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= 0001.0376.p
         (697 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...  1222   0.0  

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

 Score = 1222 bits (3161), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 620/679 (91%), Positives = 644/679 (94%)

Query: 1   MNLLFEESGDFKAGSIMTQQGESYQVEMASGKRAKVKSRDALLQFAAPSPQELLQQAQAI 60
           MNLLFEESGDFKAGSIMTQQGESYQVEMASGKRAKVK+RDALLQFA P+PQELLQQAQAI
Sbjct: 1   MNLLFEESGDFKAGSIMTQQGESYQVEMASGKRAKVKARDALLQFATPAPQELLQQAQAI 60

Query: 61  AEEIDLDFLWEVAGEEEFGFTDLAAEYFGHAPLPPEAAGLLLRLHHAPIYFYKKGRGRYK 120
           AEEIDLDFLWEVAGEEEFGFT+LA +YFGHAPLPPEAAGLLLRLH+APIYFYKKGRGRYK
Sbjct: 61  AEEIDLDFLWEVAGEEEFGFTELATDYFGHAPLPPEAAGLLLRLHNAPIYFYKKGRGRYK 120

Query: 121 AAPQASLQAALAGLEKKKQQLAAQAVYVEELKAHKLPEAFRPIALQLLFKPDKNGIEFKA 180
           AAPQASLQAALAGLEKKKQQL AQA YV+ELKAHKLP+AF PIALQLLFKPDKN IEFKA
Sbjct: 121 AAPQASLQAALAGLEKKKQQLLAQAAYVDELKAHKLPQAFAPIALQLLFKPDKNSIEFKA 180

Query: 181 LDAAAKELQTTPQRLMLAAGGVASPKDLHYARFLYEFFPRGTGFPAIDIPTPPGDLPLAD 240
           LDAAAKE+QTTPQRLMLAAGGVASPKDLHYARFL+E FPRGTGFPAIDIP PP DLP AD
Sbjct: 181 LDAAAKEMQTTPQRLMLAAGGVASPKDLHYARFLFEHFPRGTGFPAIDIPAPPTDLPTAD 240

Query: 241 VQAFSIDDVTTTEIDDALSVTRLPDGKLRVGIHIAAPALAIKRGDAIDAIARARMSTVYM 300
           VQAFSIDDVTTTEIDDALSVTRLPDGKLRVGIHIAAP LAIKRGDAIDAIARARMSTVYM
Sbjct: 241 VQAFSIDDVTTTEIDDALSVTRLPDGKLRVGIHIAAPGLAIKRGDAIDAIARARMSTVYM 300

Query: 301 PGEKITMLPDDLVATYTLDAGAARPALSLYATLDAGTWEVLATETRAERVPIAANLRHND 360
           PGEKITMLPD+LVA YTLDAGAARPALSLYATLDA  W VLATETRAE VPI ANLRHND
Sbjct: 301 PGEKITMLPDELVAAYTLDAGAARPALSLYATLDATNWAVLATETRAELVPITANLRHND 360

Query: 361 LDELVTEEALADNRGDYPHKEEISLLWQWAQLLEQGRMAKRESFGLRPEQNNRVDFNFYV 420
           LDELVTEEALA+NRG+YPHK+EI+LLWQW QLLEQGRMAKRESFGLRPEQNNRVDFNFYV
Sbjct: 361 LDELVTEEALAENRGEYPHKDEIALLWQWVQLLEQGRMAKRESFGLRPEQNNRVDFNFYV 420

Query: 421 DNDVVSIVRRRRGAPLDKIVAELMIFANSTWGKLMADHGVPGIYRAQGGGAGGWAAKMQV 480
           ++DVVSIVRRRRGAPLDKIVAELMIFANSTWGKLMADHGVPGIYRAQGGGAGGWAAKMQV
Sbjct: 421 EDDVVSIVRRRRGAPLDKIVAELMIFANSTWGKLMADHGVPGIYRAQGGGAGGWAAKMQV 480

Query: 481 RMVTHAAPHQGLGVDQYAWSTSPLRRYTDLVNQWQILACVEHGVTAPLVAPFKPRDADLF 540
           RMVTHAAPHQGLGVDQYAWSTSPLRRYTDLVNQWQILAC+EHGVTAPLVAPFKPRDADLF
Sbjct: 481 RMVTHAAPHQGLGVDQYAWSTSPLRRYTDLVNQWQILACIEHGVTAPLVAPFKPRDADLF 540

Query: 541 AIVSGFDAAYSGYADFQSTMERYWCLRWLAQENARTVEAVVLKDEILRLVDIPLVLRMPG 600
           AIVSGFDAAYSGYADFQSTMERYWCLRWLAQENAR V+AVVLKDEILRLVDIPLVLRMPG
Sbjct: 541 AIVSGFDAAYSGYADFQSTMERYWCLRWLAQENARVVDAVVLKDEILRLVDIPLVLRMPG 600

Query: 601 LPQLARGLQVKLDLLRWDEVDLSVEARLLEVPTAAAQALASDLGEEDEELLEGMAALGAE 660
           LPQLARGLQVKLDLLRWDEVDL+VEARLLEVP AAAQA+ +DLGEEDE+LLEGMAALG E
Sbjct: 601 LPQLARGLQVKLDLLRWDEVDLTVEARLLEVPAAAAQAVDADLGEEDEDLLEGMAALGEE 660

Query: 661 QQEGSEAAEEGSATQDAPP 679
           +    E      A  + PP
Sbjct: 661 EAPPPEEPAASLAADENPP 679


  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    0.391 

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: 1,921,467
Number of extensions: 75068
Number of successful extensions: 242
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 242
Number of HSP's successfully gapped: 1
Length of query: 697
Length of database: 1,619,870
Length adjustment: 92
Effective length of query: 605
Effective length of database: 1,184,250
Effective search space: 716471250
Effective search space used: 716471250
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)