 (5%)

Query: 38  MALDGIVTRAIVHELQPFIGARIGKIYQPSTHDXXXXXXXXXXXXXXXXXANPTYPRVHL 97
           M+     + A     + F  +      +    D                          +
Sbjct: 1   MSPISCHSSAAPAMKKIFSVSDFIAFGERYGIDYRFPALPQYTQSS----PVLHGDIEEI 56

Query: 98  TDRNSINPPEAPMFCMLMRKHCEGGTIDSISQVGMERIIHIQVRTRDELGDVSAKKIIIE 157
                I    + +  +   +     +      V +E  + + V  +  L           
Sbjct: 57  ALPGGICITRSDVHVLQPYETTSRHSSPLYMLVVLEGNVALAVNEQTFLLSAGMAFCSQL 116

Query: 158 LMGRHSNIILTELATGIIIDGIHHVTPTISSYRNVMPGIAYIEPP 202
              +         A   +      +                +   
Sbjct: 117 SEQQTIRAHH--GADSKLRTLSLGM---YPDGGWRERLPVSLADE 156


  Database: COG
    Posted date:  Aug 3, 2010  9:58 AM
  Number of letters in database: 38,378,431
  Number of sequences in database:  115,334
  
Lambda     K      H
   0.318    0.135    0.396 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 115334
Number of Hits to DB: 45,048,904
Number of extensions: 1742069
Number of successful extensions: 2845
Number of sequences better than 1.0e-05: 1
Number of HSP's gapped: 2840
Number of HSP's successfully gapped: 2
Length of query: 677
Length of database: 38,378,431
Length adjustment: 113
Effective length of query: 564
Effective length of database: 25,345,689
Effective search space: 14294968596
Effective search space used: 14294968596
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 119 (50.4 bits)