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= 0001.2731.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...   551   e-158
gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudou...    77   2e-15
gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudou...    67   2e-12

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

 Score =  551 bits (1421), Expect = e-158,   Method: Compositional matrix adjust.
 Identities = 270/299 (90%), Positives = 286/299 (95%)

Query: 1   MRPTPTLPMRDGLSPSYLWLQPGPWRDMLSFLAEHFTAVPAEIWRERLLRGEVRNQRGED 60
           MRPTPTLPMR+GLSPSYLWLQPGPWR MLSFLAE FTAVP  +WRERLLRGEVRNQ GE 
Sbjct: 1   MRPTPTLPMREGLSPSYLWLQPGPWRTMLSFLAERFTAVPEPVWRERLLRGEVRNQHGEA 60

Query: 61  LRPDSAYRSGDCIFYYRELPQGEERIPVEEKILHLDEHLLVADKPHFLPVIPTGRFVQET 120
           L+PD+ YRSGDCIFYYRELPQGE RIPVEEKILHLD+HLLVADKPHFLPVIPTGRFVQET
Sbjct: 61  LQPDTPYRSGDCIFYYRELPQGEARIPVEEKILHLDDHLLVADKPHFLPVIPTGRFVQET 120

Query: 121 LLVRLKKATGLQDLVPIHRLDRETAGVIVFSHQRASRGKYQSMFRERSMFKVYEAIAPLR 180
           LLVRLKKATGLQDLVPIHRLDRETAGVIVFSHQ ASRGKYQSMF++R+MFKVYEAIAPLR
Sbjct: 121 LLVRLKKATGLQDLVPIHRLDRETAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAIAPLR 180

Query: 181 PELQLPRVHRSRVEELPEQFFKMHEAQGAPNSETHISLLEARGELGLYQLEPVTGRRHQL 240
            +L+LPRVHRSRVEE+PEQFFKMHEA+GAPNSETHISL+EARG LGLY+LEPVTGRRHQL
Sbjct: 181 SDLELPRVHRSRVEEIPEQFFKMHEAEGAPNSETHISLIEARGALGLYRLEPVTGRRHQL 240

Query: 241 RVHMAALGIPILNDLFYPHAVPVGVADDLDKPLKLLARSLFFIDPLDGSERHFVSQRSL 299
           RVHMAALGIPILNDLFYP AVPVGVADDLDKPLKLLARSLFFIDPLDGSERHF S+R+L
Sbjct: 241 RVHMAALGIPILNDLFYPEAVPVGVADDLDKPLKLLARSLFFIDPLDGSERHFSSERNL 299


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

 Score = 77.0 bits (188), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 113/240 (47%), Gaps = 21/240 (8%)

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

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

Query: 144 TAGVIVFSHQRASRGKYQSMFRERSMFKVYEAIA-----PLRPELQLPRVHRSRVEELPE 198
           T+GV++ + +R++        RE +  K Y  +        R  ++LP    S     P+
Sbjct: 165 TSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKLPLFKYS----TPD 220

Query: 199 QFFKMH-EAQGAPNSETHISLLEARGELGLYQLEPVTGRRHQLRVHMAALGIPILNDLFY 257
              ++  +A G P S T  SLL   G+  L + E  TGR HQ+RVH+++ G PI+ D  Y
Sbjct: 221 GERRVRVQADGQP-SHTVFSLLRRFGDFALLEAELKTGRTHQIRVHLSSSGFPIVGDDKY 279


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

 Score = 66.6 bits (161), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/189 (32%), Positives = 88/189 (46%), Gaps = 16/189 (8%)

Query: 80  PQGEERIPVEEKILHLDEHLLVADKPHFLPVIPTGRFVQETLLVRLKKATGLQDLVP--- 136
           P G E  P+   ILH D+ L+V +KP  L V P       TLL  L         VP   
Sbjct: 111 PYGPE--PMALDILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALAKVPRAG 168

Query: 137 -IHRLDRETAGVIVFSHQRASRGKYQSMFRERSMFKVYEAIAPLRPELQLPRVHRSRVEE 195
            +HRLD++T+G++V +   A++       + RSM + Y A+    P  QL     + +  
Sbjct: 169 IVHRLDKDTSGIMVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLP--QLSGTINAPMAR 226

Query: 196 LPEQFFKMHEAQG--APNSETHISLLEARGEL-----GLYQLEPVTGRRHQLRVHMAALG 248
            P    KM  +Q   A  + TH   L A GE+      L      TGR HQ+RVH+ +LG
Sbjct: 227 HPRDRIKMAVSQSMRAKPAVTHYRRL-ATGEIDRKPVSLIHCRLETGRTHQIRVHLQSLG 285

Query: 249 IPILNDLFY 257
            P++ D  Y
Sbjct: 286 FPLVGDALY 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
   0.323    0.141    0.427 

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: 1,011,250
Number of extensions: 44927
Number of successful extensions: 110
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 106
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 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 130 (54.7 bits)