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= 0001.2403.p
         (366 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310132|ref|YP_003774224.1| type III secretion HrcU transme...   504   e-144
gi|300311341|ref|YP_003775433.1| flagellar biosynthesis FlhB tra...   162   4e-41

>gi|300310132|ref|YP_003774224.1| type III secretion HrcU
           transmembrane protein [Herbaspirillum seropedicae SmR1]
          Length = 371

 Score =  504 bits (1299), Expect = e-144,   Method: Compositional matrix adjust.
 Identities = 240/363 (66%), Positives = 286/363 (78%)

Query: 1   MSEEKNEEPTHKKIEDARKKGQIAVSRDLARLAMLVVVAELAMATESLWRGAISNLMEAG 60
           MS++KNEEPT KKIEDA+KKGQIAVSRDLARL  LV V E A+A +SLWRGA+ NLME G
Sbjct: 1   MSDDKNEEPTDKKIEDAKKKGQIAVSRDLARLVTLVAVMEAALAADSLWRGAVFNLMEGG 60

Query: 61  IHGVGQDFIPVAMTILSSAGIFVAIVIAICFVVCIVIGVAAHWGQFGMLVATEALTPKFD 120
           + GVGQDF       L++A I +A+      V+C +  V  HWGQFGML+ATEAL PK D
Sbjct: 61  VLGVGQDFQTAMNNQLTAALILLAVAFFAVLVICPLAAVVGHWGQFGMLIATEALEPKLD 120

Query: 121 KLNPVNGLKQIISKKKLVELMTTVGKALLIGWIVYVLVRGNLANIVSLSSGDPKDSYYGF 180
           KLNPVNG+KQI SKKKLVEL  TVGKA LI  ++Y  +   L  I +L+ G+PKD Y  F
Sbjct: 121 KLNPVNGIKQIFSKKKLVELFITVGKAALIAGMMYSAIHSQLGAIFTLAGGEPKDVYEAF 180

Query: 181 LTILRAIFHVIIVVCLCIGLVDFAIQKYFHKKELMMDKEEVKREHKESEGDPLIKGQRKR 240
           +T+LR IFH+IIVVCL +G++D+A+QKYFHKK+LMMD+EE+KRE KESEGDP++KGQRK+
Sbjct: 181 VTLLRNIFHLIIVVCLVLGVIDYAVQKYFHKKDLMMDQEEIKREFKESEGDPMVKGQRKQ 240

Query: 241 LARQWANEAPVAKTANANAVVVNPTHFAVALYYDATQEMVPQLLAKGKNETARAMIRRAR 300
           LARQWANEAP AKT  ANAVVVNPTHFAVA++YDA + MVP +LAKG++E A+AMI RA 
Sbjct: 241 LARQWANEAPAAKTEKANAVVVNPTHFAVAMFYDADEAMVPLVLAKGRDEIAQAMIARAH 300

Query: 301 ECGIPVIRHVWLARHLYANCDEDALIPRESYEAVAHVYAVVHELVASEQTDRHVELESQG 360
            CGIPVIRHVWLAR LYA C +D  +PR SY+AVA VYAVVHELVAS +  R VELES G
Sbjct: 301 ACGIPVIRHVWLARTLYATCQDDMPVPRSSYQAVAQVYAVVHELVASGEVQREVELESLG 360

Query: 361 IRP 363
             P
Sbjct: 361 EPP 363


>gi|300311341|ref|YP_003775433.1| flagellar biosynthesis FlhB
           transmembrane protein [Herbaspirillum seropedicae SmR1]
          Length = 391

 Score =  162 bits (410), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 124/373 (33%), Positives = 184/373 (49%), Gaps = 28/373 (7%)

Query: 4   EKNEEPTHKKIEDARKKGQIAVSRDLARLAMLVVVAELAMATESLWRGAISNLMEAGIHG 63
           E+ E  T K+IE AR++G +  SR+LA   +L+V          +W       M +G   
Sbjct: 8   ERTEPATGKRIERAREQGDVPRSRELATCLVLLV------GGSCVW-------MFSGPVV 54

Query: 64  VGQDFIPVAMTILSSAGIFVAIVI-----AICFVVCIVI----------GVAAHWGQFGM 108
              D I VAM  L  A I+  +V+     A C  V I +           +AA     G 
Sbjct: 55  TSLDRIMVAMMSLERAAIYDPVVLMNLISARCLDVAIAVIPLAFLMTLAAMAAPLTLGGW 114

Query: 109 LVATEALTPKFDKLNPVNGLKQIISKKKLVELMTTVGKALLIGWIVYVLVRGNLANIVSL 168
           L    +L PKF KLNP++G   + S   LVEL   V K LL+G + +V +R  L  ++ L
Sbjct: 115 LFNVSSLAPKFSKLNPISGFANMFSVNSLVELGKAVLKTLLVGTVAWVTIRSQLDAVMGL 174

Query: 169 SSGDPKDSYYGFLTILRAIFHVIIVVCLCIGLVDFAIQKYFHKKELMMDKEEVKREHKES 228
                K +      +L   F  ++   + I ++D   Q + + ++L M +EEVK+EHKES
Sbjct: 175 GVESLKTAGAHAAQLLWISFITMVSALIFIAVLDVPYQLWNYGRKLRMTREEVKQEHKES 234

Query: 229 EGDPLIKGQRKRLARQWANEAPVAKTANANAVVVNPTHFAVALYYDATQEMVPQLLAKGK 288
           EGDP IKG+ + + R  A    +A+   A+ VV NPTH+AVAL Y   +   P+++AKG 
Sbjct: 235 EGDPHIKGKIRAMQRAMARRRMMAEVPTADVVVTNPTHYAVALKYSEGKMGAPKVVAKGS 294

Query: 289 NETARAMIRRARECGIPVIRHVWLARHLYANCDEDALIPRESYEAVAHVYAVVHELVASE 348
           +E A  +   ARE  +P++    LAR L+ + +    IP   Y AVA V A V +L    
Sbjct: 295 DEIAAKIRELAREHRVPLLEAPPLARALHTHTEIGDEIPEALYTAVAEVLAYVFQLRTYG 354

Query: 349 QTDRHVELESQGI 361
           Q      +E  G+
Sbjct: 355 QFGGTRPVEPTGL 367


  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
   0.322    0.135    0.395 

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: 841,291
Number of extensions: 24793
Number of successful extensions: 84
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 84
Number of HSP's successfully gapped: 2
Length of query: 366
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 280
Effective length of database: 1,212,660
Effective search space: 339544800
Effective search space used: 339544800
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 (21.9 bits)
S2: 131 (55.1 bits)