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= 0001.4639.p
         (309 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300314029|ref|YP_003778121.1| permease [Herbaspirillum serope...   540   e-155

>gi|300314029|ref|YP_003778121.1| permease [Herbaspirillum
           seropedicae SmR1]
          Length = 310

 Score =  540 bits (1392), Expect = e-155,   Method: Compositional matrix adjust.
 Identities = 277/309 (89%), Positives = 291/309 (94%), Gaps = 3/309 (0%)

Query: 1   MSYTPSRPLGYGCLILSMSLVGAYVALTKPLAAMLPVFLLAWLRFAIGAVAMLRWMKKPA 60
           MSYTPSRP+GYGCLILSMSLVGAYVALTKPLAAMLPVFLLAWLRF IGAVAMLRW+KKPA
Sbjct: 1   MSYTPSRPMGYGCLILSMSLVGAYVALTKPLAAMLPVFLLAWLRFGIGAVAMLRWLKKPA 60

Query: 61  AEQALSTQSRWLVFLESFLGNFLFTLCMITGVSMTNAVSAGVIMSSIPAVVAVMSWVFLK 120
           +EQ LSTQSRWLVFLESFLGNFLFTLCMITGVSMTNAVSAGVIMS+IPAVVAVMSW+FLK
Sbjct: 61  SEQPLSTQSRWLVFLESFLGNFLFTLCMITGVSMTNAVSAGVIMSAIPAVVAVMSWIFLK 120

Query: 121 ERISLRVWGAVACGAIGIGLLSLAKDTHGAAGSSGAAPAQYAWLGNVLVFCAVLCEAAYA 180
           E+ISLRVWGAVACGA+GIGLLSLAKD HGA+ +SG    QYAWLGN LVFCAVLCEAAYA
Sbjct: 121 EKISLRVWGAVACGAVGIGLLSLAKDGHGASAASG---GQYAWLGNGLVFCAVLCEAAYA 177

Query: 181 VIGKKLTAVLTPKRISAVINLWGLLLMTPMGLYTALKFDFSTVPLNIWLLLVFYGLAASV 240
           VIGKKLTAVLTPKRISAVINLWGLLLMTPMG+YTAL FDF  VP N+W LL+FYGLAASV
Sbjct: 178 VIGKKLTAVLTPKRISAVINLWGLLLMTPMGVYTALHFDFGAVPANMWWLLLFYGLAASV 237

Query: 241 WTVWLWMTGLKVVPAARAGVFTVMLPVSAAVVGVLALGERLSALQAGAFAVALAGMFLAT 300
           WTVWLWMTGLKVVPAARAGVFTVMLPVSAA+VGVLALGE LSALQAGAFA+ALAGM LAT
Sbjct: 238 WTVWLWMTGLKVVPAARAGVFTVMLPVSAALVGVLALGESLSALQAGAFAIALAGMLLAT 297

Query: 301 LPGRAATDN 309
           LPGRAA D 
Sbjct: 298 LPGRAAADK 306


  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
   0.327    0.136    0.427 

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: 867,482
Number of extensions: 32368
Number of successful extensions: 229
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 227
Number of HSP's successfully gapped: 3
Length of query: 309
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 224
Effective length of database: 1,217,395
Effective search space: 272696480
Effective search space used: 272696480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 130 (54.7 bits)