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= 0002.0129.p
         (574 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309795|ref|YP_003773887.1| DNA polymerase I protein [Herba...  1004   0.0  

>gi|300309795|ref|YP_003773887.1| DNA polymerase I protein
           [Herbaspirillum seropedicae SmR1]
          Length = 920

 Score = 1004 bits (2596), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 479/574 (83%), Positives = 524/574 (91%)

Query: 1   VDTETTSLVPMQAQLVGISLCCEAGRAAYIPVAHNYQDMPAQLPRELVLAKLKPWLEDDS 60
           VDTETTSL  MQA+LVGISLCCE GRAAYIPVAHNYQD P QL R+ VL KLKPWLED S
Sbjct: 347 VDTETTSLEAMQAELVGISLCCEPGRAAYIPVAHNYQDAPVQLSRQHVLEKLKPWLEDAS 406

Query: 61  KPKLGQNLKYDSHIFANQGIQLRGIVHDTLLESYVFESHRTHDMDSLALRHLNRTTISYT 120
           KPKLGQ+LKYDSHIFAN G++L G+ HDTLLESYVFESHR HDMDSLA RHL R TI+Y 
Sbjct: 407 KPKLGQHLKYDSHIFANYGVRLAGVKHDTLLESYVFESHRPHDMDSLAARHLERKTITYA 466

Query: 121 DVCGKGASQICFDQVEIGRATEYAAEDADVTLALHQAMWPQVENDAKLRYIYEKIEVPTS 180
           +VCGKGASQI F++V I RATEYAAEDA+VTLALHQAMWPQ+E+D KLR+IYEKIEVPTS
Sbjct: 467 EVCGKGASQIGFNEVAIERATEYAAEDAEVTLALHQAMWPQIEHDDKLRFIYEKIEVPTS 526

Query: 181 VVLQKIERNGVLVDAAILATQSNELGKRMLEIEQQAYELAGQPFNLNSPKQLGEILFEKL 240
           VVLQKIERNGVL+D+  L  QS++LGKRMLEIEQQAY+LAGQPFNLNSPKQLGEILF KL
Sbjct: 527 VVLQKIERNGVLIDSERLGQQSHDLGKRMLEIEQQAYDLAGQPFNLNSPKQLGEILFGKL 586

Query: 241 QLPVVKKTPSGTPSTDEEVLAKLAEDYPLPKILLDYRGLSKLKSTYTDKLPKMVDPTTGR 300
           +LPVVKKT SG PSTDEEVL KLAEDYPLPK+LLDYRGL+KLKSTYTDKLPKMV+P TGR
Sbjct: 587 ELPVVKKTASGAPSTDEEVLQKLAEDYPLPKVLLDYRGLAKLKSTYTDKLPKMVNPATGR 646

Query: 301 VHTNYAQAVAVTGRLASNDPNLQNIPIRTAEGRRIREAFIAPPGSTIVSADYSQIELRIM 360
           VHTNYAQAVAVTGRL+SNDPNLQNIPIRTAEGRRIREAF+AP GS IVSADYSQIELRIM
Sbjct: 647 VHTNYAQAVAVTGRLSSNDPNLQNIPIRTAEGRRIREAFVAPEGSVIVSADYSQIELRIM 706

Query: 361 AHISGDANMLKAFADGEDIHRATASEIFGVGLADVTSEQRRYAKVINFGLIYGMSAFGLA 420
           AHIS D NMLKAFA+ EDIHRATA+EIFG+    V SEQRRYAKVINFGLIYGMSAFGLA
Sbjct: 707 AHISEDENMLKAFANNEDIHRATAAEIFGIAPEQVESEQRRYAKVINFGLIYGMSAFGLA 766

Query: 421 GNLGIERSAAQMYIDKYFQRFSSVKQYMDDTRLEAKSQGYVETVFGRRLWLPEINSPNGP 480
            NLGIER+AAQMYIDKYF RFS VK+YMD+TRL+AK++GYVETVFGRRLWLPEINSPNGP
Sbjct: 767 SNLGIERAAAQMYIDKYFMRFSGVKRYMDETRLQAKARGYVETVFGRRLWLPEINSPNGP 826

Query: 481 RRQGAERAAINAPMQGTAADLIKLAMISVQGWIEQDGLQSKLIMQVHDELVMEVPDAELA 540
           RRQGAERAAINAPMQGTAADLIK+AMI+VQ W+E + LQ+++IMQVHDELV+EVP  EL 
Sbjct: 827 RRQGAERAAINAPMQGTAADLIKMAMIAVQDWLETNSLQTRMIMQVHDELVLEVPQQELE 886

Query: 541 LVREKLPELMKNVAELKVPLIAEVGAGKNWDQAH 574
           +VREKLPELMKNVAELKVPL+AEVG GKNWD+AH
Sbjct: 887 MVREKLPELMKNVAELKVPLLAEVGIGKNWDEAH 920


  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
   0.317    0.133    0.380 

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: 1,737,425
Number of extensions: 72079
Number of successful extensions: 194
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 194
Number of HSP's successfully gapped: 1
Length of query: 574
Length of database: 1,619,870
Length adjustment: 90
Effective length of query: 484
Effective length of database: 1,193,720
Effective search space: 577760480
Effective search space used: 577760480
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: 133 (55.8 bits)