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= 0075.0038.p
         (278 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...   117   1e-27
gi|300309742|ref|YP_003773834.1| shikimate 5-dehydrogenase [Herb...    67   1e-12

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

 Score =  117 bits (292), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 80/258 (31%), Positives = 130/258 (50%), Gaps = 5/258 (1%)

Query: 7   RQITGSTKVVAILADPIGHVRTPPAFNALMAQHDVDAVMVPFNVRPDHFAQFIAAVPLIR 66
           + ITG+T++  ++  P+  V+ P  FNA    H +DA ++PF + P+ + + +       
Sbjct: 2   KAITGTTRIFPVIGWPVEQVKAPTLFNAYFEHHGIDARVIPFKIEPERYCEAVRMFMKTE 61

Query: 67  SLAGLVVTIPYKEIILQHCTTLTESAQRMGAVNIVRFDDQPDGARSLIGSNFDGIGFVGG 126
           ++ G+ V+IP+K + L+     T  A+  GA N V  D   DG   + G   DG GF+  
Sbjct: 62  NVGGIFVSIPHKPMTLEAVEQSTLRARVAGACNAVYRD--ADGV--IWGDLIDGEGFIRA 117

Query: 127 LLAQGHVLKGRRVYLAGAPXKGAGGAAKAIVHALADEGVAAIGIYNRSAVRAEHLVRELR 186
           L A+    +        A   G GG   AIV +LA +GVA I +++ +   AE L+    
Sbjct: 118 L-ARTAADRPLVWNQTRALVVGTGGVGCAIVASLAAQGVAEISVFDTNRAGAEALLARAA 176

Query: 187 QRYPRLDAHLADARPQGYTLAINSTSLGLQESDPLPFTPDGLPPGAVVAEVIMKTEITPL 246
             +P      A     G+ L +N T LG+   DP+PF  +G+   A+VA+  MK E++ L
Sbjct: 177 AAFPATRVGFAQPDASGFDLLVNCTPLGMHVGDPMPFALEGVRRDAIVADCGMKIEMSQL 236

Query: 247 LAKAGACGFAVHPGRHMM 264
           L +A A G  +  G+ M+
Sbjct: 237 LVQAQALGCRIQKGKEML 254


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

 Score = 67.0 bits (162), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 103/228 (45%), Gaps = 31/228 (13%)

Query: 18  ILADPIGHVRTPPAFNALMAQH----DVDAVMVPFNVRPDHFAQFIAAVPLI--RSLAGL 71
           ++ +PI H ++P       AQ       + ++VP +        F AAV +   R   G 
Sbjct: 6   VIGNPIAHSKSPDIHARFAAQTGQSMSYERLLVPLH-------GFKAAVQVFQRRGGRGA 58

Query: 72  VVTIPYKEIILQHCTTLTESAQRMGAVNIVRFDDQPDGARSLIGSNFDGIGFVGGLLAQ- 130
            +T+P+K         LTE A+  GAVN  +F++       ++G N DG G V  ++   
Sbjct: 59  NITVPFKLEAHALADQLTERARLAGAVNTFKFEEG-----CILGDNTDGAGLVTDIMVNA 113

Query: 131 GHVLKGRRVYLAGAPXKGAGGAAKAIVHALADEGVAAIGIYNRSAVRAEHLVRELRQRYP 190
           G  L+GRR+ L GA     GGA++  +  L  +  A + + NR+A RAE L  +     P
Sbjct: 114 GQALQGRRILLLGA-----GGASRGALLPLLQQRPAELVVVNRTASRAEELATQFAAYGP 168

Query: 191 RLDAHLADARPQGYTLAINSTSLGLQESDPLPFTPDGLPPGAVVAEVI 238
                 A      + + +N+TS  L  SD LP     LPP    +E +
Sbjct: 169 VRSTTFAGLEG-AFDVIVNATSASL--SDDLP----PLPPSVYGSETL 209


  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    0.139    0.408 

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: 876,537
Number of extensions: 35267
Number of successful extensions: 139
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 136
Number of HSP's successfully gapped: 2
Length of query: 278
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 194
Effective length of database: 1,222,130
Effective search space: 237093220
Effective search space used: 237093220
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)