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= 0231.0042.p
         (571 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312983|ref|YP_003777075.1| 30s ribosomal protein S1 [Herba...  1101   0.0  
gi|300313473|ref|YP_003777565.1| transcription accessory protein...    59   1e-09

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

 Score = 1101 bits (2848), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 544/571 (95%), Positives = 559/571 (97%)

Query: 1   MSTTTVLAPGAAGADAFAALFEESLSRQDMRSGEVISAEVVRLDHNFVIVNAGLKSEAFI 60
           MSTTTV+A G   +  FAALFEESLSRQDMRSGEVISAEVVRLDHNFVIVNAGLKSEAFI
Sbjct: 15  MSTTTVIAAGVDTSSEFAALFEESLSRQDMRSGEVISAEVVRLDHNFVIVNAGLKSEAFI 74

Query: 61  PIEEFKNDNGELEVNVGDFISVAIESLENGFGDTILSRDKAKRLASWLSLEKAMESGEIV 120
           P+EEFKNDNGE+EVNVGDFISVAIESLENGFGDTILSRDKAKRLASWLSLEKAMESGEIV
Sbjct: 75  PVEEFKNDNGEVEVNVGDFISVAIESLENGFGDTILSRDKAKRLASWLSLEKAMESGEIV 134

Query: 121 VGTVNGKVKGGLTVLTNGIRAFLPGSLVDTRPVKDTTPFEGKTLEFKVIKLDRKRNNVVL 180
            GTVNGKVKGGLTVLTNGIRAFLPGSLVDTRPVKDTTPFEGKTLEFKVIKLDRKRNNVVL
Sbjct: 135 TGTVNGKVKGGLTVLTNGIRAFLPGSLVDTRPVKDTTPFEGKTLEFKVIKLDRKRNNVVL 194

Query: 181 SRRAVIEASMGEERQKLMETLKEGTVVTGVVKNITDYGAFVDLGGIDGLLHITDLAWRRV 240
           SRRAVIEASMGEER KLMETLKEGTVVTG+VKNITDYGAFVDLGGIDGLLHITDLAWRRV
Sbjct: 195 SRRAVIEASMGEERAKLMETLKEGTVVTGIVKNITDYGAFVDLGGIDGLLHITDLAWRRV 254

Query: 241 RHPSEVLTVGQEITAKVLKYDQEKNRVSLGVKQLGDDPWTGLSRRYPQGTRLFGKVTNLT 300
           RHPSEVL+VGQEITAKVLKYDQEKNRVSLGVKQLGDDPWTGLSRRYPQGTRLFGKVTNLT
Sbjct: 255 RHPSEVLSVGQEITAKVLKYDQEKNRVSLGVKQLGDDPWTGLSRRYPQGTRLFGKVTNLT 314

Query: 301 DYGAFVEVEQGIEGLVHVSEMDWTNKNVAPNKVVQLGDEVEVMVLEIDEERRRISLGMKQ 360
           DYGAFVEVEQGIEGLVHVSEMDWTNKNVAPNKVVQLGDEVEVMVLEIDEERRRISLGMKQ
Sbjct: 315 DYGAFVEVEQGIEGLVHVSEMDWTNKNVAPNKVVQLGDEVEVMVLEIDEERRRISLGMKQ 374

Query: 361 CKANPWDDFAVTHKKGDKVKGAIKSITDFGVFIGLTGNIDGLVHLSDLSWTETGEEAVRK 420
           CK NPWDDFA++HKKGDKVKG+IKSITDFGVFIGL GNIDGLVHLSDLSWTE GEEAVRK
Sbjct: 375 CKPNPWDDFAMSHKKGDKVKGSIKSITDFGVFIGLPGNIDGLVHLSDLSWTEAGEEAVRK 434

Query: 421 FKKGDELEAVVLAIDVERERVSLGVKQLEGDPFNNFAAMNDKGALVNGTVKSVEPKGAVI 480
           FKKGDELEAVVLAIDVERERVSLGVKQLEGDPFNNFAA+NDKGA+V GTVKSVEPKGAVI
Sbjct: 435 FKKGDELEAVVLAIDVERERVSLGVKQLEGDPFNNFAALNDKGAIVTGTVKSVEPKGAVI 494

Query: 481 QLSEEVEGYLRASEISRDRVEDAGTHLKVGDSVEALVINIDRKARSIQLSIKAKDNAETQ 540
           QL++EVEGYLRASEISRDRVEDAGTHLKVGDSVEALVINIDRKARSIQLSIKAKDNAETQ
Sbjct: 495 QLTDEVEGYLRASEISRDRVEDAGTHLKVGDSVEALVINIDRKARSIQLSIKAKDNAETQ 554

Query: 541 EAMQKMSSDSSAASGTTSLGALLKAKLDNKN 571
           EAMQKMS+DS+AASGTTSLGALLKAKLDNKN
Sbjct: 555 EAMQKMSADSNAASGTTSLGALLKAKLDNKN 585


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

 Score = 58.5 bits (140), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/95 (34%), Positives = 57/95 (60%), Gaps = 2/95 (2%)

Query: 198 METLKEGTVVTGVVKNITDYGAFVDLG-GIDGLLHITDLAWRRVRHPSEVLTVGQEITAK 256
           ++ L+   ++ GVV N+  +GAFVD+G   DGL+HI+ L+   V+ P  V+  GQ +  K
Sbjct: 657 IKDLRPDMILEGVVTNVAAFGAFVDIGVHQDGLVHISALSNTYVKDPHTVVKAGQVVKVK 716

Query: 257 VLKYDQEKNRVSLGVKQLGDDPWTGLSRRYPQGTR 291
           VL+ D+++ R++L ++     P  G +R   +G R
Sbjct: 717 VLEVDEKRKRIALTMRLNDTAPAPG-ARNEQRGDR 750



 Score = 57.4 bits (137), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 36/88 (40%), Positives = 55/88 (62%), Gaps = 4/88 (4%)

Query: 292 LFGKVTNLTDYGAFVEVEQGIEGLVHVSEMDWTNKNVA-PNKVVQLGDEVEVMVLEIDEE 350
           L G VTN+  +GAFV++    +GLVH+S +  +N  V  P+ VV+ G  V+V VLE+DE+
Sbjct: 666 LEGVVTNVAAFGAFVDIGVHQDGLVHISAL--SNTYVKDPHTVVKAGQVVKVKVLEVDEK 723

Query: 351 RRRISLGMKQCKANPWDDFAVTHKKGDK 378
           R+RI+L M+     P    A   ++GD+
Sbjct: 724 RKRIALTMRLNDTAPAPG-ARNEQRGDR 750


  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
   0.314    0.133    0.366 

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: 1,480,983
Number of extensions: 58537
Number of successful extensions: 162
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 145
Number of HSP's successfully gapped: 4
Length of query: 571
Length of database: 1,619,870
Length adjustment: 90
Effective length of query: 481
Effective length of database: 1,193,720
Effective search space: 574179320
Effective search space used: 574179320
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 133 (55.8 bits)