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= 0005.0061.p
         (452 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312262|ref|YP_003776354.1| 23S rRNA (Uracil-5-)-methyltran...   785   0.0  

>gi|300312262|ref|YP_003776354.1| 23S rRNA
           (Uracil-5-)-methyltransferase [Herbaspirillum
           seropedicae SmR1]
          Length = 453

 Score =  785 bits (2027), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 372/453 (82%), Positives = 407/453 (89%), Gaps = 1/453 (0%)

Query: 1   MQQNII-NIKALDMDGRGVGHVANEDGTQGKVIFVEGALPGEQVSFQSYRRKPKWEAATM 59
           MQQ+II  IK+LDMDGRGVGH+ NEDGTQGKVIFVEGALPGE+VSFQSYR+KPKWEA  M
Sbjct: 1   MQQDIIIEIKSLDMDGRGVGHLENEDGTQGKVIFVEGALPGERVSFQSYRKKPKWEAGVM 60

Query: 60  TALHRESSLRVKPQCDYFGLCGGCAMQHLEPSAQVAMKQRVLEDNLWHLSKLKAETMLRP 119
           T LH ESSLRVKP+CDYFG CGGCAMQHLEPSAQVAMKQRVLEDNLWHL K KAE MLRP
Sbjct: 61  TTLHSESSLRVKPRCDYFGTCGGCAMQHLEPSAQVAMKQRVLEDNLWHLGKTKAEVMLRP 120

Query: 120 IYGPTWGYRYRARISVKNVVKKGTVLVGFHEKKSPFVSDMKTCEILPPHVSAMLMPLRAL 179
           IYGPTWGYRYRARISV++V KKG VLVGFHEK+S F++DMKTCEILPP+VSAML+PLR L
Sbjct: 121 IYGPTWGYRYRARISVRHVAKKGGVLVGFHEKRSSFIADMKTCEILPPNVSAMLVPLREL 180

Query: 180 IGSLSIIDRLPQIELAIGEGDNGVKTTVMVLRVMEPPSADDELKLKAFADEHKVEWWLQP 239
           +  LSI DR+PQIELA+GEGD+G K TV+VLR+ME  S  DE+ LK+FADEHK+EWWLQ 
Sbjct: 181 VAGLSIRDRMPQIELAVGEGDDGNKVTVLVLRIMEALSPADEVLLKSFADEHKIEWWLQT 240

Query: 240 KGPDTAHPFYPPQSNLHYTLPEFGIRMPFKPTDFTQVNHQINRVLVARALRLLDVQPEDR 299
           KGPDTA P+YP QS L YTLPEFGIRMPFKPTDFTQVNHQINRVLVARALRLLDVQP+DR
Sbjct: 241 KGPDTAAPYYPAQSRLQYTLPEFGIRMPFKPTDFTQVNHQINRVLVARALRLLDVQPQDR 300

Query: 300 VADLFCGLGNFTLPIATLAREVVGIEGSTALTERAAENAKVNGIAGKTAFYCRNLFEATT 359
           VADLFCGLGNFTLPIATLAREVVGIEGSTALTERA +NAKVNG+  KT+FYCRNLFEA  
Sbjct: 301 VADLFCGLGNFTLPIATLAREVVGIEGSTALTERALDNAKVNGVDAKTSFYCRNLFEAKP 360

Query: 360 EDFIALGKFDRMLIDPPREGALEVCKAIAGLGAQHAHLKPRRIVYVSCNPATLARDAGEL 419
           EDF+ALGKFDRMLIDPPREGA+EVCKA+  L  +  HLKP+RIVYVSCNPATLARDAG L
Sbjct: 361 EDFVALGKFDRMLIDPPREGAMEVCKALVELPPEQQHLKPKRIVYVSCNPATLARDAGML 420

Query: 420 VNLGGYRLTLAGVVNMFPHTAHVESMAVFDLAD 452
           V+LGGY L  AGVVNMFPHTAHVES+AVFDL +
Sbjct: 421 VHLGGYALKYAGVVNMFPHTAHVESIAVFDLPE 453


  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
   0.321    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: 1,419,183
Number of extensions: 57438
Number of successful extensions: 124
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 124
Number of HSP's successfully gapped: 1
Length of query: 452
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 364
Effective length of database: 1,203,190
Effective search space: 437961160
Effective search space used: 437961160
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: 132 (55.5 bits)