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= 0092.0053.p
         (404 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311255|ref|YP_003775347.1| sigma-E factor regulatory (nega...   298   7e-82
gi|300311254|ref|YP_003775346.1| transmembrane sigma-E factor ne...    65   7e-12

>gi|300311255|ref|YP_003775347.1| sigma-E factor regulatory
           (negative regulator) transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 338

 Score =  298 bits (762), Expect = 7e-82,   Method: Compositional matrix adjust.
 Identities = 151/271 (55%), Positives = 190/271 (70%), Gaps = 35/271 (12%)

Query: 168 LSAVXRGKNEIEKLEVLDGKPREYIRNNDDVACYVPEAKTVLIEKRVTRDVFPAILAANP 227
           ++ V  GKNE+EKLE+LDGKP E+IR+ND+VA Y+P+++T+ +EKRVTRDVFPAI+   P
Sbjct: 69  VTHVVVGKNELEKLELLDGKPAEFIRSNDEVASYLPQSRTIRMEKRVTRDVFPAIVDVRP 128

Query: 228 TDLVDYYSVKMGETGRVAGHDCQAVILEPKDKLRYGYKLWADKATGLLLRAENLX-RG-- 284
            DL   Y ++ G   RVAG DC+ V+LEP+DKLRYGY+ W DKATGLLLRA+ L  +G  
Sbjct: 129 QDLGAQYHLRAGSDERVAGRDCRVVMLEPRDKLRYGYRFWTDKATGLLLRAQTLDGQGEV 188

Query: 285 -------------------------------ENSVMSQVNLSGWSVTPPPGFKKIQEVKR 313
                                          E +VM+ ++L  W VTPPPGF+KIQ+V+R
Sbjct: 189 IEQIAFTQIEIGGIDRARVNPTYKDTHGWHIEKAVMTPIDLPQWQVTPPPGFRKIQQVRR 248

Query: 314 LISDTQNTGTSAAQHGVTTQREVSQIVFSDGLAAISVFIEPGSQSRTEGSMQQGAMNIVG 373
           L++ +   G + AQ+    +REVSQIVFSDGLAAISVFIEPGS  R EGS QQGAM+I+G
Sbjct: 249 LMAGSAADGAAPAQN-RAAEREVSQIVFSDGLAAISVFIEPGSPGREEGSAQQGAMHILG 307

Query: 374 RRQGDYWLTVVGEVPGPAIRQVSNSIEFKSK 404
           R QGDYWLTVVGEVP  AIRQV++SIE KSK
Sbjct: 308 RPQGDYWLTVVGEVPAAAIRQVADSIELKSK 338


>gi|300311254|ref|YP_003775346.1| transmembrane sigma-E factor
          negative regulatory transcription regulator protein
          [Herbaspirillum seropedicae SmR1]
          Length = 232

 Score = 65.5 bits (158), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 32/57 (56%), Positives = 43/57 (75%), Gaps = 1/57 (1%)

Query: 1  MALTVLRQPEE-HVTWDLYHQIGDVMRSEEMAFSLSDGFAAKMSARLDAEPTIIAPQ 56
          +AL  LR  ++    W+ YH+IG+V+RSEEM   LS GF+A+MSA L+AEPTI+APQ
Sbjct: 26 IALAGLRSSKDAQQAWEDYHRIGEVLRSEEMDVPLSAGFSARMSALLEAEPTIVAPQ 82


  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
   0.319    0.132    0.381 

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: 1,180,711
Number of extensions: 44336
Number of successful extensions: 125
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 123
Number of HSP's successfully gapped: 2
Length of query: 404
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 317
Effective length of database: 1,207,925
Effective search space: 382912225
Effective search space used: 382912225
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 (21.8 bits)
S2: 132 (55.5 bits)