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= 0001.0424.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...   876   0.0  
gi|300312690|ref|YP_003776782.1| sugar ABC transporter periplasm...   114   2e-26

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

 Score =  876 bits (2263), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 435/451 (96%), Positives = 445/451 (98%)

Query: 1   MSKLARPRASGFTCVRFTLAAAAISTLFAAGLAHAEPVTLNIASINNPDMIELQKLAPAF 60
           MSKL RPRA GFT VRFTLAAAAISTLFAAGLA AEPVTLNIASINNPDMIELQKLAPAF
Sbjct: 1   MSKLVRPRAFGFTRVRFTLAAAAISTLFAAGLAQAEPVTLNIASINNPDMIELQKLAPAF 60

Query: 61  EKANPDIKLRWVTMEESVLRQRLTTDIATNSGQFDLMTIGAYEAPIWAKKGWLAPMTGLP 120
           EKANPDIKLRWVTMEESVLRQRLTTDIATNSGQFDLMTIGAYEAPIWAKKGWLAPMTGLP
Sbjct: 61  EKANPDIKLRWVTMEESVLRQRLTTDIATNSGQFDLMTIGAYEAPIWAKKGWLAPMTGLP 120

Query: 121 ADYDEADLIKPVREGLSVDGKLYALPFYAESSMTYYRKDLFEQKKLTMPQRPTWDDIAKL 180
           ADYDEADLIKPVREGLSVDGKLYALPFYAESSMTYYRKDLFEQKKLTMPQRPTWD+IAKL
Sbjct: 121 ADYDEADLIKPVREGLSVDGKLYALPFYAESSMTYYRKDLFEQKKLTMPQRPTWDEIAKL 180

Query: 181 AAQLHDPAKGVYGICLRGRAGWGENMAILTTMANAWGGRWFDEQWQPQLSSPEWKAAVGF 240
           AAQLHDPAKGVYGICLRGRAGWGENMAI+TTMANAWGGRWFDEQWQPQLSSPEWK +V F
Sbjct: 181 AAQLHDPAKGVYGICLRGRAGWGENMAIITTMANAWGGRWFDEQWQPQLSSPEWKKSVAF 240

Query: 241 YVDLMRKYGPPGASSNGFNENLVLFSSGKCGMWVDATVAAGMLYHGKDSKVADKTAFAPA 300
           YVDLMRKYGPPGASSNGFNENLVLFSSGKCGMWVDATVAAGMLYHGKDSKVADKTAFAP+
Sbjct: 241 YVDLMRKYGPPGASSNGFNENLVLFSSGKCGMWVDATVAAGMLYHGKDSKVADKTAFAPS 300

Query: 301 PMQVTDKGSHWLWIWSLAVPKSSKSQDAAKKFAAWATSKDYINLVAKDAGWALVPPGTRN 360
           PMQVTDKGSHWLWIWSLAVPKSSKSQDAAKKFAAWATSK+YINLVAKD+GWALVPPGTRN
Sbjct: 301 PMQVTDKGSHWLWIWSLAVPKSSKSQDAAKKFAAWATSKEYINLVAKDSGWALVPPGTRN 360

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

Query: 421 GALAGKTSADAALDAAQAQAVRMMRQGRYLK 451
           GALAGKT++DAALDAAQAQAVRMMRQGRY+K
Sbjct: 421 GALAGKTTSDAALDAAQAQAVRMMRQGRYIK 451


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

 Score =  114 bits (284), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 98/326 (30%), Positives = 147/326 (45%), Gaps = 22/326 (6%)

Query: 29  AAGLAHAEPVTLNIASINNPDMIEL-----------QKLAPAFEKANPDIKLRWVTMEES 77
            A L  A P+  +  S N P +  L           + LA   +++   I++ +    + 
Sbjct: 20  CAVLGAALPLVASAQSCNVPVLKVLAQKSLGLTVMEKSLADYQKRSGTRIEISYFGENDR 79

Query: 78  VLRQRLTTDIATNSGQFDLMTIGAYEAPIWAKKGWLAPMTG-LPADYDEADLIKPVREGL 136
             + RL  D AT +G + +  +       +A  GW+ P+    P D D  D +   R   
Sbjct: 80  RAKSRL--DAATKAGSYQVYYVDEANVAEFASAGWIVPLLKYFPKDADYDDFLPGRRAVA 137

Query: 137 SVDGKLYALPFYAESSMTYYRKDLFEQKKLTMPQRPTWDDIAKLAAQLHDPAKGVYGICL 196
           S     Y  P    S   +YR+DL E+  L +P+  T D++     +LH P   VYG   
Sbjct: 138 SYKDVAYFAPLIGGSDFLFYRRDLLEKAGLPVPR--TLDELVADIKKLHSPP-SVYGWVA 194

Query: 197 RGRAGWGENMAILTTMANAWGGRWFDEQWQPQLSSPEWKAAVGFYVDLMRKYGPPGASSN 256
           RG+ G G N+        A GG+W D+  QP  +SP    A   Y DL  KY PPGA++ 
Sbjct: 195 RGQRGSGMNVWRWAPFMLAQGGQWTDKNNQPAFNSPAAVKATQLYADLF-KYAPPGAATY 253

Query: 257 GFNENLVLFSSGKCGMWVDATVAAGMLYHGKDSKVADKTAFA--PAPMQVTDKGSHWLWI 314
            ++  L  F SGK    +++T  A  +     S VADK  +A  PAP+     G H L I
Sbjct: 254 DWSNALEAFRSGKVAFMIESTPFADWMEDSSKSSVADKVGYARPPAPLPSAAYG-HGLAI 312

Query: 315 WSLAVPKSSKSQDAAKKFAAWATSKD 340
            ++   K   ++ AA KF A+AT K+
Sbjct: 313 SAVGA-KDECTRQAAGKFIAFATGKE 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
   0.317    0.131    0.404 

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: 1,414,487
Number of extensions: 58998
Number of successful extensions: 174
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 174
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)