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= 0131.0002.p
         (227 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...   235   2e-63
gi|300311211|ref|YP_003775303.1| ribosomal large subunit pseudou...    57   1e-09

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

 Score =  235 bits (600), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 117/171 (68%), Positives = 131/171 (76%), Gaps = 1/171 (0%)

Query: 58  TGLADLTPIHRLDRETAGVLIFSHNPASRGAYQAMFQQRTMDKTYEALAGMLEGRSFPFV 117
           TGL DL PIHRLDRETAGV++FSH PASRG YQ+MFQQR M K YEA+A +      P V
Sbjct: 129 TGLQDLVPIHRLDRETAGVIVFSHQPASRGKYQSMFQQRAMFKVYEAIAPLRSDLELPRV 188

Query: 118 HRSRMVD-ADKFFLMREEEGEPNSETHIDLIERRGALGLYRLNPVTGRKHQLRVHMAALG 176
           HRSR+ +  ++FF M E EG PNSETHI LIE RGALGLYRL PVTGR+HQLRVHMAALG
Sbjct: 189 HRSRVEEIPEQFFKMHEAEGAPNSETHISLIEARGALGLYRLEPVTGRRHQLRVHMAALG 248

Query: 177 IPIVNDNFYPHVVPAGTADNYDAPLKLLARSIAFTDPLSGDVRYFESLRTL 227
           IPI+ND FYP  VP G AD+ D PLKLLARS+ F DPL G  R+F S R L
Sbjct: 249 IPILNDLFYPEAVPVGVADDLDKPLKLLARSLFFIDPLDGSERHFSSERNL 299



 Score = 65.5 bits (158), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 29/55 (52%), Positives = 37/55 (67%), Gaps = 2/55 (3%)

Query: 1  MKPTAPLPLKDGVAPSYLWLQEAADLWSNMLDFLTARFPGVTEEAWRQRMARGEV 55
          M+PT  LP+++G++PSYLWLQ     W  ML FL  RF  V E  WR+R+ RGEV
Sbjct: 1  MRPTPTLPMREGLSPSYLWLQPGP--WRTMLSFLAERFTAVPEPVWRERLLRGEV 53


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

 Score = 57.0 bits (136), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 51/166 (30%), Positives = 74/166 (44%), Gaps = 14/166 (8%)

Query: 63  LTPIHRLDRETAGVLIFSHNPASRGAYQAMFQQRTMDKTYEALA-----GMLEGRSFPFV 117
           L  +HRLDR+T+GVL+ +   ++        ++ T DK Y  L         +    P  
Sbjct: 155 LELVHRLDRDTSGVLLIAKKRSALTNLHDQMREGTTDKRYFTLVQGDWKNARQHVKLPLF 214

Query: 118 HRSRMVDADKFFLMREEEGEPNSETHIDLIERRGALGLYRLNPVTGRKHQLRVHMAALGI 177
             S   D ++   + + +G+P S T   L+ R G   L      TGR HQ+RVH+++ G 
Sbjct: 215 KYS-TPDGERRVRV-QADGQP-SHTVFSLLRRFGDFALLEAELKTGRTHQIRVHLSSSGF 271

Query: 178 PIVNDNFYPHVV---PAGTADNYDAPLK---LLARSIAFTDPLSGD 217
           PIV D+ Y           AD      K   L A  I+F  P SGD
Sbjct: 272 PIVGDDKYGDFALNKALQKADGRRIAFKRMFLHAWRISFRHPESGD 317


  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    0.137    0.415 

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: 775,565
Number of extensions: 33224
Number of successful extensions: 84
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 81
Number of HSP's successfully gapped: 3
Length of query: 227
Length of database: 1,619,870
Length adjustment: 82
Effective length of query: 145
Effective length of database: 1,231,600
Effective search space: 178582000
Effective search space used: 178582000
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: 129 (54.3 bits)