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= 0021.0002.p
         (685 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...   913   0.0  

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

 Score =  913 bits (2360), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 430/645 (66%), Positives = 516/645 (80%), Gaps = 1/645 (0%)

Query: 4   QRAGFLLTRHWRDTPAGTEVEFWLATDDGPQLVRLPPQHSVAFIPAEQREQAEALLRNER 63
           +RAGF+LTRHWRDTPAG E+E WLATD G Q +RLPPQ +VAF+P  ++ + + LLR   
Sbjct: 5   ERAGFILTRHWRDTPAGVEIELWLATDTGAQCLRLPPQQAVAFVPQSEQARVQDLLRGVA 64

Query: 64  EVELRPLQ-LTDFSHRPVLGVYCRQHRQLIKIEKQFRDYGLAIYEADIRPPERYLMERFI 122
            VEL+PL+ L DFS RPV+G+Y R +RQL+++EKQ    G+++YEADIRPPERYLMERFI
Sbjct: 65  GVELKPLEALKDFSQRPVMGLYARHYRQLLRLEKQLVAAGISVYEADIRPPERYLMERFI 124

Query: 123 TAPVLFSGDANGTNPLLNTQLKPAPDYRPQLKLVSLDIETTMGGDLYSIALEGCGQRQVY 182
            APV F G  +G   L   +L+P P YRP L+L SLDIET+  G+LYSIA+EGCGQR VY
Sbjct: 125 NAPVAFGGVDDGQGVLGQARLRPLPGYRPPLRLASLDIETSWQGELYSIAIEGCGQRTVY 184

Query: 183 MLGPPNGDASGLDFDMEYCDTRAQMLEKLNQWMARHDPDAIIGWNVVQFDLRVLREHAAR 242
            L P +G    +DF + +CD+R +++E LN WMARHDPD IIGWN++QFDL VL++ A +
Sbjct: 185 TLAPASGAVQAVDFALHFCDSRRELIEALNAWMARHDPDVIIGWNLIQFDLNVLQKQADQ 244

Query: 243 FGIPLRFGRDGSELEWREHGFQQNHYFASAAGRLIIDGIEALRSATWSFPSFSLESVSQT 302
           +   L  GR    LEWR+HG +  H   SA GRL+IDGIE+LRSA W+FPSFSLE+V+QT
Sbjct: 245 YQTRLLPGRAAQPLEWRKHGLRAGHLLVSAPGRLVIDGIESLRSAFWNFPSFSLENVAQT 304

Query: 303 LLGEGKAINNPYQRMDEIDRRFAEDKPALATYNLKDCELVTRIFAKTELLSFLLERASVT 362
           LLGEGKAI  PYQRMDEIDR FAED+ ALATYNLKDCELVTRIFA T++LSFLLERASVT
Sbjct: 305 LLGEGKAIATPYQRMDEIDRMFAEDRAALATYNLKDCELVTRIFAVTDILSFLLERASVT 364

Query: 363 GLPADRNGGSVAAFGHLYMPHMHRLGFVAPNLGDTPGEPSPGGFVMDSQSGLFDSVLVLD 422
           GLPADR+GGSVAAF HLY+P +HR G+VAPNLGD     SPGGFVMDS+SGL+DSV+VLD
Sbjct: 365 GLPADRSGGSVAAFTHLYLPQLHRKGYVAPNLGDAEALASPGGFVMDSRSGLYDSVIVLD 424

Query: 423 YKSLYPSIIRTFLIDPVGLIEGLAHPGDADSVPGFRGARFSRSKHSLPAIVEKIWQGREV 482
           YKSLYPSIIR+FLIDP GL++G  +  +A +VPGF GARFSR  HSLPAI+E+IWQ RE 
Sbjct: 425 YKSLYPSIIRSFLIDPAGLVDGTLNESEAQTVPGFNGARFSRRSHSLPAIIEQIWQAREQ 484

Query: 483 AKRQQNKPLSQALKIIMNSLYGVLGSTGCRFFDARLASSITMRGHEIMHRTRELIEAQGY 542
           AK Q NK L QALKIIMNS YGVLGSTGCRFFD+RLASSIT RGHEIMHRTRELIE QGY
Sbjct: 485 AKAQGNKALQQALKIIMNSFYGVLGSTGCRFFDSRLASSITRRGHEIMHRTRELIEEQGY 544

Query: 543 EVIYGDTDSTFVWLRKAHDEASADAIGNALVRHVNDWWAAHLKETYGLDNALELEYETHY 602
           EVIYGDTDSTFVWLR AH +  A +IG AL   +NDWW  HL++ YGL++ALEL+YE HY
Sbjct: 545 EVIYGDTDSTFVWLRSAHSDEEARSIGLALTSRINDWWRLHLRQQYGLESALELQYEVHY 604

Query: 603 RRFLMPNVRGTDFGSKKRYAGMIIKPDGREEMIYKGLESHRSAWS 647
           +RFLMP VRG+D GSKKRYAG +   +G +++ YKGLE+ R+ W+
Sbjct: 605 QRFLMPTVRGSDTGSKKRYAGYVRTAEGEDKVTYKGLETVRTDWT 649


  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    0.421 

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: 2,380,950
Number of extensions: 106477
Number of successful extensions: 255
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 254
Number of HSP's successfully gapped: 1
Length of query: 685
Length of database: 1,619,870
Length adjustment: 92
Effective length of query: 593
Effective length of database: 1,184,250
Effective search space: 702260250
Effective search space used: 702260250
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: 134 (56.2 bits)