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= 0092.0055.p
         (241 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311253|ref|YP_003775345.1| RNA polymerase sigma-E factor (...   284   5e-78
gi|300311252|ref|YP_003775344.1| flagellar hook-length control p...   115   3e-27
gi|300311734|ref|YP_003775826.1| RNA polymerase sigma-E factor p...    65   4e-12
gi|300310115|ref|YP_003774207.1| RNA polymerase sigma-24 factor ...    59   4e-10

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

 Score =  284 bits (726), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 137/152 (90%), Positives = 142/152 (93%)

Query: 90  DSVPRETFXRRARALPQFRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAET 149
           + V +E F +  RALPQFRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAET
Sbjct: 49  EDVVQEAFIKAYRALPQFRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAET 108

Query: 150 FDDGEHLRDINTPESMLATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIAEAMGC 209
           FDD +HLRDINTPESMLATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIA+AM C
Sbjct: 109 FDDADHLRDINTPESMLATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIADAMNC 168

Query: 210 PIGTVRSRIFRAREAIAEKLRPLLGTALDKRW 241
           PIGTVRSRIFRAREAIAEKLRPLL TA DKRW
Sbjct: 169 PIGTVRSRIFRAREAIAEKLRPLLDTAADKRW 200


>gi|300311252|ref|YP_003775344.1| flagellar hook-length control
           protein [Herbaspirillum seropedicae SmR1]
          Length = 166

 Score =  115 bits (288), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 62/109 (56%), Positives = 74/109 (67%), Gaps = 12/109 (11%)

Query: 18  VLRSRTAVWLHISGTGQIRLVEHHVAVRAKPGSQVMNGGLAQLLAGSTVWPNLLLLRLRL 77
           VLR R  +WLHISGTGQIR+VEH +A  ++   QVM+ GLAQLLAGST+WP +L LRLRL
Sbjct: 64  VLRERKTIWLHISGTGQIRVVEHLLAASSRTKPQVMSAGLAQLLAGSTIWPGMLFLRLRL 123

Query: 78  ENGRTRTIPILPDSVPRETFXRRARALPQFRGDSAFYTWLYRIGINTAK 126
           E+G+TRTIP+L DSV  +T          FR  S    WL  I  NTAK
Sbjct: 124 ESGKTRTIPVLSDSVSEDT----------FRALSVACRWL--ISHNTAK 160


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

 Score = 65.5 bits (158), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 39/119 (32%), Positives = 59/119 (49%), Gaps = 11/119 (9%)

Query: 107 FRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDDGEHLRDINTPESML 166
           + G S   TW++ I        L     R  T  E D E   +        ++  PE  L
Sbjct: 71  YNGQSKVSTWIFAIAYKQGLKAL----SRVDTPVEMDMETMVS-------DELVEPEHQL 119

Query: 167 ATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIAEAMGCPIGTVRSRIFRAREAI 225
           +  Q+ + +  A+E L  E RT +TL    G+SY+EIA+ MGC I TV++R+F AR+ +
Sbjct: 120 SETQLRRHIGGALERLSFEHRTVMTLTYFHGMSYEEIADTMGCSINTVKTRMFYARQKL 178


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

 Score = 58.9 bits (141), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 45/137 (32%), Positives = 67/137 (48%), Gaps = 9/137 (6%)

Query: 90  DSVPRETFXRRARALPQFRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAET 149
           + V + TF    +   +F G S   TWL+ IG+N A+N +    RR      AD  E   
Sbjct: 95  EDVVQNTFIEAVKCAHRFSGLSKPSTWLFGIGLNLARNQV----RR----NSADRYEMVE 146

Query: 150 FDDGEHLRDINTPESMLAT-KQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIAEAMG 208
            +  E L D +   +M+   +QIAQ V+  +  LP  +R           +Y+E A+ + 
Sbjct: 147 ENFMEQLVDASADPAMVYELRQIAQKVDDMLSELPPHIRHTFEAVLDGDATYEEAAQHLN 206

Query: 209 CPIGTVRSRIFRAREAI 225
            PIGTVRSR+ R R A+
Sbjct: 207 IPIGTVRSRVSRVRAAV 223


  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    0.135    0.398 

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: 657,048
Number of extensions: 23100
Number of successful extensions: 84
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 84
Number of HSP's successfully gapped: 4
Length of query: 241
Length of database: 1,619,870
Length adjustment: 83
Effective length of query: 158
Effective length of database: 1,226,865
Effective search space: 193844670
Effective search space used: 193844670
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: 129 (54.3 bits)