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= 0002.0566.p
         (807 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313473|ref|YP_003777565.1| transcription accessory protein...  1438   0.0  
gi|300312983|ref|YP_003777075.1| 30s ribosomal protein S1 [Herba...    58   3e-09

>gi|300313473|ref|YP_003777565.1| transcription accessory protein
           [Herbaspirillum seropedicae SmR1]
          Length = 783

 Score = 1438 bits (3723), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 700/766 (91%), Positives = 736/766 (96%)

Query: 1   MLPSIEQRLALELVAKPVQVAAAIALLDEGATVPFIARYRKEATGGLDDTQLRLLEERLR 60
           MLPSIEQRLALEL AKPVQVAAAIALLDEGATVPFIARYRKE TGGLDD QLRLLEERLR
Sbjct: 1   MLPSIEQRLALELAAKPVQVAAAIALLDEGATVPFIARYRKEVTGGLDDVQLRLLEERLR 60

Query: 61  YLRELEDRRTAIISSIEEQGKMTPVLLDAIVHAEDKTRLEDLYLPYKLKRRTKAQIAAEA 120
           YLRELE RR AII+SIEEQGKMTPVLLDAI HAEDKTRLEDLYLPYK KRRTKAQIAAEA
Sbjct: 61  YLRELESRRAAIIASIEEQGKMTPVLLDAITHAEDKTRLEDLYLPYKPKRRTKAQIAAEA 120

Query: 121 GLTELADALLNDPMLNPEEEAAKYLKPAFTTDSGDNPGVADAKAALDGARQILMERFAED 180
           GLTELADALLNDP LNPEEEAAK++KPAFTTD+GDNPGV D KAALDGARQILMERF+ED
Sbjct: 121 GLTELADALLNDPTLNPEEEAAKFIKPAFTTDNGDNPGVPDTKAALDGARQILMERFSED 180

Query: 181 AELLQALREYITEHGVVESKVIEGKQDAGEKFADYFDYSETIGTIPSHRALALFRGRREE 240
           AELLQ+LREY+TEHGVVESKVIEGKQDAGEKFADYFDYSET  TIPSHRALALFRGRREE
Sbjct: 181 AELLQSLREYLTEHGVVESKVIEGKQDAGEKFADYFDYSETYSTIPSHRALALFRGRREE 240

Query: 241 MLTVVLRLDTEEEKPKWDAPHNPCENRIAARFGVSSKGRPADKWLADTVRWAWRVKVFMH 300
           ML V+LRLD+EEEKPKWDAPHNPCE RIA+RFGVS+KGR ADKWL+DTVRWAWRVKVFMH
Sbjct: 241 MLNVILRLDSEEEKPKWDAPHNPCEGRIASRFGVSNKGRAADKWLSDTVRWAWRVKVFMH 300

Query: 301 LETELMTGLRERSEAEAINVFARNLKDLLLAAPAGPRATMGLDPGLRTGVKVAVVDATGK 360
           LETELMT LRE++EAEAINVFARNLKDLLLAAPAGPRATMGLDPGLRTGVKVA+VDATGK
Sbjct: 301 LETELMTNLREKAEAEAINVFARNLKDLLLAAPAGPRATMGLDPGLRTGVKVAIVDATGK 360

Query: 361 VVDTTAIFPHQPRNDWEGSLHTLAKLAEKHNVSLISIGNGTASRETDKLAQELIKMRPEL 420
           VV T  I+PHQPRNDW GSLHTL++LAEKHNVSLISIGNGTASRETDKLAQ+LIK+RPEL
Sbjct: 361 VVATDTIYPHQPRNDWNGSLHTLSQLAEKHNVSLISIGNGTASRETDKLAQDLIKLRPEL 420

Query: 421 KLTKIVVSEAGASVYSASEFASKELPDLDVSIRGAVSIARRLQDPLAELVKIDPKSIGVG 480
           KLTKIVVSEAGASVYSASEFASKELPDLDVS+RGAVSIARRLQDPLAELVKIDPKSIGVG
Sbjct: 421 KLTKIVVSEAGASVYSASEFASKELPDLDVSLRGAVSIARRLQDPLAELVKIDPKSIGVG 480

Query: 481 QYQHDVGQSQLARSLDAVVEDCVNAVGVDVNTASAPLLARVSGLNASVAQSIVSYRDMKG 540
           QYQHDV QSQLARSLDAVVEDCVNAVGVDVNTASAPLLARVSGLNASVAQSIVSYRDMKG
Sbjct: 481 QYQHDVSQSQLARSLDAVVEDCVNAVGVDVNTASAPLLARVSGLNASVAQSIVSYRDMKG 540

Query: 541 MFTSRAGLREVPRLGDKTFEQAAGFLRVMNGENPLDASAVHPESYPLVNKILADIKKDVK 600
           MF+SRA LREVPRLG+KTFEQAAGFLRVMNGENPLDASAVHPESYPLV KILADIKKDVK
Sbjct: 541 MFSSRAALREVPRLGEKTFEQAAGFLRVMNGENPLDASAVHPESYPLVEKILADIKKDVK 600

Query: 601 GVLGESALLKSLSPAKYADEKFGVPTVTDILKELEKPGRDPRPEFTTATFKDGVEEIKDL 660
            VLG+++LLK LSPAKYADEKFGVPTVTDILKEL+KPGRDPRPEFTTATFK+GVEEIKDL
Sbjct: 601 SVLGQTSLLKGLSPAKYADEKFGVPTVTDILKELDKPGRDPRPEFTTATFKEGVEEIKDL 660

Query: 661 RPDMILEGVVTNVAAFGAFVDIGVHQDGLVHISALSNTFVKDPHTVVKAGQVVKVKVLEV 720
           RPDMILEGVVTNVAAFGAFVDIGVHQDGLVHISALSNT+VKDPHTVVKAGQVVKVKVLEV
Sbjct: 661 RPDMILEGVVTNVAAFGAFVDIGVHQDGLVHISALSNTYVKDPHTVVKAGQVVKVKVLEV 720

Query: 721 DEKRKRIALTMRLSDSAPAAGSKPEQRGDRNDARRLSQHQGQQSRQ 766
           DEKRKRIALTMRL+D+APA G++ EQRGDR D+RRLSQHQ Q+ R+
Sbjct: 721 DEKRKRIALTMRLNDTAPAPGARNEQRGDRTDSRRLSQHQNQRGRE 766


>gi|300312983|ref|YP_003777075.1| 30s ribosomal protein S1
           [Herbaspirillum seropedicae SmR1]
          Length = 585

 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 52/85 (61%), Gaps = 1/85 (1%)

Query: 657 IKDLRPDMILEGVVTNVAAFGAFVDIGVHQDGLVHISALSNTFVKDPHTVVKAGQVVKVK 716
           ++ L+   ++ G+V N+  +GAFVD+G   DGL+HI+ L+   V+ P  V+  GQ +  K
Sbjct: 212 METLKEGTVVTGIVKNITDYGAFVDLG-GIDGLLHITDLAWRRVRHPSEVLSVGQEITAK 270

Query: 717 VLEVDEKRKRIALTMRLSDSAPAAG 741
           VL+ D+++ R++L ++     P  G
Sbjct: 271 VLKYDQEKNRVSLGVKQLGDDPWTG 295


  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
   0.316    0.133    0.373 

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: 2,357,296
Number of extensions: 95541
Number of successful extensions: 324
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 323
Number of HSP's successfully gapped: 2
Length of query: 807
Length of database: 1,619,870
Length adjustment: 93
Effective length of query: 714
Effective length of database: 1,179,515
Effective search space: 842173710
Effective search space used: 842173710
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 (21.6 bits)
S2: 134 (56.2 bits)