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= 0007.0018.p
         (166 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312008|ref|YP_003776100.1| RNA polymerase sigma-E factor [...   184   3e-48
gi|300311734|ref|YP_003775826.1| RNA polymerase sigma-E factor p...    67   8e-13
gi|300311253|ref|YP_003775345.1| RNA polymerase sigma-E factor (...    58   3e-10
gi|300310115|ref|YP_003774207.1| RNA polymerase sigma-24 factor ...    57   7e-10

>gi|300312008|ref|YP_003776100.1| RNA polymerase sigma-E factor
           [Herbaspirillum seropedicae SmR1]
          Length = 163

 Score =  184 bits (467), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 110/163 (67%), Positives = 125/163 (76%), Gaps = 3/163 (1%)

Query: 7   LLACLPRLRRYARALVGDRAGADDLVQDTMERAWQKLSSWRKGSDMRPWLFSIMHNLHVD 66
           +LACLPRLRRYARAL G R  ADDLVQDT+ERAWQKL SW++GS MRPWLFSIMHNLH D
Sbjct: 1   MLACLPRLRRYARALTGAREAADDLVQDTLERAWQKLDSWQRGSPMRPWLFSIMHNLHAD 60

Query: 67  QRRKPVIPTVALDDEDALATPAYAPDRLVGYDLESALRLLAAEQREILLLVVLEEMTYEE 126
            RR+    TVALD+   +     A D  V  DLE+AL+LL  EQRE+LLLVVLEEM YEE
Sbjct: 61  ARRRASPATVALDEYGEIDQAQVALDPGVLLDLETALQLLPPEQREVLLLVVLEEMRYEE 120

Query: 127 VAATLSIPLGTVMSRLSRARERLRALVEGRPRH---STLKVVK 166
           VA TL IP GTVMSRLSRARERLR +++G+      S+LKVVK
Sbjct: 121 VAVTLGIPTGTVMSRLSRARERLRRVMQGQGESSPGSSLKVVK 163


>gi|300311734|ref|YP_003775826.1| RNA polymerase sigma-E factor
           protein [Herbaspirillum seropedicae SmR1]
          Length = 186

 Score = 67.0 bits (162), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 39/150 (26%), Positives = 74/150 (49%), Gaps = 6/150 (4%)

Query: 9   ACLPRLRRYARALVGDRAGADDLVQDTMERAWQKLSSWRKGSDMRPWLFSIMHNLHVDQR 68
           +  PRL ++ R LV D   +++++ DTM   W K  ++   S +  W+F+I +   +   
Sbjct: 34  SYFPRLAQFLRRLVWDGPLSEEIINDTMFVVWTKAQTYNGQSKVSTWIFAIAYKQGLKAL 93

Query: 69  RKPVIPTVALDDEDALATPAYAPDRLVGY-----DLESALRLLAAEQREILLLVVLEEMT 123
            +   P V +D E  ++     P+  +        +  AL  L+ E R ++ L     M+
Sbjct: 94  SRVDTP-VEMDMETMVSDELVEPEHQLSETQLRRHIGGALERLSFEHRTVMTLTYFHGMS 152

Query: 124 YEEVAATLSIPLGTVMSRLSRARERLRALV 153
           YEE+A T+   + TV +R+  AR++L+  +
Sbjct: 153 YEEIADTMGCSINTVKTRMFYARQKLKVFL 182


>gi|300311253|ref|YP_003775345.1| RNA polymerase sigma-E factor
           (sigma-24) transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 200

 Score = 58.2 bits (139), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 46/150 (30%), Positives = 72/150 (48%), Gaps = 15/150 (10%)

Query: 13  RLRRYARALVGDRAGADDLVQDTMERAWQKLSSWRKGSDMRPWLFSIMHNLHVDQ----- 67
           +L R    LV D+A A+D+VQ+   +A++ L  +R  S    WL+ I  N   +      
Sbjct: 33  KLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQFRGDSAFYTWLYRIGINTAKNYLVTMG 92

Query: 68  RRKPVIPTV------ALDDEDAL---ATP-AYAPDRLVGYDLESALRLLAAEQREILLLV 117
           RR P             DD D L    TP +    + +   +  A+  L  E R  + L 
Sbjct: 93  RRAPTSTEADAEEAETFDDADHLRDINTPESMLATKQIAQTVNVAMEALPEELRTAITLR 152

Query: 118 VLEEMTYEEVAATLSIPLGTVMSRLSRARE 147
            +E ++Y+E+A  ++ P+GTV SR+ RARE
Sbjct: 153 EIEGLSYDEIADAMNCPIGTVRSRIFRARE 182


>gi|300310115|ref|YP_003774207.1| RNA polymerase sigma-24 factor
           protein [Herbaspirillum seropedicae SmR1]
          Length = 244

 Score = 57.0 bits (136), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 47/146 (32%), Positives = 68/146 (46%), Gaps = 8/146 (5%)

Query: 13  RLRRYARALVGDRAGADDLVQDTMERAWQKLSSWRKGSDMRPWLFSIMHNLHVDQRRKPV 72
            L R+    VG+   A+D+VQ+T   A +    +   S    WLF I  NL  +Q R+  
Sbjct: 79  HLLRFVLRYVGNHEDAEDVVQNTFIEAVKCAHRFSGLSKPSTWLFGIGLNLARNQVRRNS 138

Query: 73  IPTVALDDE-------DALATPAYAPD-RLVGYDLESALRLLAAEQREILLLVVLEEMTY 124
                + +E       DA A PA   + R +   ++  L  L    R     V+  + TY
Sbjct: 139 ADRYEMVEENFMEQLVDASADPAMVYELRQIAQKVDDMLSELPPHIRHTFEAVLDGDATY 198

Query: 125 EEVAATLSIPLGTVMSRLSRARERLR 150
           EE A  L+IP+GTV SR+SR R  +R
Sbjct: 199 EEAAQHLNIPIGTVRSRVSRVRAAVR 224


  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    0.134    0.389 

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: 491,316
Number of extensions: 18801
Number of successful extensions: 81
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 79
Number of HSP's successfully gapped: 4
Length of query: 166
Length of database: 1,619,870
Length adjustment: 78
Effective length of query: 88
Effective length of database: 1,250,540
Effective search space: 110047520
Effective search space used: 110047520
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: 127 (53.5 bits)