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= 0001.0022.p
         (299 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylat...   605   e-175
gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudou...    66   3e-12
gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudou...    61   1e-10

>gi|300312000|ref|YP_003776092.1| 23S RNA-specific pseudouridylate
           synthase [Herbaspirillum seropedicae SmR1]
          Length = 299

 Score =  605 bits (1561), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 299/299 (100%), Positives = 299/299 (100%)

Query: 1   MRPTPTLPMREGLSPSYLWLQPGPWRTMLSFLAERFTAVPEPVWRERLLRGEVRNQHGEA 60
           MRPTPTLPMREGLSPSYLWLQPGPWRTMLSFLAERFTAVPEPVWRERLLRGEVRNQHGEA
Sbjct: 1   MRPTPTLPMREGLSPSYLWLQPGPWRTMLSFLAERFTAVPEPVWRERLLRGEVRNQHGEA 60

Query: 61  LQPDTPYRSGDCIFYYRELPQGEARIPVEEKILHLDDHLLVADKPHFLPVIPTGRFVQET 120
           LQPDTPYRSGDCIFYYRELPQGEARIPVEEKILHLDDHLLVADKPHFLPVIPTGRFVQET
Sbjct: 61  LQPDTPYRSGDCIFYYRELPQGEARIPVEEKILHLDDHLLVADKPHFLPVIPTGRFVQET 120

Query: 121 LLVRLKKATGLQDLVPIHRLDRETAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAIAPLR 180
           LLVRLKKATGLQDLVPIHRLDRETAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAIAPLR
Sbjct: 121 LLVRLKKATGLQDLVPIHRLDRETAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAIAPLR 180

Query: 181 SDLELPRVHRSRVEEIPEQFFKMHEAEGAPNSETHISLIEARGALGLYRLEPVTGRRHQL 240
           SDLELPRVHRSRVEEIPEQFFKMHEAEGAPNSETHISLIEARGALGLYRLEPVTGRRHQL
Sbjct: 181 SDLELPRVHRSRVEEIPEQFFKMHEAEGAPNSETHISLIEARGALGLYRLEPVTGRRHQL 240

Query: 241 RVHMAALGIPILNDLFYPEAVPVGVADDLDKPLKLLARSLFFIDPLDGSERHFSSERNL 299
           RVHMAALGIPILNDLFYPEAVPVGVADDLDKPLKLLARSLFFIDPLDGSERHFSSERNL
Sbjct: 241 RVHMAALGIPILNDLFYPEAVPVGVADDLDKPLKLLARSLFFIDPLDGSERHFSSERNL 299


>gi|300311211|ref|YP_003775303.1| ribosomal large subunit
           pseudouridine synthase C [Herbaspirillum seropedicae
           SmR1]
          Length = 355

 Score = 66.2 bits (160), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 111/246 (45%), Gaps = 29/246 (11%)

Query: 30  SFLAERFTAVPEPVWRERLLRGEVRNQHGEALQPDTPYR--SGDCIFY--YRELPQGEAR 85
           +FL      VP+      L  GEVR   G   + D  YR   GD +     R   + E  
Sbjct: 49  NFLLRVCKGVPKSHIYRVLRSGEVRVNKG---RIDQTYRLAEGDVVRVPPIRVAEKQETV 105

Query: 86  IPVEE-KILHLDDHLLVADKPHFLPVIPTGRFVQETLLVRLKKAT-GLQDLVPIHRLDRE 143
           +P  E +IL  D HLLV DKP  + V   G  V   ++ +L+ A    + L  +HRLDR+
Sbjct: 106 VPGAEFRILLEDSHLLVIDKPAGVAV-HGGSGVSYGVIEQLRAARPQAKFLELVHRLDRD 164

Query: 144 TAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAIAPLRSDLELPRVHRSRVEEIPEQFFKM 203
           T+GV++ + + ++        ++    K Y  +  ++ D +  R H      +    FK 
Sbjct: 165 TSGVLLIAKKRSALTNLHDQMREGTTDKRYFTL--VQGDWKNARQH------VKLPLFKY 216

Query: 204 H----------EAEGAPNSETHISLIEARGALGLYRLEPVTGRRHQLRVHMAALGIPILN 253
                      +A+G P S T  SL+   G   L   E  TGR HQ+RVH+++ G PI+ 
Sbjct: 217 STPDGERRVRVQADGQP-SHTVFSLLRRFGDFALLEAELKTGRTHQIRVHLSSSGFPIVG 275

Query: 254 DLFYPE 259
           D  Y +
Sbjct: 276 DDKYGD 281


>gi|300312307|ref|YP_003776399.1| ribosomal large subunit
           pseudouridine synthase D [Herbaspirillum seropedicae
           SmR1]
          Length = 370

 Score = 60.8 bits (146), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 55/185 (29%), Positives = 82/185 (44%), Gaps = 20/185 (10%)

Query: 87  PVEEKILHLDDHLLVADKPHFLPVIPTGRFVQETLLVRLKKATGLQDLVP----IHRLDR 142
           P+   ILH D  L+V +KP  L V P       TLL  L         VP    +HRLD+
Sbjct: 116 PMALDILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALAKVPRAGIVHRLDK 175

Query: 143 ETAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAIA----PLRSDLELP--RVHRSRVEEI 196
           +T+G++V +   A++       Q R+M + Y A+      L   +  P  R  R R++  
Sbjct: 176 DTSGIMVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINAPMARHPRDRIKMA 235

Query: 197 PEQFFKMHEAEGAPNSETHISLIEA----RGALGLYRLEPVTGRRHQLRVHMAALGIPIL 252
             Q  +      A  + TH   +      R  + L      TGR HQ+RVH+ +LG P++
Sbjct: 236 VSQSMR------AKPAVTHYRRLATGEIDRKPVSLIHCRLETGRTHQIRVHLQSLGFPLV 289

Query: 253 NDLFY 257
            D  Y
Sbjct: 290 GDALY 294


  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
   0.322    0.140    0.426 

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: 1,018,096
Number of extensions: 45477
Number of successful extensions: 113
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 110
Number of HSP's successfully gapped: 3
Length of query: 299
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 214
Effective length of database: 1,217,395
Effective search space: 260522530
Effective search space used: 260522530
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)