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= 0078.0008.p
         (343 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311755|ref|YP_003775847.1| DNA polymerase II protein [Herb...   474   e-135

>gi|300311755|ref|YP_003775847.1| DNA polymerase II protein
           [Herbaspirillum seropedicae SmR1]
          Length = 790

 Score =  474 bits (1220), Expect = e-135,   Method: Compositional matrix adjust.
 Identities = 226/341 (66%), Positives = 270/341 (79%)

Query: 1   MERFITAPVLFSGDANGAGPLLNTQLKPAPDYRPQLRLVSLDIETTMGGDLYSIALEGCG 60
           MERFI APV F G  +G G L   +L+P P YRP LRL SLDIET+  G+LYSIA+EGCG
Sbjct: 120 MERFINAPVAFGGVDDGQGVLGQARLRPLPGYRPPLRLASLDIETSWQGELYSIAIEGCG 179

Query: 61  QRQVYMLGPPNGDAGGLDFDMEYCDSRAQMLEKLNQWMAQHDPDAIIGWNVVQFDLRVLR 120
           QR VY L P +G    +DF + +CDSR +++E LN WMA+HDPD IIGWN++QFDL VL+
Sbjct: 180 QRTVYTLAPASGAVQAVDFALHFCDSRRELIEALNAWMARHDPDVIIGWNLIQFDLNVLQ 239

Query: 121 EHAARFGIPLRFGRDGSELEWREHGFQQNHYFASAAGRLIIDGIEALRSATWSFPSFSLE 180
           + A ++   L  GR    LEWR+HG +  H   SA GRL+IDGIE+LRSA W+FPSFSLE
Sbjct: 240 KQADQYQTRLLPGRAAQPLEWRKHGLRAGHLLVSAPGRLVIDGIESLRSAFWNFPSFSLE 299

Query: 181 SVSQTLLGEGKAIDNAYQRMDEIDRRFAEDKPALATYNLKDCELVTRIFAKTELLSFLLE 240
           +V+QTLLGEGKAI   YQRMDEIDR FAED+ ALATYNLKDCELVTRIFA T++LSFLLE
Sbjct: 300 NVAQTLLGEGKAIATPYQRMDEIDRMFAEDRAALATYNLKDCELVTRIFAVTDILSFLLE 359

Query: 241 RASVTGLPADRNGGSVAAFGHLYMPHMHRLGFVAPNLGDTPGEPSPGGFVMDSQSGLFDS 300
           RASVTGLPADR+GGSVAAF HLY+P +HR G+VAPNLGD     SPGGFVMDS+SGL+DS
Sbjct: 360 RASVTGLPADRSGGSVAAFTHLYLPQLHRKGYVAPNLGDAEALASPGGFVMDSRSGLYDS 419

Query: 301 VLVLDYKSLYPSIIRTFLIDPVGLIEGLAHPDDADSVPGYT 341
           V+VLDYKSLYPSIIR+FLIDP GL++G  +  +A +VPG+ 
Sbjct: 420 VIVLDYKSLYPSIIRSFLIDPAGLVDGTLNESEAQTVPGFN 460


  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    0.140    0.426 

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: 1,241,566
Number of extensions: 55870
Number of successful extensions: 126
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 126
Number of HSP's successfully gapped: 1
Length of query: 343
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 257
Effective length of database: 1,212,660
Effective search space: 311653620
Effective search space used: 311653620
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: 131 (55.1 bits)