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= 0001.0390.p
         (346 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309754|ref|YP_003773846.1| tRNA-dihydrouridine synthase or...   635   0.0  
gi|300312882|ref|YP_003776974.1| hypothetical protein Hsero_3587...    80   3e-16

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

 Score =  635 bits (1639), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 320/342 (93%), Positives = 326/342 (95%), Gaps = 2/342 (0%)

Query: 5   VNIGPYSLRNNVFVAPMAGVTDRPFRQLCKQLGAGYAVSEMAASDPRLWHSEKTSRRINH 64
           +NIGPYSLRNNVFVAPMAGVTDRPFRQLCKQLGAGYAVSEMAASDPRLW SEKTSRRINH
Sbjct: 1   MNIGPYSLRNNVFVAPMAGVTDRPFRQLCKQLGAGYAVSEMAASDPRLWQSEKTSRRINH 60

Query: 65  DGEMEPKAVQIAGADPAMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEEL 124
           DGEMEPKAVQIAGADP MLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEEL
Sbjct: 61  DGEMEPKAVQIAGADPVMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEEL 120

Query: 125 VARILDAVVSAVDVPVTLKFRTGWNRANKNALKIAARAEAAGIAMLTLHGRTRADGYSGE 184
           VARILDAVVSAVDVPVTLKFRTGWNRANKNALKIAARAEAAGIAMLTLHGRTRADGYSGE
Sbjct: 121 VARILDAVVSAVDVPVTLKFRTGWNRANKNALKIAARAEAAGIAMLTLHGRTRADGYSGE 180

Query: 185 AEYETIAAVKAAVKIPVVANGDITTPEKAREVLRITGADAVMVGRAAQGRPWIFREIDHF 244
           AEYETIAAVKAAVKIPVVANGDITTPEKAR+VL +T ADAVMVGRAAQGRPWIFREIDHF
Sbjct: 181 AEYETIAAVKAAVKIPVVANGDITTPEKARDVLLLTKADAVMVGRAAQGRPWIFREIDHF 240

Query: 245 LRTGDFLPAPLVSEVEHLMAEHLQAHYAFYGEYLGVRTARKHIGWYVRDLPGGEQFRRSM 304
           LRTG+ LPAPLVSEVE LM EHLQAHYAFYG+YLGVRTARKHIGWYVRDLPGGEQFRRSM
Sbjct: 241 LRTGEHLPAPLVSEVEQLMDEHLQAHYAFYGDYLGVRTARKHIGWYVRDLPGGEQFRRSM 300

Query: 305 NRIEDCGQQLQAVRQFFADQAAHGERLQYERAQEMQEVPLAA 346
           NRIEDC QQLQAVRQFFA QAA GERLQY  A  + EV LAA
Sbjct: 301 NRIEDCAQQLQAVRQFFASQAAFGERLQYGLA--VDEVALAA 340


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

 Score = 80.1 bits (196), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 86/332 (25%), Positives = 144/332 (43%), Gaps = 29/332 (8%)

Query: 18  VAPMAGVTDRPFRQLCKQLG-AGYAVSEMAASDPRLWHSEKTSRRINHDGEMEPKAVQIA 76
           VAPM   TDR  R   +Q+    +  +EM  +   L H +   R ++ D +  P A+Q+ 
Sbjct: 29  VAPMMDWTDRHCRVFHRQITRHTWLYTEMVTTGA-LLHGD-VPRHLDFDEQEHPVALQLG 86

Query: 77  GADPAMLADCAKYNVERGAQIIDINMGCPVKKVCNSWCGSALLQDEELVARILDAVVSAV 136
           G++PA LA  AK   + G   I++N GCP ++V     G+ L+ +  LVA  + A+  AV
Sbjct: 87  GSEPADLAHSAKLGEQWGYDEINLNCGCPSERVQKGAFGACLMGEPTLVADCVKAMRDAV 146

Query: 137 DVPVTLKFRTGWNRANKNAL--KIAARAEAAGIAMLTLHGRTRADGYSGEAEYETIAAVK 194
            + VT+K R G +             +   AG     +H R          E   I  +K
Sbjct: 147 SIDVTVKHRIGIDEVESYDFVRDFVGQIAEAGCQTFIVHARNAILKGLSPKENREIPPLK 206

Query: 195 AAV---------KIPVVANGDITTPEKAREVLRITGADAVMVGRAAQGRPWIFREIDHFL 245
                        + ++ NG I T  +  E L+    D VM+GR A   P++    D   
Sbjct: 207 YDYAYQLKKDFPSLEILINGGIKTLPEIDEHLK--HVDGVMLGREAYHNPYLMAGFD--A 262

Query: 246 RTGDFLPAPLV---SEVEHLMAEHLQAHYAFYGEY---LGVRTARKHIGWYVRDLPGGEQ 299
           R    L   L    +EV   M  +++     +G+    L + +  +H+   +  +PG   
Sbjct: 263 RYYAALEGGLQRSRAEVIEAMLPYIKRQLELHGDNGRGLRLNSITRHMLGLMAGMPGARA 322

Query: 300 FRRSMNR-----IEDCGQQLQAVRQFFADQAA 326
           FR++++      + D    L+A+++  A QAA
Sbjct: 323 FRQTLSDSKRLALGDPALLLEALQRTQAAQAA 354


  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    0.135    0.405 

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: 1,018,882
Number of extensions: 40062
Number of successful extensions: 155
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 154
Number of HSP's successfully gapped: 2
Length of query: 346
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 260
Effective length of database: 1,212,660
Effective search space: 315291600
Effective search space used: 315291600
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)