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= 0001.2406.p
         (219 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310129|ref|YP_003774221.1| type III secretion HrcR transme...   360   e-101
gi|300311365|ref|YP_003775457.1| flagellar biosynthetic protein ...   119   3e-28

>gi|300310129|ref|YP_003774221.1| type III secretion HrcR
           transmembrane protein [Herbaspirillum seropedicae SmR1]
          Length = 220

 Score =  360 bits (925), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 178/220 (80%), Positives = 204/220 (92%), Gaps = 1/220 (0%)

Query: 1   MLNNQFDVVSFSILLALLALIPLLVVTTTSFLKISLVLLVLRNAIGVQQVPPTLAIYGIS 60
           ML+ QFDVVSFS+LLAL+AL+PL+VVTTTSFLKISLVLLVLRNAIGVQQVPPTLAIYGI+
Sbjct: 1   MLSGQFDVVSFSVLLALMALVPLMVVTTTSFLKISLVLLVLRNAIGVQQVPPTLAIYGIA 60

Query: 61  LALSVFIMAPTVQEIGVHALQMDSSQ-VSSRTTPLLVKAQESFEPLRKFMMKVSRPEQRE 119
           LALSVFIMAPTVQE+G  A+ +D S   +SRT P+L +AQ++F+PLRKFM+K+S  EQRE
Sbjct: 61  LALSVFIMAPTVQEVGKRAMAVDVSHPAASRTVPILERAQDAFDPLRKFMLKMSHAEQRE 120

Query: 120 LFLASARKLWPKDVAKEARPSDALVLIPAFVVSELQAGYEIGFLIYIPFVIIDLLISNLL 179
           +FLASA+KLWPK+ AK+A+P+DAL+LIPAFVVSELQ GYEIGFLIYIPFV+IDLLISNLL
Sbjct: 121 MFLASAKKLWPKEAAKDAQPTDALILIPAFVVSELQTGYEIGFLIYIPFVVIDLLISNLL 180

Query: 180 MALGMQQVSPQTITIPLKLLLFTLVAGWGKLLNALALSYV 219
           MALGMQQVSPQTITIPLKLLLFTLV GW KLLNALA+SYV
Sbjct: 181 MALGMQQVSPQTITIPLKLLLFTLVGGWAKLLNALAMSYV 220


>gi|300311365|ref|YP_003775457.1| flagellar biosynthetic protein
           FliP [Herbaspirillum seropedicae SmR1]
          Length = 244

 Score =  119 bits (297), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 74/209 (35%), Positives = 125/209 (59%), Gaps = 14/209 (6%)

Query: 13  ILLALLALIPLLVVTTTSFLKISLVLLVLRNAIGVQQVPPTLAIYGISLALSVFIMAPTV 72
           +LL  L+ +P  ++  T F +I +VL +LR A+G Q  PPT  + G+SL L+ F+M+P  
Sbjct: 46  LLLTSLSFLPAALLMMTCFTRIVIVLSLLRQALGTQSTPPTQVLVGLSLFLTFFVMSPVF 105

Query: 73  QEIGVHALQMDSSQVSSRTTPLLVKAQESFEPLRKFMMKVSRPEQRELFLASARK---LW 129
             I   A Q      +     ++    +  +PL++FM+K +R     L++  +R      
Sbjct: 106 DRIYTDAYQ----PFAENKIQMMEALDKGAQPLKEFMLKQTRESDLALYVKLSRGPALQG 161

Query: 130 PKDVAKEARPSDALVLIPAFVVSELQAGYEIGFLIYIPFVIIDLLISNLLMALGMQQVSP 189
           P+DV          +L+PAFV SEL+  ++IGF I++PF+IID++++++LM++GM  +SP
Sbjct: 162 PEDVPLR-------LLVPAFVTSELKTAFQIGFAIFLPFLIIDMVVASILMSMGMMMMSP 214

Query: 190 QTITIPLKLLLFTLVAGWGKLLNALALSY 218
             +++P KL+LF LV GW  L+ +LA S+
Sbjct: 215 ALVSLPFKLMLFVLVDGWQLLIGSLAQSF 243


  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
   0.326    0.139    0.386 

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: 529,184
Number of extensions: 18189
Number of successful extensions: 83
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 78
Number of HSP's successfully gapped: 2
Length of query: 219
Length of database: 1,619,870
Length adjustment: 82
Effective length of query: 137
Effective length of database: 1,231,600
Effective search space: 168729200
Effective search space used: 168729200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 128 (53.9 bits)