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= 0037.0001.p
         (309 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

PA1735 [R] COG0679 Predicted permeases                                 51   2e-06

>PA1735 [R] COG0679 Predicted permeases
          Length = 295

 Score = 51.2 bits (121), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 64/262 (24%), Positives = 106/262 (40%), Gaps = 19/262 (7%)

Query: 46  SPAIILDTLATAEI---SFGDVYKTLAFSXXXXXXXXXXXXXXGRVLKLAPAEAAGLTLI 102
           SP +IL TLA   +   SFG +    A                GR       E   L   
Sbjct: 43  SPCLILATLAHTRVDLHSFGRMALASALICVCMAALGWAAARLGR------QEWQVLVPA 96

Query: 103 STFTNSVNYGLPLVLLAFGQLGLDKASVYVIAQMVIVNTIGVYFAARSQFSAGSAVRSVF 162
            +F N  N GLP+ L AFG+ G+  A  + +   +   ++GV++      S   + RS+ 
Sbjct: 97  YSFPNVGNMGLPVCLYAFGEAGMTLAVAFYLIMSIGNFSLGVFW-----MSGERSWRSLL 151

Query: 163 SXXXXXXXXXXXXXXXXXXHMPQEIASGVSMVAGAYSPVVLAILGVQMVRVQTAQVARNV 222
                               +P+ +A+ V ++AG   P++L  LGV +  ++  Q+    
Sbjct: 152 GNPILLSVLLALLLMGLDLQLPRWMANTVDLMAGLTIPLMLITLGVSLASIRPRQLGNGF 211

Query: 223 QLAFWTGMSVRXXXXXXXXXXXXXXXNISGTLFAVLLILASMPVAVNSVVLAERFGSSPA 282
                    +R                +      VL++ +SMPVAV + + A R   SP 
Sbjct: 212 FYG-----GLRLLLGALVGWSVALALQLPPLAQGVLVVQSSMPVAVFNYLYALRGNRSPD 266

Query: 283 LVSRCILWTTLASFLVLPILIS 304
            V+  +L +TL SF  +P+L++
Sbjct: 267 QVASLVLCSTLLSFAFIPLLLT 288


  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
   0.325    0.137    0.380 

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: 16,220,973
Number of extensions: 528278
Number of successful extensions: 1500
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 1500
Number of HSP's successfully gapped: 3
Length of query: 309
Length of database: 38,378,431
Length adjustment: 106
Effective length of query: 203
Effective length of database: 26,153,027
Effective search space: 5309064481
Effective search space used: 5309064481
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 116 (49.3 bits)