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= 0098.0034.p
         (745 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...   617   e-177
gi|300312260|ref|YP_003776352.1| nucleoside-diphosphate kinase [...   174   2e-44

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

 Score =  617 bits (1591), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 297/378 (78%), Positives = 325/378 (85%), Gaps = 4/378 (1%)

Query: 15  MQQNII-NIKALDMDGRGVGHLANEDGTQGKVIFVEGALPGEQVSFQSYRRKPKWEAATM 73
           MQQ+II  IK+LDMDGRGVGHL NEDGTQGKVIFVEGALPGE+VSFQSYR+KPKWEA  M
Sbjct: 1   MQQDIIIEIKSLDMDGRGVGHLENEDGTQGKVIFVEGALPGERVSFQSYRKKPKWEAGVM 60

Query: 74  TTLHRESSLRVKPQCDYFGLCGGCAMQHLEPSAQVAMKQRVLEDNLWHLSKLKAETMLRP 133
           TTLH ESSLRVKP+CDYFG CGGCAMQHLEPSAQVAMKQRVLEDNLWHL K KAE MLRP
Sbjct: 61  TTLHSESSLRVKPRCDYFGTCGGCAMQHLEPSAQVAMKQRVLEDNLWHLGKTKAEVMLRP 120

Query: 134 IYGPTWGYRYRARISVKNVVKKGTVLVGFHEKKSPFVSDMKTCEILPPHVSAMLMPLRAL 193
           IYGPTWGYRYRARISV++V KKG VLVGFHEK+S F++DMKTCEILPP+VSAML+PLR L
Sbjct: 121 IYGPTWGYRYRARISVRHVAKKGGVLVGFHEKRSSFIADMKTCEILPPNVSAMLVPLREL 180

Query: 194 IGSLSIIDRLPQIELAIGEGDNGVKTTVMVLRVMEPPSADDEIKLKAFADEYKVEWWLQP 253
           +  LSI DR+PQIELA+GEGD+G K TV+VLR+ME  S  DE+ LK+FADE+K+EWWLQ 
Sbjct: 181 VAGLSIRDRMPQIELAVGEGDDGNKVTVLVLRIMEALSPADEVLLKSFADEHKIEWWLQT 240

Query: 254 KGPDTAHPFYPPQSNLHYTLPEFGIRMPFKPTDFTQVNHQINRVLVARALRLLDVQPEDR 313
           KGPDTA P+YP QS L YTLPEFGIRMPFKPTDFTQVNHQINRVLVARALRLLDVQP+DR
Sbjct: 241 KGPDTAAPYYPAQSRLQYTLPEFGIRMPFKPTDFTQVNHQINRVLVARALRLLDVQPQDR 300

Query: 314 VADLFCGLGNFTLPIATLAREVVGIEGSTALTERAAENAKVNAVAGKTGGGSAFSLKLSA 373
           VADLFCGLGNFTLPIATLAREVVGIEGSTALTERA +NAKVN V  KT   S +   L  
Sbjct: 301 VADLFCGLGNFTLPIATLAREVVGIEGSTALTERALDNAKVNGVDAKT---SFYCRNLFE 357

Query: 374 AQSVAIAAQDAQDREQVD 391
           A+     A    DR  +D
Sbjct: 358 AKPEDFVALGKFDRMLID 375


>gi|300312260|ref|YP_003776352.1| nucleoside-diphosphate kinase
           [Herbaspirillum seropedicae SmR1]
          Length = 141

 Score =  174 bits (441), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 84/96 (87%), Positives = 91/96 (94%)

Query: 643 KIIAARMIHLSRAEAEGFYAVHRERPFFKDLVDFMVSGPVIVQALEGDNAILKHRDLMGA 702
           K+IAARM  LSRAEAEGFYAVHRERPFFKDLVDFMVSGPV++Q LEG+ AILK+RDLMGA
Sbjct: 33  KVIAARMAQLSRAEAEGFYAVHRERPFFKDLVDFMVSGPVMIQVLEGEGAILKNRDLMGA 92

Query: 703 TDPKKAEKGTIRADFADSIDANAVHGSDAAETAKLK 738
           TDPKKAEKGTIRADFADSIDANAVHGSDA ETAK++
Sbjct: 93  TDPKKAEKGTIRADFADSIDANAVHGSDADETAKVE 128


  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
   0.318    0.133    0.393 

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: 2,213,519
Number of extensions: 89826
Number of successful extensions: 229
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 229
Number of HSP's successfully gapped: 2
Length of query: 745
Length of database: 1,619,870
Length adjustment: 92
Effective length of query: 653
Effective length of database: 1,184,250
Effective search space: 773315250
Effective search space used: 773315250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 134 (56.2 bits)