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= 0002.0066.p
         (451 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309781|ref|YP_003773873.1| sugar ABC transporter periplasm...   882   0.0  
gi|300312690|ref|YP_003776782.1| sugar ABC transporter periplasm...   115   9e-27

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

 Score =  882 bits (2279), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 440/451 (97%), Positives = 445/451 (98%)

Query: 1   MSKLVRTRASGFTRVRFTLAAAAISTLFAAGHAQAEPVTLNIASINNPDMIELQKLAPAF 60
           MSKLVR RA GFTRVRFTLAAAAISTLFAAG AQAEPVTLNIASINNPDMIELQKLAPAF
Sbjct: 1   MSKLVRPRAFGFTRVRFTLAAAAISTLFAAGLAQAEPVTLNIASINNPDMIELQKLAPAF 60

Query: 61  EKANPDIKLRWVTMEESVLRQRLTTDIATNSGQFDLMTIGAYEAPIWAKKGWLAPMSGLP 120
           EKANPDIKLRWVTMEESVLRQRLTTDIATNSGQFDLMTIGAYEAPIWAKKGWLAPM+GLP
Sbjct: 61  EKANPDIKLRWVTMEESVLRQRLTTDIATNSGQFDLMTIGAYEAPIWAKKGWLAPMTGLP 120

Query: 121 ADYDEADLIKPVREGLSVDGKLYALPFYAESSMTYYRKDLFEQKKLTMPQHPTWDEVAKL 180
           ADYDEADLIKPVREGLSVDGKLYALPFYAESSMTYYRKDLFEQKKLTMPQ PTWDE+AKL
Sbjct: 121 ADYDEADLIKPVREGLSVDGKLYALPFYAESSMTYYRKDLFEQKKLTMPQRPTWDEIAKL 180

Query: 181 AAQLHDPAKGVYGICLRGRAGWGENMAIITTMANAWGGRWFDEQWQPQLSSPEWKKSVNF 240
           AAQLHDPAKGVYGICLRGRAGWGENMAIITTMANAWGGRWFDEQWQPQLSSPEWKKSV F
Sbjct: 181 AAQLHDPAKGVYGICLRGRAGWGENMAIITTMANAWGGRWFDEQWQPQLSSPEWKKSVAF 240

Query: 241 YVDLMRKYGPPGASSNGFNENLVLFSSGKCGMWVDATVAAGMLYHGKDSKVADKTAFAPS 300
           YVDLMRKYGPPGASSNGFNENLVLFSSGKCGMWVDATVAAGMLYHGKDSKVADKTAFAPS
Sbjct: 241 YVDLMRKYGPPGASSNGFNENLVLFSSGKCGMWVDATVAAGMLYHGKDSKVADKTAFAPS 300

Query: 301 PQQVTDKGSHWLWIWSLAVPKSSKSQDAAKKFAAWATSKEYINLVAKDSGWALVPPGTRN 360
           P QVTDKGSHWLWIWSLAVPKSSKSQDAAKKFAAWATSKEYINLVAKDSGWALVPPGTRN
Sbjct: 301 PMQVTDKGSHWLWIWSLAVPKSSKSQDAAKKFAAWATSKEYINLVAKDSGWALVPPGTRN 360

Query: 361 STYASAEYKKVSPFSDFVLDAIQTADANKPTLKPVPYTGVQFATIPEFQSIGTVTGQAIA 420
           STYASAEYKKVSPFSDFVLDAIQTADANKPT+KPVPYTGVQFATIPEFQSIGTVTGQAIA
Sbjct: 361 STYASAEYKKVSPFSDFVLDAIQTADANKPTVKPVPYTGVQFATIPEFQSIGTVTGQAIA 420

Query: 421 GALAGKTSADAALDAAQAQAVRMMRQGRYIK 451
           GALAGKT++DAALDAAQAQAVRMMRQGRYIK
Sbjct: 421 GALAGKTTSDAALDAAQAQAVRMMRQGRYIK 451


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

 Score =  115 bits (287), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 94/316 (29%), Positives = 144/316 (45%), Gaps = 9/316 (2%)

Query: 27  LFAAGHAQAEPVTLNIASINNPDMIELQKLAPAFEKANPDIKLRWVTMEESVLRQRLTTD 86
           L A+  +   PV   +A  +    +  + LA   +++   I++ +    +   + RL  D
Sbjct: 29  LVASAQSCNVPVLKVLAQKSLGLTVMEKSLADYQKRSGTRIEISYFGENDRRAKSRL--D 86

Query: 87  IATNSGQFDLMTIGAYEAPIWAKKGWLAPM-SGLPADYDEADLIKPVREGLSVDGKLYAL 145
            AT +G + +  +       +A  GW+ P+    P D D  D +   R   S     Y  
Sbjct: 87  AATKAGSYQVYYVDEANVAEFASAGWIVPLLKYFPKDADYDDFLPGRRAVASYKDVAYFA 146

Query: 146 PFYAESSMTYYRKDLFEQKKLTMPQHPTWDEVAKLAAQLHDPAKGVYGICLRGRAGWGEN 205
           P    S   +YR+DL E+  L +P+  T DE+     +LH P   VYG   RG+ G G N
Sbjct: 147 PLIGGSDFLFYRRDLLEKAGLPVPR--TLDELVADIKKLHSP-PSVYGWVARGQRGSGMN 203

Query: 206 MAIITTMANAWGGRWFDEQWQPQLSSPEWKKSVNFYVDLMRKYGPPGASSNGFNENLVLF 265
           +        A GG+W D+  QP  +SP   K+   Y DL  KY PPGA++  ++  L  F
Sbjct: 204 VWRWAPFMLAQGGQWTDKNNQPAFNSPAAVKATQLYADLF-KYAPPGAATYDWSNALEAF 262

Query: 266 SSGKCGMWVDATVAAGMLYHGKDSKVADKTAFAPSPQQVTDKG-SHWLWIWSLAVPKSSK 324
            SGK    +++T  A  +     S VADK  +A  P  +      H L I ++   K   
Sbjct: 263 RSGKVAFMIESTPFADWMEDSSKSSVADKVGYARPPAPLPSAAYGHGLAISAVGA-KDEC 321

Query: 325 SQDAAKKFAAWATSKE 340
           ++ AA KF A+AT KE
Sbjct: 322 TRQAAGKFIAFATGKE 337


  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    0.397 

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: 1,391,924
Number of extensions: 57698
Number of successful extensions: 176
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 176
Number of HSP's successfully gapped: 2
Length of query: 451
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 363
Effective length of database: 1,203,190
Effective search space: 436757970
Effective search space used: 436757970
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 (21.7 bits)
S2: 132 (55.5 bits)