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= 0001.0378.p
         (271 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309742|ref|YP_003773834.1| shikimate 5-dehydrogenase [Herb...   476   e-135
gi|300313060|ref|YP_003777152.1| shikimate 5-dehydrogenase [Herb...    59   4e-10

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

 Score =  476 bits (1225), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 234/271 (86%), Positives = 246/271 (90%)

Query: 1   MDEYVVIGNPIAHSKSPEIHARFAVQTGQQLHYDRLLVPLRGFKAAVQVFQRRGGCGANV 60
           MDEYVVIGNPIAHSKSP+IHARFA QTGQ + Y+RLLVPL GFKAAVQVFQRRGG GAN+
Sbjct: 1   MDEYVVIGNPIAHSKSPDIHARFAAQTGQSMSYERLLVPLHGFKAAVQVFQRRGGRGANI 60

Query: 61  TVPFKLEAHALADQLTERARLAGAVNTLKFEGGRILGDNTDGAGLVTDIMSNAGQALAGR 120
           TVPFKLEAHALADQLTERARLAGAVNT KFE G ILGDNTDGAGLVTDIM NAGQAL GR
Sbjct: 61  TVPFKLEAHALADQLTERARLAGAVNTFKFEEGCILGDNTDGAGLVTDIMVNAGQALQGR 120

Query: 121 RILLLGAGGAARGALLPLLQQKPRELVIVNRTATKAAELAKLFVEYGPVRSVAYAELDGV 180
           RILLLGAGGA+RGALLPLLQQ+P ELV+VNRTA++A ELA  F  YGPVRS  +A L+G 
Sbjct: 121 RILLLGAGGASRGALLPLLQQRPAELVVVNRTASRAEELATQFAAYGPVRSTTFAGLEGA 180

Query: 181 FDVIINATSASLSDDLPPLPVSVYGCETLAYDMMYGRQPTVFMHSAQQHGASVRDGLGML 240
           FDVI+NATSASLSDDLPPLP SVYG ETLAYDMMYGR PTVFM SAQQHGA VRDGLGML
Sbjct: 181 FDVIVNATSASLSDDLPPLPPSVYGSETLAYDMMYGRGPTVFMQSAQQHGAHVRDGLGML 240

Query: 241 VEQAAEAFQWWRGVRPATAEVFASLRQQLSQ 271
           VEQAAEAFQWWRGVRPATAEVFASLRQQLSQ
Sbjct: 241 VEQAAEAFQWWRGVRPATAEVFASLRQQLSQ 271


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

 Score = 59.3 bits (142), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 65/258 (25%), Positives = 106/258 (41%), Gaps = 12/258 (4%)

Query: 4   YVVIGNPIAHSKSPEIHARFAVQTGQQLHYDRLLVPLRGFKAAVQVFQRRGGCGA-NVTV 62
           + VIG P+   K+P +   +    G         +    +  AV++F +    G   V++
Sbjct: 11  FPVIGWPVEQVKAPTLFNAYFEHHGIDARVIPFKIEPERYCEAVRMFMKTENVGGIFVSI 70

Query: 63  PFKLEAHALADQLTERARLAGAVNTLKFEG-GRILGDNTDGAGLVTDIMSNAGQ---ALA 118
           P K       +Q T RAR+AGA N +  +  G I GD  DG G +  +   A        
Sbjct: 71  PHKPMTLEAVEQSTLRARVAGACNAVYRDADGVIWGDLIDGEGFIRALARTAADRPLVWN 130

Query: 119 GRRILLLGAGGAARGALLPLLQQKPRELVIVNRTATKAAELAKLFVEYGPVRSVAYAELD 178
             R L++G GG     +  L  Q   E+ + +     A  L        P   V +A+ D
Sbjct: 131 QTRALVVGTGGVGCAIVASLAAQGVAEISVFDTNRAGAEALLARAAAAFPATRVGFAQPD 190

Query: 179 GV-FDVIINATSASLSDDLPPLPVSVYGC--ETLAYDMMYGRQPTVFMHSAQQHGASVRD 235
              FD+++N T   +     P+P ++ G   + +  D     + +  +  AQ  G  ++ 
Sbjct: 191 ASGFDLLVNCTPLGMHVG-DPMPFALEGVRRDAIVADCGMKIEMSQLLVQAQALGCRIQK 249

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


  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
   0.321    0.136    0.394 

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: 739,209
Number of extensions: 27270
Number of successful extensions: 102
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 102
Number of HSP's successfully gapped: 2
Length of query: 271
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 187
Effective length of database: 1,222,130
Effective search space: 228538310
Effective search space used: 228538310
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)