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= 0001.2407.p
         (383 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310128|ref|YP_003774220.1| type III secretion system prote...   152   5e-38

>gi|300310128|ref|YP_003774220.1| type III secretion system protein
           [Herbaspirillum seropedicae SmR1]
          Length = 400

 Score =  152 bits (384), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 133/359 (37%), Positives = 174/359 (48%), Gaps = 25/359 (6%)

Query: 46  APKVSASLAALTRKVGRGLRMVLPPQQAELTLRLAPASPGTQAANAA--LLLSGAAGSVR 103
           AP + A  A L+R +GRG+R+ L      L    A A+  +  A  A  L L  A G + 
Sbjct: 46  APLIGAEQAQLSRLLGRGVRLALGRDDMALLALPASATAASAVAAMAPDLRLQTADGVLL 105

Query: 104 LDDGARWLRVLTGIDLTAALADASGQDCPDWLTAAVAAKLQGTPLC--RTSQIRRAPITS 161
           L  G R L  LTGID  AA   A G+  P WL AA+A +LQ T L    T Q   A   +
Sbjct: 106 LAQGERLLAGLTGID-PAASRHADGRFAP-WLAAALAGRLQQTALASLHTVQPCAAGDAA 163

Query: 162 EPQTCALEFSLHQDGHLMLGSFHATPQTWLRLLEECEVTALRAPEDDFLEIPWCQPVVLG 221
           +    AL   L    H +     A P  W   LE  E   ++ P   +  +P    V+L 
Sbjct: 164 QAGLVALRLRLRDPTHAIETLAWAAPSLWRCWLEAAE--PMQMPLSAWSGLPLSSTVLLA 221

Query: 222 WHRLGESACASLAAGDIILPSRPAFERSGMGRLNLAGRNWRVRYIAPGQLQLISSESGLD 281
            HRL      +L  GD++LP RP F+  G GR+ L  R WRVRYIA  +LQ+IS E+ L+
Sbjct: 222 THRLPSRVMEALRVGDLLLPERPLFDIHGHGRMTLGARQWRVRYIAHQRLQIISQENALN 281

Query: 282 MES---VEDLDLGAAPDSPA-------------GGRGQH-DDASAPLEELSLTLVFELGR 324
            ++       DL A PD  A             G  G+  +D      EL LTL  ELGR
Sbjct: 282 HDTDLAQSSADLDADPDDEAFHDADASAASAEEGDEGRDGEDGPDVAVELPLTLQVELGR 341

Query: 325 IALPLGTLRSLAPQSILALQSGHPGNIGIFCAGRRVGQGEVVDVEGALGIRIVHWGGTC 383
           ++L L  LR+L  Q +L L       + I  AG  +G+GEVV V+G LG+RIV W G C
Sbjct: 342 LSLSLSQLRALGEQVVLELHGASAQALRITSAGVELGRGEVVSVDGRLGVRIVRWSGAC 400


  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
   0.319    0.136    0.417 

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: 1,363,970
Number of extensions: 60728
Number of successful extensions: 200
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 197
Number of HSP's successfully gapped: 1
Length of query: 383
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 296
Effective length of database: 1,207,925
Effective search space: 357545800
Effective search space used: 357545800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 131 (55.1 bits)