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= 0008.0053.p
         (326 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312882|ref|YP_003776974.1| hypothetical protein Hsero_3587...   645   0.0  
gi|300309754|ref|YP_003773846.1| tRNA-dihydrouridine synthase or...    73   4e-14

>gi|300312882|ref|YP_003776974.1| hypothetical protein Hsero_3587
           [Herbaspirillum seropedicae SmR1]
          Length = 357

 Score =  645 bits (1663), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 307/323 (95%), Positives = 315/323 (97%)

Query: 1   MMDWTDRHCRVFHRQITRHTWLYTEMVTTGALLHGDVPRHLDFDEQEHPVALQLGGSEPS 60
           MMDWTDRHCRVFHRQITRHTWLYTEMVTTGALLHGDVPRHLDFDEQEHPVALQLGGSEP+
Sbjct: 32  MMDWTDRHCRVFHRQITRHTWLYTEMVTTGALLHGDVPRHLDFDEQEHPVALQLGGSEPA 91

Query: 61  DLAHSAKLGEQWGYDEINLNCGCPSERVQKGAFGACLMGEPTLVADCVKAMKDAVSIDVT 120
           DLAHSAKLGEQWGYDEINLNCGCPSERVQKGAFGACLMGEPTLVADCVKAM+DAVSIDVT
Sbjct: 92  DLAHSAKLGEQWGYDEINLNCGCPSERVQKGAFGACLMGEPTLVADCVKAMRDAVSIDVT 151

Query: 121 VKHRIGIDDVQSYDFVRDFVGQIAEAGCKTFIVHARNAILKGLSPKENREIPPLKYHYAY 180
           VKHRIGID+V+SYDFVRDFVGQIAEAGC+TFIVHARNAILKGLSPKENREIPPLKY YAY
Sbjct: 152 VKHRIGIDEVESYDFVRDFVGQIAEAGCQTFIVHARNAILKGLSPKENREIPPLKYDYAY 211

Query: 181 QLKQDFPELEILINGGIKTLPEIDEHLKHVDGVMLGREAYHNPYLMATFDARYYGDLDGG 240
           QLK+DFP LEILINGGIKTLPEIDEHLKHVDGVMLGREAYHNPYLMA FDARYY  L+GG
Sbjct: 212 QLKKDFPSLEILINGGIKTLPEIDEHLKHVDGVMLGREAYHNPYLMAGFDARYYAALEGG 271

Query: 241 RQPSRAEVIEAMLPYIKRQLELHGDNGRGLRLNSITRHMLGLLTGMPGARAFRQTLSDSK 300
            Q SRAEVIEAMLPYIKRQLELHGDNGRGLRLNSITRHMLGL+ GMPGARAFRQTLSDSK
Sbjct: 272 LQRSRAEVIEAMLPYIKRQLELHGDNGRGLRLNSITRHMLGLMAGMPGARAFRQTLSDSK 331

Query: 301 RLALGDPALLLEALQRTQAAQAA 323
           RLALGDPALLLEALQRTQAAQAA
Sbjct: 332 RLALGDPALLLEALQRTQAAQAA 354


>gi|300309754|ref|YP_003773846.1| tRNA-dihydrouridine synthase or
           NifR3-like protein [Herbaspirillum seropedicae SmR1]
          Length = 340

 Score = 72.8 bits (177), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 82/328 (25%), Positives = 141/328 (42%), Gaps = 27/328 (8%)

Query: 1   MMDWTDRHCRVFHRQITRHTWLYTEMVTTGALL--HGDVPRHLDFDEQEHPVALQLGGSE 58
           M   TDR  R   +Q+    +  +EM  +   L       R ++ D +  P A+Q+ G++
Sbjct: 17  MAGVTDRPFRQLCKQLG-AGYAVSEMAASDPRLWQSEKTSRRINHDGEMEPKAVQIAGAD 75

Query: 59  PSDLAHSAKLGEQWGYDEINLNCGCPSERVQKGAFGACLMGEPTLVADCVKAMKDAVSID 118
           P  LA  AK   + G   I++N GCP ++V     G+ L+ +  LVA  + A+  AV + 
Sbjct: 76  PVMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEELVARILDAVVSAVDVP 135

Query: 119 VTVKHRIGIDDVQSYDFVRDFVGQIAEAGCKTFIVHARNAILKGLSPKENREIPPLKYHY 178
           VT+K R G +             +   AG     +H R          E   I  +K   
Sbjct: 136 VTLKFRTGWNRANKNAL--KIAARAEAAGIAMLTLHGRTRADGYSGEAEYETIAAVKAAV 193

Query: 179 AYQLKQDFPELEILINGGIKTLPEIDEH---LKHVDGVMLGREAYHNPYLMATFDARYYG 235
                    ++ ++ NG I T PE       L   D VM+GR A   P++    D  +  
Sbjct: 194 ---------KIPVVANGDITT-PEKARDVLLLTKADAVMVGRAAQGRPWIFREID-HFLR 242

Query: 236 DLDGGRQPSRAEVIEAMLPYIKRQLELHGDNGRGLRLNSITRHMLGLLTGMPGARAFRQT 295
             +    P  +EV + M  +++     +GD    L + +  +H+   +  +PG   FR++
Sbjct: 243 TGEHLPAPLVSEVEQLMDEHLQAHYAFYGDY---LGVRTARKHIGWYVRDLPGGEQFRRS 299

Query: 296 LSDSKRLALGDPALLLEALQRTQAAQAA 323
           ++      + D A  L+A+++  A+QAA
Sbjct: 300 MNR-----IEDCAQQLQAVRQFFASQAA 322


  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    0.138    0.422 

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: 1,024,023
Number of extensions: 43826
Number of successful extensions: 111
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 110
Number of HSP's successfully gapped: 2
Length of query: 326
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 241
Effective length of database: 1,217,395
Effective search space: 293392195
Effective search space used: 293392195
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: 131 (55.1 bits)