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= 0035.0012.p
         (322 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudou...   276   2e-75
gi|300311212|ref|YP_003775304.1| phosphoglycolate phosphatase [H...   202   2e-53

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

 Score =  276 bits (706), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 174/356 (48%), Positives = 211/356 (59%), Gaps = 64/356 (17%)

Query: 1   MKDLARFSGKTPEKPESPASTQSAPAS---PQVQLLTISEEEAGQRIDNFLLRVCKGVPK 57
           MKDLARFS    E  ++  ++++A AS   PQVQLLTIS+EEAGQRIDNFLLRVCKGVPK
Sbjct: 1   MKDLARFSRGASESAKAAPASRNATASQSVPQVQLLTISDEEAGQRIDNFLLRVCKGVPK 60

Query: 58  SHIYRVLRSGEVRVNKGRIDQTYRLQDGDILRVPPIRIAEKASAAVAPGAEFKILLEDNH 117
           SHIYRVLRSGEVRVNKGRIDQTYRL +GD++RVPPIR+AEK    V PGAEF+ILLED+H
Sbjct: 61  SHIYRVLRSGEVRVNKGRIDQTYRLAEGDVVRVPPIRVAEKQE-TVVPGAEFRILLEDSH 119

Query: 118 LLIIDXRARARAARDLGLPIPDKSAASYVIGLGLQDAMQAAIPDVDPKYYPRIVERYRHH 177
           LL+ID  A        G+ +   S  SY    G+ + ++AA P      +  +V R    
Sbjct: 120 LLVIDKPA--------GVAVHGGSGVSY----GVIEQLRAARPQAK---FLELVHRLDRD 164

Query: 178 YLG-------QDKDLSLFDGVREMLDDLGQQGYFLAVA--------------------TG 210
             G       +    +L D +RE   D   + YF  V                      G
Sbjct: 165 TSGVLLIAKKRSALTNLHDQMREGTTD---KRYFTLVQGDWKNARQHVKLPLFKYSTPDG 221

Query: 211 KSRV-------------GLNRALNSTNLLSAFDATRCXGTNLLSAFDATRGFPIVGDDKY 257
           + RV              L R      LL A    +   T+ +    ++ GFPIVGDDKY
Sbjct: 222 ERRVRVQADGQPSHTVFSLLRRFGDFALLEA--ELKTGRTHQIRVHLSSSGFPIVGDDKY 279

Query: 258 GDFPLNKSLQKADGERGAFKRMFLHAHQITFTHPDSGKTVTLKAGLPPECQRFLKS 313
           GDF LNK+LQKADG R AFKRMFLHA +I+F HP+SG TVTLKAGLP EC  FL+S
Sbjct: 280 GDFALNKALQKADGRRIAFKRMFLHAWRISFRHPESGDTVTLKAGLPQECASFLRS 335


>gi|300311212|ref|YP_003775304.1| phosphoglycolate phosphatase
           [Herbaspirillum seropedicae SmR1]
          Length = 219

 Score =  202 bits (515), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 97/111 (87%), Positives = 102/111 (91%)

Query: 124 RARARAARDLGLPIPDKSAASYVIGLGLQDAMQAAIPDVDPKYYPRIVERYRHHYLGQDK 183
           R    AARDLGLPIPDKSAASYVIGLGLQDAMQAAIPDVDPKYYPRIVERYRHHYLGQDK
Sbjct: 26  RCIQAAARDLGLPIPDKSAASYVIGLGLQDAMQAAIPDVDPKYYPRIVERYRHHYLGQDK 85

Query: 184 DLSLFDGVREMLDDLGQQGYFLAVATGKSRVGLNRALNSTNLLSAFDATRC 234
           DL+LF+GV EML DL QQGYFLAVATGKSRVGLNRA+N+T LLS FDA+RC
Sbjct: 86  DLTLFEGVPEMLADLSQQGYFLAVATGKSRVGLNRAMNTTGLLSMFDASRC 136


  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
   0.319    0.137    0.394 

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: 933,504
Number of extensions: 37385
Number of successful extensions: 116
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 114
Number of HSP's successfully gapped: 3
Length of query: 322
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 237
Effective length of database: 1,217,395
Effective search space: 288522615
Effective search space used: 288522615
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 (21.8 bits)
S2: 130 (54.7 bits)