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= 0003.0008.p
         (281 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313060|ref|YP_003777152.1| shikimate 5-dehydrogenase [Herb...   508   e-145
gi|300309742|ref|YP_003773834.1| shikimate 5-dehydrogenase [Herb...    71   1e-13

>gi|300313060|ref|YP_003777152.1| shikimate 5-dehydrogenase
           [Herbaspirillum seropedicae SmR1]
          Length = 281

 Score =  508 bits (1309), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 261/281 (92%), Positives = 271/281 (96%)

Query: 1   MKEITGTTRIFPVIGWPVEQVKAPTLFNAYFKRHGLDARVIPFKIEPERYCEAVRMFMKT 60
           MK ITGTTRIFPVIGWPVEQVKAPTLFNAYF+ HG+DARVIPFKIEPERYCEAVRMFMKT
Sbjct: 1   MKAITGTTRIFPVIGWPVEQVKAPTLFNAYFEHHGIDARVIPFKIEPERYCEAVRMFMKT 60

Query: 61  ENVGGIFVSIPHKPMTLEAVEQATLRARVAGACNAVYRDAEGVVWGDLIDGEGFIRALAR 120
           ENVGGIFVSIPHKPMTLEAVEQ+TLRARVAGACNAVYRDA+GV+WGDLIDGEGFIRALAR
Sbjct: 61  ENVGGIFVSIPHKPMTLEAVEQSTLRARVAGACNAVYRDADGVIWGDLIDGEGFIRALAR 120

Query: 121 TAADRPLVWNKTRALVVGTGGVGCAIVASLAAQGIAEISVFDTNRAGAEALLARVEAAYP 180
           TAADRPLVWN+TRALVVGTGGVGCAIVASLAAQG+AEISVFDTNRAGAEALLAR  AA+P
Sbjct: 121 TAADRPLVWNQTRALVVGTGGVGCAIVASLAAQGVAEISVFDTNRAGAEALLARAAAAFP 180

Query: 181 ATRVRFAQPDASGVDLLVNCTPLGMHVGDPMPFALEGVSTEAIVADCGMKIEMSQLLVQA 240
           ATRV FAQPDASG DLLVNCTPLGMHVGDPMPFALEGV  +AIVADCGMKIEMSQLLVQA
Sbjct: 181 ATRVGFAQPDASGFDLLVNCTPLGMHVGDPMPFALEGVRRDAIVADCGMKIEMSQLLVQA 240

Query: 241 QAKGCRIQKGKEMLIEQAPLYLELFGWPGVAADDFRHLEAL 281
           QA GCRIQKGKEMLIEQAPLYLELFGWPGV+ADDFR LEAL
Sbjct: 241 QALGCRIQKGKEMLIEQAPLYLELFGWPGVSADDFRALEAL 281


>gi|300309742|ref|YP_003773834.1| shikimate 5-dehydrogenase
           [Herbaspirillum seropedicae SmR1]
          Length = 271

 Score = 70.9 bits (172), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 68/258 (26%), Positives = 111/258 (43%), Gaps = 12/258 (4%)

Query: 11  FPVIGWPVEQVKAPTLFNAYFKRHGLDARVIPFKIEPERYCEAVRMFMKTENVGGIFVSI 70
           + VIG P+   K+P +   +  + G         +    +  AV++F +    G   +++
Sbjct: 4   YVVIGNPIAHSKSPDIHARFAAQTGQSMSYERLLVPLHGFKAAVQVFQRRGGRGAN-ITV 62

Query: 71  PHKPMTLEAVEQATLRARVAGACNAVYRDAEGVVWGDLIDGEGFIRALARTAADRPLVWN 130
           P K       +Q T RAR+AGA N  ++  EG + GD  DG G +  +   A        
Sbjct: 63  PFKLEAHALADQLTERARLAGAVN-TFKFEEGCILGDNTDGAGLVTDIMVNAGQ---ALQ 118

Query: 131 KTRALVVGTGGVGCAIVASLAAQGIAEISVFDTNRAGAEALLARVEAAYPATRVRFAQPD 190
             R L++G GG     +  L  Q  AE+ V +   + AE L  +  A  P     FA  +
Sbjct: 119 GRRILLLGAGGASRGALLPLLQQRPAELVVVNRTASRAEELATQFAAYGPVRSTTFAGLE 178

Query: 191 ASGVDLLVNCTPLGMHVG-DPMPFALEGVSTEAIVADCGMKIEMSQLLVQAQAKGCRIQK 249
            +  D++VN T   +     P+P ++ G  +E +  D       +  +  AQ  G  ++ 
Sbjct: 179 GA-FDVIVNATSASLSDDLPPLPPSVYG--SETLAYDMMYGRGPTVFMQSAQQHGAHVRD 235

Query: 250 GKEMLIEQAPLYLELFGW 267
           G  ML+EQA    E F W
Sbjct: 236 GLGMLVEQAA---EAFQW 250


  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
   0.323    0.138    0.416 

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: 872,163
Number of extensions: 35627
Number of successful extensions: 160
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 158
Number of HSP's successfully gapped: 2
Length of query: 281
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 197
Effective length of database: 1,222,130
Effective search space: 240759610
Effective search space used: 240759610
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 130 (54.7 bits)