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= 0028.0124.p
         (225 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...   416   e-117
gi|300312307|ref|YP_003776399.1| ribosomal large subunit pseudou...    83   2e-17

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

 Score =  416 bits (1068), Expect = e-117,   Method: Compositional matrix adjust.
 Identities = 208/224 (92%), Positives = 216/224 (96%)

Query: 1   VHGGSGVSYGVIEQLRAARPQAKFLELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTT 60
           VHGGSGVSYGVIEQLRAARPQAKFLELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTT
Sbjct: 131 VHGGSGVSYGVIEQLRAARPQAKFLELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTT 190

Query: 61  DKRYFTLVQGDWKNARQHVKLPLFKYSTPDGERRVRVQADGQASHTIFSLLRRFGEFALL 120
           DKRYFTLVQGDWKNARQHVKLPLFKYSTPDGERRVRVQADGQ SHT+FSLLRRFG+FALL
Sbjct: 191 DKRYFTLVQGDWKNARQHVKLPLFKYSTPDGERRVRVQADGQPSHTVFSLLRRFGDFALL 250

Query: 121 EAELKTGRTHQIRVHLSSSGFPIVGDDKYGDFTLNKSLQKADGNRVAFKRMFLHAWRISF 180
           EAELKTGRTHQIRVHLSSSGFPIVGDDKYGDF LNK+LQKADG R+AFKRMFLHAWRISF
Sbjct: 251 EAELKTGRTHQIRVHLSSSGFPIVGDDKYGDFALNKALQKADGRRIAFKRMFLHAWRISF 310

Query: 181 RHPESGETVTLKAGLPEECARFLRSLEGGAEGDLLPHNMLAGTE 224
           RHPESG+TVTLKAGLP+ECA FLRSLEGG EG+LLP+ MLA  E
Sbjct: 311 RHPESGDTVTLKAGLPQECASFLRSLEGGEEGELLPYGMLACAE 354


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

 Score = 83.2 bits (204), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 63/185 (34%), Positives = 94/185 (50%), Gaps = 21/185 (11%)

Query: 27  LVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKLPLFKY 86
           +VHRLD+DTSG++++AK  +A T+L  Q++  +  ++Y  LV G        +  P+ ++
Sbjct: 169 IVHRLDKDTSGIMVVAKTLAAQTDLVRQLQARSMKRQYLALVWG-LPQLSGTINAPMARH 227

Query: 87  STPDGERRVRVQADGQASHTIFSLLRRF--GEF-----ALLEAELKTGRTHQIRVHLSSS 139
             P    ++ V    +A   + +  RR   GE      +L+   L+TGRTHQIRVHL S 
Sbjct: 228 --PRDRIKMAVSQSMRAKPAV-THYRRLATGEIDRKPVSLIHCRLETGRTHQIRVHLQSL 284

Query: 140 GFPIVGDDKYGDFTLNKSLQKADGNRVAFKRMFLHAWRISFRHPESGETVTLKAGLPEEC 199
           GFP+VGD  YG   L             F R  L A R+   HP +G+     A LPE+ 
Sbjct: 285 GFPLVGDALYGKHHLVS----------VFPRQALLAGRLGLLHPSTGKFRQWAAPLPEDI 334

Query: 200 ARFLR 204
              L+
Sbjct: 335 VALLQ 339


  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
   0.320    0.137    0.402 

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: 733,401
Number of extensions: 29685
Number of successful extensions: 79
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 77
Number of HSP's successfully gapped: 2
Length of query: 225
Length of database: 1,619,870
Length adjustment: 82
Effective length of query: 143
Effective length of database: 1,231,600
Effective search space: 176118800
Effective search space used: 176118800
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: 129 (54.3 bits)