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= 0002.0305.p
         (436 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311574|ref|YP_003775666.1| DNA polymerase, Y family protei...   458   e-130

>gi|300311574|ref|YP_003775666.1| DNA polymerase, Y family protein
           [Herbaspirillum seropedicae SmR1]
          Length = 466

 Score =  458 bits (1179), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 249/443 (56%), Positives = 304/443 (68%), Gaps = 7/443 (1%)

Query: 1   MRRGGVLALLPQAPMHDRAPEREAQTLFGAATALLQYTPQASFSDDATVLLDIGASLRLF 60
           MRRGGV  L P+A + +R P RE   L   A ALLQYTPQ S +  A VLL++ ASLRLF
Sbjct: 24  MRRGGVQLLAPEAQLQERDPAREQAALEQTALALLQYTPQVSLAPQACVLLEVSASLRLF 83

Query: 61  GGIRMLCQRVRCTMHRLGLTAIISCAPTAAGAALLARHGGVRIMKKERLHQCLDRLPVSA 120
           GGIR LC++VR ++ RLGL+A +SCA TA GA +LAR+G VR +++  L + LDRLPV  
Sbjct: 84  GGIRALCRKVRVSISRLGLSATLSCAVTATGAWMLARYGDVRTVRERSLRRRLDRLPVVL 143

Query: 121 LLTVAPYLDWLEGIGCRTLSDLRRLPRAGLQRRGHTHMLDTLDCAYGNAPELHAWIEMPP 180
           L     +L+WL G+GCR L  LR LPRAGLQRR    +LD L+ AYG APE+H W+  PP
Sbjct: 144 LSAAQAHLEWLHGLGCRQLGQLRALPRAGLQRRCGKALLDMLEHAYGEAPEVHDWVVAPP 203

Query: 181 TFRQRIELNERIEHADAALHTVQALLAQLCGWLSARQLAVKQVHVQLEHERGRQAVTPTA 240
            F+ R+EL +RIE  D      QALL QL GWL+ARQLAVKQ+ + LEHERGRQAV PT 
Sbjct: 204 VFQARVELPDRIEQTDILTAYAQALLTQLAGWLTARQLAVKQLRLWLEHERGRQAVAPTD 263

Query: 241 IQLALAESTWQDSHLIRLLKERLAHLEISAPIIAVVLEAAETEPMAPASDKLFPEPGGSP 300
           +++AL+   WQ+ HL  L+KE+LA   + AP IA+ L A E E   PASD LFPEPGGS 
Sbjct: 264 LRIALSAPAWQEDHLYSLVKEKLARSTLPAPAIALGLAAEELERRQPASDMLFPEPGGSA 323

Query: 301 ADYKRLVELLVARLGADKVLQASPLADYRPEQANRWVPVMATATSL------DHRPLPPR 354
            D++RL+ELLVARLGADKV QA+P ADYRPE ANRW  VM  A SL      D   LPPR
Sbjct: 324 EDHQRLLELLVARLGADKVRQAAPRADYRPELANRWCSVMQPAASLPAPLSTDAARLPPR 383

Query: 355 PTWLLEQPVVLPLRAHRPYYGARLRPVSPPERIEAGWWNGLLVTRDYYIAEGANHCHYWI 414
           P WLL++PV L +  H+P+Y   L   SPPERIEAGWW G   TRDY+    A H +YWI
Sbjct: 384 PLWLLDEPVPLRVLQHKPFYRTPLEFTSPPERIEAGWWEGRPSTRDYFTVRDAQHAYYWI 443

Query: 415 YRE-RIGDVDGREPHWYLHGLFG 436
           +R+   G+    EP W+LHGLFG
Sbjct: 444 FRQWHGGECPEEEPQWFLHGLFG 466


  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
   0.323    0.137    0.435 

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: 1,498,639
Number of extensions: 65183
Number of successful extensions: 201
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 199
Number of HSP's successfully gapped: 1
Length of query: 436
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 348
Effective length of database: 1,203,190
Effective search space: 418710120
Effective search space used: 418710120
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 132 (55.5 bits)