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= 0231.0011.p
         (406 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310549|ref|YP_003774641.1| periplasmic component of the To...   565   e-162

>gi|300310549|ref|YP_003774641.1| periplasmic component of the Tol
           biopolymer transport system protein [Herbaspirillum
           seropedicae SmR1]
          Length = 428

 Score =  565 bits (1457), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 271/316 (85%), Positives = 298/316 (94%)

Query: 58  ISGVGASQIPVAIAAFPGEEGAPQQITSIVKADLARSGVFKLIDNSDSLSDASAINYGDW 117
           I+GVGASQIP+AI AFPGEE APQQITS+VKADLARSGVFKLIDN D+LSD+SA+NY DW
Sbjct: 34  ITGVGASQIPIAITAFPGEESAPQQITSVVKADLARSGVFKLIDNGDALSDSSAVNYADW 93

Query: 118 KNRGANALAVGSVQRLADGRFDVRYRLFDTIKAAQLSALSFGSQPQLMRLTAHKIADDIY 177
           + RGANALAVGSV RLADGRFDVRYRLFDT++++QLSALS G+QPQL+RLTAHKIADDIY
Sbjct: 94  QKRGANALAVGSVTRLADGRFDVRYRLFDTVQSSQLSALSIGAQPQLLRLTAHKIADDIY 153

Query: 178 EKLTGIPGIFSTRIAYVTRSGKEYRLEVADADGEGVQVALRSNEPIISPSWSPDGGKVAY 237
           +KLTGIPGIFSTRI+YVT+SG EYRLEVADADGEG QVALRSNEPIISPSWSPDG KVAY
Sbjct: 154 QKLTGIPGIFSTRISYVTKSGGEYRLEVADADGEGTQVALRSNEPIISPSWSPDGTKVAY 213

Query: 238 VSFEAKKPVIYIQNLVTRQRTLVANFKGSNSAPAWAPDGQRLAVALTRDGLTQVYVINAD 297
           VSFE KKPV+YIQNLVTRQR++VANFKGSNSAPAW+PDG RLAVALTRDGLTQVYVINAD
Sbjct: 214 VSFEMKKPVVYIQNLVTRQRSIVANFKGSNSAPAWSPDGSRLAVALTRDGLTQVYVINAD 273

Query: 298 GSGLRRLTNTAGIDTEPRFSPDGNYVYFTSDRSGGPQIYKVSPNGGDAQRVTFSGSYNIS 357
           GSGLRRLTN+AGIDTEP+FSPDG  +YFTSDRSGGPQ+YKV  +GG  QRVTF+GSYNIS
Sbjct: 274 GSGLRRLTNSAGIDTEPQFSPDGGSIYFTSDRSGGPQVYKVGLDGGSPQRVTFNGSYNIS 333

Query: 358 PRISPDGKTLAYISRR 373
           PRISPDGKTLA+ISRR
Sbjct: 334 PRISPDGKTLAFISRR 349



 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 50/159 (31%), Positives = 80/159 (50%), Gaps = 8/159 (5%)

Query: 194 VTRSGKEYRLEVADADGEGVQVALRSNEPIISPSWSPDGGKVAYVSFEAKKPVIYIQNL- 252
           +TR G   ++ V +ADG G++    S      P +SPDGG + + S  +  P +Y   L 
Sbjct: 259 LTRDGLT-QVYVINADGSGLRRLTNSAGIDTEPQFSPDGGSIYFTSDRSGGPQVYKVGLD 317

Query: 253 -VTRQRTLVANFKGS-NSAPAWAPDGQRLAVALTRDGLTQVYVINADGSGLRRLTNTAGI 310
             + QR     F GS N +P  +PDG+ LA    RDG  Q+Y ++       RL++ +  
Sbjct: 318 GGSPQRV---TFNGSYNISPRISPDGKTLAFISRRDGQFQLYALDLTNGQEIRLSDGSR- 373

Query: 311 DTEPRFSPDGNYVYFTSDRSGGPQIYKVSPNGGDAQRVT 349
           D  P F+P+G Y+ + ++      +  VS +G   QR+T
Sbjct: 374 DQSPSFAPNGKYIMYATEAGRRGSLAVVSVDGRIKQRLT 412


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.318    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 1,248,570
Number of extensions: 51929
Number of successful extensions: 153
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 148
Number of HSP's successfully gapped: 4
Length of query: 406
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 319
Effective length of database: 1,207,925
Effective search space: 385328075
Effective search space used: 385328075
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: 132 (55.5 bits)