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= 0001.0119.p
         (286 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310430|ref|YP_003774522.1| transcription regulator protein...   580   e-167
gi|300311078|ref|YP_003775170.1| transcription regulator protein...   106   3e-24

>gi|300310430|ref|YP_003774522.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 286

 Score =  580 bits (1494), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 286/286 (100%), Positives = 286/286 (100%)

Query: 1   MSMLLDSIRTHINSLSKSEKKVAATILANPQLALAENLTALAKNAEVSEPTVIRFCRAIG 60
           MSMLLDSIRTHINSLSKSEKKVAATILANPQLALAENLTALAKNAEVSEPTVIRFCRAIG
Sbjct: 1   MSMLLDSIRTHINSLSKSEKKVAATILANPQLALAENLTALAKNAEVSEPTVIRFCRAIG 60

Query: 61  YEGWHDFKLKLAQSLALALPGADETLAQDDLAADLVNKICSRSINTLLDLRNHLNPDAIQ 120
           YEGWHDFKLKLAQSLALALPGADETLAQDDLAADLVNKICSRSINTLLDLRNHLNPDAIQ
Sbjct: 61  YEGWHDFKLKLAQSLALALPGADETLAQDDLAADLVNKICSRSINTLLDLRNHLNPDAIQ 120

Query: 121 LALDVLARANKIEFYGQGTSGIVANDAQHKFFRSGVPTVAYSDPHIHSIAASLLKAGDCV 180
           LALDVLARANKIEFYGQGTSGIVANDAQHKFFRSGVPTVAYSDPHIHSIAASLLKAGDCV
Sbjct: 121 LALDVLARANKIEFYGQGTSGIVANDAQHKFFRSGVPTVAYSDPHIHSIAASLLKAGDCV 180

Query: 181 VAISQRGGNAALLRSIQLARKGGADIIVLGPSGTPLAELATVLVPIDLSFNIDPYTPISA 240
           VAISQRGGNAALLRSIQLARKGGADIIVLGPSGTPLAELATVLVPIDLSFNIDPYTPISA
Sbjct: 181 VAISQRGGNAALLRSIQLARKGGADIIVLGPSGTPLAELATVLVPIDLSFNIDPYTPISA 240

Query: 241 RLAHLVVIDILAVGLALRRGPEFRKKMQNAQKSLQKFDMQFDSFFR 286
           RLAHLVVIDILAVGLALRRGPEFRKKMQNAQKSLQKFDMQFDSFFR
Sbjct: 241 RLAHLVVIDILAVGLALRRGPEFRKKMQNAQKSLQKFDMQFDSFFR 286


>gi|300311078|ref|YP_003775170.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 294

 Score =  106 bits (264), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 83/260 (31%), Positives = 136/260 (52%), Gaps = 10/260 (3%)

Query: 4   LLDSIRTHINSLSKSEKKVAATILANPQLALAENLTALAKNAEVSEPTVIRFCRAIGYEG 63
           ++  I    ++L  +E+KVA  IL +   A + ++  LA  A VS  +V RF +A+G   
Sbjct: 7   IISRITERSSTLRLAEQKVAEAILGDLHAAASASIGELADKAGVSVASVTRFAKAMGCRD 66

Query: 64  WHDFKLKLAQSLALA---LPGADETLA-QDDLAADLVNKICSRSINTLLDL-RNHLNPDA 118
             +FK  LAQ++A+      GA    + Q    AD+V     R I+ +L+L R  LN D 
Sbjct: 67  VREFKFLLAQAVAVGQRFFDGAKTVPSEQPPELADVVY----RDIHAVLELNRAMLNADM 122

Query: 119 IQLALDVLARANKIEFYGQGT-SGIVANDAQHKFFRSGVPTVAYSDPHIHSIAASLLKAG 177
           +  A  +L  A  I  +G G  S +++++A+++  R G P  +Y D  +  + A+ L   
Sbjct: 123 LMQAAHLLLGARMIYCFGMGGGSTMMSDEARYRLVRLGRPVASYHDAVLQKMVAATLDKD 182

Query: 178 DCVVAISQRGGNAALLRSIQLARKGGADIIVLGPSGTPLAELATVLVPIDLSFNIDPYTP 237
           D ++  S  G    LL S ++AR+ G  +I +   G+PLA+LA VL+PI        + P
Sbjct: 183 DVLLVFSTTGSVPELLASCEVAREYGVKLIAITALGSPLAKLADVLLPIKTLETDLIFKP 242

Query: 238 ISARLAHLVVIDILAVGLAL 257
            S+R A +  +D+L + LAL
Sbjct: 243 SSSRYAMMATLDMLVLELAL 262


  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    0.380 

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: 804,637
Number of extensions: 32299
Number of successful extensions: 157
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 153
Number of HSP's successfully gapped: 3
Length of query: 286
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 202
Effective length of database: 1,222,130
Effective search space: 246870260
Effective search space used: 246870260
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: 130 (54.7 bits)