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= 0001.0329.p
         (417 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309698|ref|YP_003773790.1| type II secretion system protei...   532   e-152

>gi|300309698|ref|YP_003773790.1| type II secretion system protein
           [Herbaspirillum seropedicae SmR1]
          Length = 415

 Score =  532 bits (1370), Expect = e-152,   Method: Compositional matrix adjust.
 Identities = 312/418 (74%), Positives = 345/418 (82%), Gaps = 4/418 (0%)

Query: 1   LPAPERQPSTRPFRWEGLDRHGRPQRGLLQATDETQARAQLRRQGLRVARLRADVQAHAP 60
           +PAPER    R FRWEGLDRHGRPQRG+LQA D T AR  LRR G+RVARL+    A A 
Sbjct: 1   MPAPERSQGGR-FRWEGLDRHGRPQRGVLQARDATAARQALRRDGVRVARLQPADTAAAT 59

Query: 61  NHAGPRPRPLAKGRISDKQIALFTRQLATMLQAGLPLLQALDIAIRGSGQGAMAGLLTSV 120
              G   R   + RI+DKQI LFTRQLATMLQAGLPLLQALDIAIRG+G  A+ GLL ++
Sbjct: 60  PAPGISARR-GRRRITDKQIVLFTRQLATMLQAGLPLLQALDIAIRGAGADALGGLLATI 118

Query: 121 RQAVSRGDSLHAALAQHPRHFDALFCNLVRAAEDAGLLDTMLERIALYREKSLALKGKVR 180
           RQ V+RGDSLHAALA+HP+ FDALFC LVRAAE AG+LD+ML RIA YREKSLAL+GKVR
Sbjct: 119 RQDVARGDSLHAALARHPQRFDALFCQLVRAAESAGVLDSMLARIASYREKSLALRGKVR 178

Query: 181 AALAYPCAVVLVAIVVTVVIMLWVVPAFEQMFQQFGAELPLATRMVMSTARLLGQYGHLL 240
           AALAYPCAVVLVA+ VTVVIMLWVVPAFEQMF+ FGAELPL TR+VMS A  L Q     
Sbjct: 179 AALAYPCAVVLVAVAVTVVIMLWVVPAFEQMFRHFGAELPLPTRIVMSLAHALTQ-AWPW 237

Query: 241 LLSGIALAVLVR-QAWLRYPPMRRAAQRLSLSLPLFGPLLRQAALARWSRTFGALFGAGI 299
           LL G+A+AVL   QAW R+ P+ + AQRLSL LPL G LLRQAALARWSRTFG L GAGI
Sbjct: 238 LLPGLAIAVLAGLQAWRRWLPLGQHAQRLSLRLPLLGGLLRQAALARWSRTFGTLLGAGI 297

Query: 300 ALVEALETVAGAAGNVVYAEASLAVRDAVRNGASLHTAMQASGVFPDLAIQMTAVGEEAG 359
           ALV+ALETVAGAAGNVV  +ASLAVRDAVRNGASLH AMQA+GVFPDLA+QMTAVGEE G
Sbjct: 298 ALVQALETVAGAAGNVVIGQASLAVRDAVRNGASLHAAMQATGVFPDLAVQMTAVGEETG 357

Query: 360 ALDAMLGKIAELNEREVDDAVAALTSLMEPVIMAVLGVVIGGLVVAMYLPVFRMGALV 417
            LDAML KIAELNEREVDD V ALTSLMEP IM VLG+VIGGLV+A+YLPVFRMG++V
Sbjct: 358 TLDAMLIKIAELNEREVDDTVTALTSLMEPAIMTVLGLVIGGLVIALYLPVFRMGSVV 415


  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
   0.325    0.136    0.393 

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: 1,052,214
Number of extensions: 37287
Number of successful extensions: 229
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 225
Number of HSP's successfully gapped: 1
Length of query: 417
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 329
Effective length of database: 1,203,190
Effective search space: 395849510
Effective search space used: 395849510
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: 132 (55.5 bits)