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= 0001.2508.p
         (279 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...   132   4e-32
gi|300311078|ref|YP_003775170.1| transcription regulator protein...    74   1e-14

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

 Score =  132 bits (331), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 78/260 (30%), Positives = 131/260 (50%)

Query: 5   LLQQIVREQEEMKPAELRIAHFVSQAPGEVIHMSMASLAERCAVSDPTIVRFCRRFGFNG 64
           LL  I      +  +E ++A  +   P   +  ++ +LA+   VS+PT++RFCR  G+ G
Sbjct: 4   LLDSIRTHINSLSKSEKKVAATILANPQLALAENLTALAKNAEVSEPTVIRFCRAIGYEG 63

Query: 65  YQEFKLNLAQSLVPAAPFVYEQITRDDDIDTIVRKTCRNSLSAIQRALDDLVPQQIEQAA 124
           + +FKL LAQSL  A P   E + +DD    +V K C  S++ +    + L P  I+ A 
Sbjct: 64  WHDFKLKLAQSLALALPGADETLAQDDLAADLVNKICSRSINTLLDLRNHLNPDAIQLAL 123

Query: 125 ALLHSATWIGIYASGISEITALDAEHKFQRLGLRCAAVMEEKKQWMHAEKSRPNEVALIF 184
            +L  A  I  Y  G S I A DA+HKF R G+   A  +     + A   +  +  +  
Sbjct: 124 DVLARANKIEFYGQGTSGIVANDAQHKFFRSGVPTVAYSDPHIHSIAASLLKAGDCVVAI 183

Query: 185 SQSGHTKRMVELAMAARAGGARVVAVTAADSPLAQVTDALIAVLPYDQTEFMTPLASRLN 244
           SQ G    ++     AR GGA ++ +  + +PLA++   L+ +      +  TP+++RL 
Sbjct: 184 SQRGGNAALLRSIQLARKGGADIIVLGPSGTPLAELATVLVPIDLSFNIDPYTPISARLA 243

Query: 245 HHLVVNMLVTAIAVASNSEF 264
           H +V+++L   +A+    EF
Sbjct: 244 HLVVIDILAVGLALRRGPEF 263


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

 Score = 73.9 bits (180), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/260 (25%), Positives = 119/260 (45%), Gaps = 10/260 (3%)

Query: 5   LLQQIVREQEEMKPAELRIAHFVSQAPGEVIHMSMASLAERCAVSDPTIVRFCRRFGFNG 64
           ++ +I      ++ AE ++A  +          S+  LA++  VS  ++ RF +  G   
Sbjct: 7   IISRITERSSTLRLAEQKVAEAILGDLHAAASASIGELADKAGVSVASVTRFAKAMGCRD 66

Query: 65  YQEFKLNLAQSLVPAAPFVYEQITRDDD-----IDTIVRKTCRNSLSAIQRALDDLVPQQ 119
            +EFK  LAQ++     F     T   +      D + R    +++  + RA+  L    
Sbjct: 67  VREFKFLLAQAVAVGQRFFDGAKTVPSEQPPELADVVYRDI--HAVLELNRAM--LNADM 122

Query: 120 IEQAAALLHSATWIGIYA-SGISEITALDAEHKFQRLGLRCAAVMEEKKQWMHAEKSRPN 178
           + QAA LL  A  I  +   G S + + +A ++  RLG   A+  +   Q M A     +
Sbjct: 123 LMQAAHLLLGARMIYCFGMGGGSTMMSDEARYRLVRLGRPVASYHDAVLQKMVAATLDKD 182

Query: 179 EVALIFSQSGHTKRMVELAMAARAGGARVVAVTAADSPLAQVTDALIAVLPYDQTEFMTP 238
           +V L+FS +G    ++     AR  G +++A+TA  SPLA++ D L+ +   +      P
Sbjct: 183 DVLLVFSTTGSVPELLASCEVAREYGVKLIAITALGSPLAKLADVLLPIKTLETDLIFKP 242

Query: 239 LASRLNHHLVVNMLVTAIAV 258
            +SR      ++MLV  +A+
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    0.130    0.373 

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: 724,991
Number of extensions: 23397
Number of successful extensions: 94
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 93
Number of HSP's successfully gapped: 2
Length of query: 279
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 195
Effective length of database: 1,222,130
Effective search space: 238315350
Effective search space used: 238315350
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)