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= 0001.3354.p
         (433 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...   852   0.0  
gi|300309781|ref|YP_003773873.1| sugar ABC transporter periplasm...   118   9e-28

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

 Score =  852 bits (2201), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 412/433 (95%), Positives = 424/433 (97%)

Query: 1   LNDKNTRRQTVNKICLGAACAVLGAALPLVASAQSCNVPVLKVLAQKSLGLTVMEKSLPD 60
           + DKN RRQTVNKICLGAACAVLGAALPLVASAQSCNVPVLKVLAQKSLGLTVMEKSL D
Sbjct: 1   MIDKNIRRQTVNKICLGAACAVLGAALPLVASAQSCNVPVLKVLAQKSLGLTVMEKSLAD 60

Query: 61  YQKRTGTRIEISYFGENDRRAKSRLDAATKAGSYQVYYVDEANVAEFASAGWIVPLLKYY 120
           YQKR+GTRIEISYFGENDRRAKSRLDAATKAGSYQVYYVDEANVAEFASAGWIVPLLKY+
Sbjct: 61  YQKRSGTRIEISYFGENDRRAKSRLDAATKAGSYQVYYVDEANVAEFASAGWIVPLLKYF 120

Query: 121 PKDADYEDFLPGRRAVASYKDVAYFAPLIGGSDFLFYRRDLLEKAGLPVPRTLDELVADI 180
           PKDADY+DFLPGRRAVASYKDVAYFAPLIGGSDFLFYRRDLLEKAGLPVPRTLDELVADI
Sbjct: 121 PKDADYDDFLPGRRAVASYKDVAYFAPLIGGSDFLFYRRDLLEKAGLPVPRTLDELVADI 180

Query: 181 KKLHSPPSVYGWVARGQRGSGMNVWRWAPFMLAAGGSWTDKNNQPSFNSPAAVKATQLYA 240
           KKLHSPPSVYGWVARGQRGSGMNVWRWAPFMLA GG WTDKNNQP+FNSPAAVKATQLYA
Sbjct: 181 KKLHSPPSVYGWVARGQRGSGMNVWRWAPFMLAQGGQWTDKNNQPAFNSPAAVKATQLYA 240

Query: 241 DLFKYAPPGAATYDWSNALEAFRSGKVAFMIESTPFADWMEDASKSSVADKVGYARPPAP 300
           DLFKYAPPGAATYDWSNALEAFRSGKVAFMIESTPFADWMED+SKSSVADKVGYARPPAP
Sbjct: 241 DLFKYAPPGAATYDWSNALEAFRSGKVAFMIESTPFADWMEDSSKSSVADKVGYARPPAP 300

Query: 301 LPSAAYGHGLAISAVGAKDECTRQAAGKFIAFATGKQQEQARLREKVFSDYNRSSTIQSD 360
           LPSAAYGHGLAISAVGAKDECTRQAAGKFIAFATGK+QEQARLREKVFSDYNRSSTIQSD
Sbjct: 301 LPSAAYGHGLAISAVGAKDECTRQAAGKFIAFATGKEQEQARLREKVFSDYNRSSTIQSD 360

Query: 361 YFQKNVKPQILAGLKDTTPVSKLTIWPSPQWPDIGDNLGVALEEIFTGTQKDIPGALNDA 420
           YFQKNVKPQILAGLKDTTPVSKLTIWPSPQWPDIGDNLGVALEE+FTGTQKDI  AL++A
Sbjct: 361 YFQKNVKPQILAGLKDTTPVSKLTIWPSPQWPDIGDNLGVALEEVFTGTQKDITRALDEA 420

Query: 421 NQYAREAMEHVRK 433
            QYA++AMEH RK
Sbjct: 421 AQYAQDAMEHARK 433


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

 Score =  118 bits (296), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 101/324 (31%), Positives = 147/324 (45%), Gaps = 18/324 (5%)

Query: 20  CAVLGAALPLVASAQSCNVPVLKVLAQKSLGLTVMEKSLPDYQKRTGTRIEISYFGENDR 79
            A L  A P+  +  S N P +  L + +      EK+ PD + R  T        E+  
Sbjct: 29  AAGLAQAEPVTLNIASINNPDMIELQKLA---PAFEKANPDIKLRWVT------MEESVL 79

Query: 80  RAKSRLDAATKAGSYQVYYVDEANVAEFASAGWIVPLLKYYPKDADYEDFLPGRRAVASY 139
           R +   D AT +G + +  +       +A  GW+ P+    P D D  D +   R   S 
Sbjct: 80  RQRLTTDIATNSGQFDLMTIGAYEAPIWAKKGWLAPMTGL-PADYDEADLIKPVREGLSV 138

Query: 140 KDVAYFAPLIGGSDFLFYRRDLLEKAGLPVPR--TLDELVADIKKLHSPP-SVYGWVARG 196
               Y  P    S   +YR+DL E+  L +P+  T DE+     +LH P   VYG   RG
Sbjct: 139 DGKLYALPFYAESSMTYYRKDLFEQKKLTMPQRPTWDEIAKLAAQLHDPAKGVYGICLRG 198

Query: 197 QRGSGMNVWRWAPFMLAAGGSWTDKNNQPSFNSPAAVKATQLYADLF-KYAPPGAATYDW 255
           + G G N+        A GG W D+  QP  +SP   K+   Y DL  KY PPGA++  +
Sbjct: 199 RAGWGENMAIITTMANAWGGRWFDEQWQPQLSSPEWKKSVAFYVDLMRKYGPPGASSNGF 258

Query: 256 SNALEAFRSGKVAFMIESTPFADWMEDASKSSVADKVGYARPPAPLPSAAYG-HGLAISA 314
           +  L  F SGK    +++T  A  +     S VADK  +A  P+P+     G H L I +
Sbjct: 259 NENLVLFSSGKCGMWVDATVAAGMLYHGKDSKVADKTAFA--PSPMQVTDKGSHWLWIWS 316

Query: 315 VGA-KDECTRQAAGKFIAFATGKQ 337
           +   K   ++ AA KF A+AT K+
Sbjct: 317 LAVPKSSKSQDAAKKFAAWATSKE 340


  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    0.132    0.398 

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: 1,362,058
Number of extensions: 58674
Number of successful extensions: 155
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 153
Number of HSP's successfully gapped: 2
Length of query: 433
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 345
Effective length of database: 1,203,190
Effective search space: 415100550
Effective search space used: 415100550
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)