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= 0229.0056.p
         (287 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312690|ref|YP_003776782.1| sugar ABC transporter periplasm...   417   e-118
gi|300309781|ref|YP_003773873.1| sugar ABC transporter periplasm...    86   3e-18

>gi|300312690|ref|YP_003776782.1| sugar ABC transporter periplasmic
           protein [Herbaspirillum seropedicae SmR1]
          Length = 433

 Score =  417 bits (1073), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 193/276 (69%), Positives = 231/276 (83%)

Query: 1   LYGGGDFLYYRKDLLEKAHIAVPQTLSELQTAIKKLNNPPNVYGWVARGQRGSGMNVWRW 60
           L GG DFL+YR+DLLEKA + VP+TL EL   IKKL++PP+VYGWVARGQRGSGMNVWRW
Sbjct: 148 LIGGSDFLFYRRDLLEKAGLPVPRTLDELVADIKKLHSPPSVYGWVARGQRGSGMNVWRW 207

Query: 61  SPFFTAMGGEWVGKDGKASFNSAAGVKATQTYMDLLKYAPPGSATYDWSNAIEAFRAGKV 120
           +PF  A GG+W  K+ + +FNS A VKATQ Y DL KYAPPG+ATYDWSNA+EAFR+GKV
Sbjct: 208 APFMLAQGGQWTDKNNQPAFNSPAAVKATQLYADLFKYAPPGAATYDWSNALEAFRSGKV 267

Query: 121 AFMIESTPFADWMEDASKSSVASTVGYARPPAPLSSAGFGHGFAIAAYGSKDECTRQAAG 180
           AFMIESTPFADWMED+SKSSVA  VGYARPPAPL SA +GHG AI+A G+KDECTRQAAG
Sbjct: 268 AFMIESTPFADWMEDSSKSSVADKVGYARPPAPLPSAAYGHGLAISAVGAKDECTRQAAG 327

Query: 181 KFIAWASSKEQEQARLKDGVFSDYNRTSTIASPFFKQHVKPGIVTGLNAISDTTKLNIWS 240
           KFIA+A+ KEQEQARL++ VFSDYNR+STI S +F+++VKP I+ GL   +  +KL IW 
Sbjct: 328 KFIAFATGKEQEQARLREKVFSDYNRSSTIQSDYFQKNVKPQILAGLKDTTPVSKLTIWP 387

Query: 241 SPVWPQVGDNLGVVLEELFTGTRTNVKAALDDAAKY 276
           SP WP +GDNLGV LEE+FTGT+ ++  ALD+AA+Y
Sbjct: 388 SPQWPDIGDNLGVALEEVFTGTQKDITRALDEAAQY 423


>gi|300309781|ref|YP_003773873.1| sugar ABC transporter periplasmic
           protein [Herbaspirillum seropedicae SmR1]
          Length = 451

 Score = 86.3 bits (212), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 81/273 (29%), Positives = 123/273 (45%), Gaps = 13/273 (4%)

Query: 1   LYGGGDFLYYRKDLLEKAHIAVPQ--TLSELQTAIKKLNNPPN-VYGWVARGQRGSGMNV 57
            Y      YYRKDL E+  + +PQ  T  E+     +L++P   VYG   RG+ G G N+
Sbjct: 147 FYAESSMTYYRKDLFEQKKLTMPQRPTWDEIAKLAAQLHDPAKGVYGICLRGRAGWGENM 206

Query: 58  WRWSPFFTAMGGEWVGKDGKASFNSAAGVKATQTYMDLL-KYAPPGSATYDWSNAIEAFR 116
              +    A GG W  +  +   +S    K+   Y+DL+ KY PPG+++  ++  +  F 
Sbjct: 207 AIITTMANAWGGRWFDEQWQPQLSSPEWKKSVAFYVDLMRKYGPPGASSNGFNENLVLFS 266

Query: 117 AGKVAFMIESTPFADWMEDASKSSVASTVGYARPPAPLSSAGFGHGFAIAAYGSKDECTR 176
           +GK    +++T  A  +     S VA    +A  P  ++  G    +  +    K   ++
Sbjct: 267 SGKCGMWVDATVAAGMLYHGKDSKVADKTAFAPSPMQVTDKGSHWLWIWSLAVPKSSKSQ 326

Query: 177 QAAGKFIAWASSKEQEQARLKD---GVFSDYNRTSTIASPFFKQHVKPGIVTGLNAI--S 231
            AA KF AWA+SKE      KD    +     R ST AS  +K+ V P     L+AI  +
Sbjct: 327 DAAKKFAAWATSKEYINLVAKDSGWALVPPGTRNSTYASAEYKK-VSPFSDFVLDAIQTA 385

Query: 232 DTTKLNIWSSPVWPQVGDNLGVVLEELFTGTRT 264
           D  K  +   PV P  G     + E    GT T
Sbjct: 386 DANKPTV--KPV-PYTGVQFATIPEFQSIGTVT 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
   0.316    0.130    0.400 

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: 969,005
Number of extensions: 40074
Number of successful extensions: 96
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 93
Number of HSP's successfully gapped: 2
Length of query: 287
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 203
Effective length of database: 1,222,130
Effective search space: 248092390
Effective search space used: 248092390
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 (21.6 bits)
S2: 130 (54.7 bits)