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= 0001.2176.p
         (795 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...  1410   0.0  

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

 Score = 1410 bits (3649), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 678/790 (85%), Positives = 729/790 (92%)

Query: 6   LRPGERAGFIVSRHWRDTPAGVEIELWLATDEGPQCLRLPPQPAVAFVPQEQAERVQALI 65
           +RPGERAGFI++RHWRDTPAGVEIELWLATD G QCLRLPPQ AVAFVPQ +  RVQ L+
Sbjct: 1   MRPGERAGFILTRHWRDTPAGVEIELWLATDTGAQCLRLPPQQAVAFVPQSEQARVQDLL 60

Query: 66  QGERGMELRPLDHLKDLSQRPVLGLYARQYRKLLKMEKTLLAAGIAVYEADIRPPERYLM 125
           +G  G+EL+PL+ LKD SQRPV+GLYAR YR+LL++EK L+AAGI+VYEADIRPPERYLM
Sbjct: 61  RGVAGVELKPLEALKDFSQRPVMGLYARHYRQLLRLEKQLVAAGISVYEADIRPPERYLM 120

Query: 126 ERFINAPLAFQGVDDGHGALVEARIRPLPGYRPPLKLASLDIETSWQGELYSIAIEGCGQ 185
           ERFINAP+AF GVDDG G L +AR+RPLPGYRPPL+LASLDIETSWQGELYSIAIEGCGQ
Sbjct: 121 ERFINAPVAFGGVDDGQGVLGQARLRPLPGYRPPLRLASLDIETSWQGELYSIAIEGCGQ 180

Query: 186 RSVYALGPPSGAVEAVDFELQFCATRKELIDCLNAWMARHDPDAIIGWNLVQFDLNVLQK 245
           R+VY L P SGAV+AVDF L FC +R+ELI+ LNAWMARHDPD IIGWNL+QFDLNVLQK
Sbjct: 181 RTVYTLAPASGAVQAVDFALHFCDSRRELIEALNAWMARHDPDVIIGWNLIQFDLNVLQK 240

Query: 246 QAQKYQTTLRLGRAGRVLEWRQHGLRANHLLVSAPGRLVIDGIESLRSAFWNFPSFSLEN 305
           QA +YQT L  GRA + LEWR+HGLRA HLLVSAPGRLVIDGIESLRSAFWNFPSFSLEN
Sbjct: 241 QADQYQTRLLPGRAAQPLEWRKHGLRAGHLLVSAPGRLVIDGIESLRSAFWNFPSFSLEN 300

Query: 306 VAQSLLGEGKAIATPYQRMDEIDRMFAEDKAALATYNLKDCELVTRIFAKTEILSFLLER 365
           VAQ+LLGEGKAIATPYQRMDEIDRMFAED+AALATYNLKDCELVTRIFA T+ILSFLLER
Sbjct: 301 VAQTLLGEGKAIATPYQRMDEIDRMFAEDRAALATYNLKDCELVTRIFAVTDILSFLLER 360

Query: 366 ASVTGLQADRSGGSVAAFTHLYLPHMHRKGYVAPNLGEAEALASPGGFVMDSRPGLYDSV 425
           ASVTGL ADRSGGSVAAFTHLYLP +HRKGYVAPNLG+AEALASPGGFVMDSR GLYDSV
Sbjct: 361 ASVTGLPADRSGGSVAAFTHLYLPQLHRKGYVAPNLGDAEALASPGGFVMDSRSGLYDSV 420

Query: 426 IVLDYKSLYPSIIRTFLIDPVGLVDGTLNEPEAQTVPGFNGARFSRRSHSLPAIIEQIWQ 485
           IVLDYKSLYPSIIR+FLIDP GLVDGTLNE EAQTVPGFNGARFSRRSHSLPAIIEQIWQ
Sbjct: 421 IVLDYKSLYPSIIRSFLIDPAGLVDGTLNESEAQTVPGFNGARFSRRSHSLPAIIEQIWQ 480

Query: 486 GREVAKAQGNKPLQQALKIIMNSFYGVLGSTACRFFDSRLASSITRRGHEIMHRTRELIE 545
            RE AKAQGNK LQQALKIIMNSFYGVLGST CRFFDSRLASSITRRGHEIMHRTRELIE
Sbjct: 481 AREQAKAQGNKALQQALKIIMNSFYGVLGSTGCRFFDSRLASSITRRGHEIMHRTRELIE 540

Query: 546 QQGVEVIYGDTDSTFVWLRKPHDDAQARQIGLQLTALINDWWRRHLSEQYGLESALELQF 605
           +QG EVIYGDTDSTFVWLR  H D +AR IGL LT+ INDWWR HL +QYGLESALELQ+
Sbjct: 541 EQGYEVIYGDTDSTFVWLRSAHSDEEARSIGLALTSRINDWWRLHLRQQYGLESALELQY 600

Query: 606 EVHYQRFLMPNIRGSDTGSKKRYAGYVRSADGQDKVTYKGLETVRTDWSPLAQRFQQALY 665
           EVHYQRFLMP +RGSDTGSKKRYAGYVR+A+G+DKVTYKGLETVRTDW+PLAQRFQQ LY
Sbjct: 601 EVHYQRFLMPTVRGSDTGSKKRYAGYVRTAEGEDKVTYKGLETVRTDWTPLAQRFQQELY 660

Query: 666 LRIFRGEPYRDFITGYVADLLAGRLDELLVYRKRLRRQLDHYEKNVPPHVRAARLADQVN 725
           LRIFRGE YRD++  YVA+LLAGRLDELLVYRKRLRRQLDHYEKNVPPHVRAAR+ADQVN
Sbjct: 661 LRIFRGETYRDYVRSYVAELLAGRLDELLVYRKRLRRQLDHYEKNVPPHVRAARMADQVN 720

Query: 726 EEGGRPLQYQQGGWINYVMTTAGPEPLEKRRAAIDYAHYLERQLAPVADAILVFVGDSFA 785
           ++ GRPLQYQQGGWI YVMTTAGPEPLEKR AAIDY HYLERQLAPVADAILVFVGDSFA
Sbjct: 721 QDDGRPLQYQQGGWITYVMTTAGPEPLEKRSAAIDYGHYLERQLAPVADAILVFVGDSFA 780

Query: 786 AVTSPQQELF 795
           A+TSPQQELF
Sbjct: 781 ALTSPQQELF 790


  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    0.138    0.416 

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: 2,660,622
Number of extensions: 117538
Number of successful extensions: 312
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 312
Number of HSP's successfully gapped: 1
Length of query: 795
Length of database: 1,619,870
Length adjustment: 93
Effective length of query: 702
Effective length of database: 1,179,515
Effective search space: 828019530
Effective search space used: 828019530
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)