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= 0002.0062.p
         (664 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309740|ref|YP_003773832.1| exoribonuclease R protein [Herb...  1038   0.0  

>gi|300309740|ref|YP_003773832.1| exoribonuclease R protein
           [Herbaspirillum seropedicae SmR1]
          Length = 684

 Score = 1038 bits (2685), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 519/654 (79%), Positives = 571/654 (87%), Gaps = 21/654 (3%)

Query: 1   MNLFFEESGDFKAGAVLSQQGEAYQVEMASGKRTKVKSKDVMLQFASPAPAQLLEEAQAV 60
           MNL FEESGDFKAG++++QQGE+YQVEMASGKR KVK++D +LQFA+PAP +LL++AQA+
Sbjct: 1   MNLLFEESGDFKAGSIMTQQGESYQVEMASGKRAKVKARDALLQFATPAPQELLQQAQAI 60

Query: 61  LQDIDLDFLWEVAGEDEFGFAELGTEYFGHAPLPHEAAGLLLRLHSAPIYFYKKGKGRYK 120
            ++IDLDFLWEVAGE+EFGF EL T+YFGHAPLP EAAGLLLRLH+APIYFYKKG+GRYK
Sbjct: 61  AEEIDLDFLWEVAGEEEFGFTELATDYFGHAPLPPEAAGLLLRLHNAPIYFYKKGRGRYK 120

Query: 121 AAPLASLQAAQAGLEKKKQQALVQAQYVDELKAGKLPESFKPLALTLLFRPDKNSIEFKA 180
           AAP ASLQAA AGLEKKKQQ L QA YVDELKA KLP++F P+AL LLF+PDKNSIEFKA
Sbjct: 121 AAPQASLQAALAGLEKKKQQLLAQAAYVDELKAHKLPQAFAPIALQLLFKPDKNSIEFKA 180

Query: 181 LDAACKELQTTPQRLMLQTGGLASPKDLHYAKFLFEFFPKGSGFPEVTIPAVPKDLPLAD 240
           LDAA KE+QTTPQRLML  GG+ASPKDLHYA+FLFE FP+G+GFP + IPA P DLP AD
Sbjct: 181 LDAAAKEMQTTPQRLMLAAGGVASPKDLHYARFLFEHFPRGTGFPAIDIPAPPTDLPTAD 240

Query: 241 VQAFSIDDVTTTEIDDALSVVRLADGNVRVGIHIAAPGLGIKRDDALDAIARQRMSTVYM 300
           VQAFSIDDVTTTEIDDALSV RL DG +RVGIHIAAPGL IKR DA+DAIAR RMSTVYM
Sbjct: 241 VQAFSIDDVTTTEIDDALSVTRLPDGKLRVGIHIAAPGLAIKRGDAIDAIARARMSTVYM 300

Query: 301 PGEKITMLPDVLVEAFTLDEGKNCPALSLYATLNPADWSVISTETRAEIVPISANLRHND 360
           PGEKITMLPD LV A+TLD G   PALSLYATL+  +W+V++TETRAE+VPI+ANLRHND
Sbjct: 301 PGEKITMLPDELVAAYTLDAGAARPALSLYATLDATNWAVLATETRAELVPITANLRHND 360

Query: 361 LDALVTEEALANNSGEYPHKDDITLLWQWVQVLEQGRMAKRESFGLRPEYTR-------- 412
           LD LVTEEALA N GEYPHKD+I LLWQWVQ+LEQGRMAKRESFGLRPE           
Sbjct: 361 LDELVTEEALAENRGEYPHKDEIALLWQWVQLLEQGRMAKRESFGLRPEQNNRVDFNFYV 420

Query: 413 -------------AXLDKIVAELMIFANSTWGKFMADHGVPGIYRAQGGGAGGWAAKMQV 459
                        A LDKIVAELMIFANSTWGK MADHGVPGIYRAQGGGAGGWAAKMQV
Sbjct: 421 EDDVVSIVRRRRGAPLDKIVAELMIFANSTWGKLMADHGVPGIYRAQGGGAGGWAAKMQV 480

Query: 460 RMVTHAAPHQGLGVDQYAWSTSPLRRYTDLVNQWQILACLEHGVTAPLAAPFKPRDADLF 519
           RMVTHAAPHQGLGVDQYAWSTSPLRRYTDLVNQWQILAC+EHGVTAPL APFKPRDADLF
Sbjct: 481 RMVTHAAPHQGLGVDQYAWSTSPLRRYTDLVNQWQILACIEHGVTAPLVAPFKPRDADLF 540

Query: 520 AIVSGFDSAYSGYADFQSGMERYWCLRWLAQEQARQVDAVVLKDEILRLVDIPLVIRLPG 579
           AIVSGFD+AYSGYADFQS MERYWCLRWLAQE AR VDAVVLKDEILRLVDIPLV+R+PG
Sbjct: 541 AIVSGFDAAYSGYADFQSTMERYWCLRWLAQENARVVDAVVLKDEILRLVDIPLVLRMPG 600

Query: 580 MPQVARGLQVKLDLLRWDEVDLTVEARLLDIPAAQPAEGAEPMDEEEEALLDGM 633
           +PQ+ARGLQVKLDLLRWDEVDLTVEARLL++PAA        + EE+E LL+GM
Sbjct: 601 LPQLARGLQVKLDLLRWDEVDLTVEARLLEVPAAAAQAVDADLGEEDEDLLEGM 654


  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
   0.318    0.134    0.396 

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: 2,003,146
Number of extensions: 84568
Number of successful extensions: 230
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 229
Number of HSP's successfully gapped: 1
Length of query: 664
Length of database: 1,619,870
Length adjustment: 91
Effective length of query: 573
Effective length of database: 1,188,985
Effective search space: 681288405
Effective search space used: 681288405
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: 134 (56.2 bits)