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= 0012.0091.p
         (169 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311984|ref|YP_003776076.1| HD-GYP domain-containing protei...    60   6e-11
gi|300310279|ref|YP_003774371.1| HD-GYP domain-containing protei...    58   4e-10
gi|300314021|ref|YP_003778113.1| HD-GYP domain-containing protei...    57   1e-09

>gi|300311984|ref|YP_003776076.1| HD-GYP domain-containing protein
           [Herbaspirillum seropedicae SmR1]
          Length = 406

 Score = 60.5 bits (145), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 38/114 (33%), Positives = 61/114 (53%), Gaps = 6/114 (5%)

Query: 18  QHHESPDGRGYPYG-TKRELSELSQMIRFADIFTAKYSARKTRASMPPRQAAQSVYLVSD 76
            HHE  DG GYPY  + R++S  ++M    D++ A  S R  ++   P ++ Q +   S 
Sbjct: 253 HHHEKMDGTGYPYKLSGRDISMTARMGAICDVYDAITSDRPYKSGWDPSRSIQHMAQ-SK 311

Query: 77  GH---PIASALLKEFGIYPPGCFVLLKSGETAVTI-RRGNTPTAPLVAVVRDKN 126
           GH    +  A +K  GIYP G  VL+++G  A+ + +R ++  APLV +    N
Sbjct: 312 GHFDFDVLQAFVKAVGIYPVGSCVLMQTGHLAMVLEQRPDSLLAPLVRIFYSTN 365


>gi|300310279|ref|YP_003774371.1| HD-GYP domain-containing protein
           [Herbaspirillum seropedicae SmR1]
          Length = 408

 Score = 58.2 bits (139), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 40/112 (35%), Positives = 56/112 (50%), Gaps = 6/112 (5%)

Query: 13  LQAVEQHHESPDGRGYPYGTK-RELSELSQMIRFADIFTAKYSARKTRASMPPRQAAQSV 71
           L     HHE  DG GYP   +  ++S  S+M    D++ A  S R  ++   P ++  S 
Sbjct: 236 LDVCLHHHEKIDGSGYPSRHQGNQISVYSRMAAVCDVYDAVTSERPYKSGWDPAESL-SR 294

Query: 72  YLVSDGH---PIASALLKEFGIYPPGCFVLLKSGETAVTIRRGNTP-TAPLV 119
                GH   PI  A +K  GIYP G  V L+SG TA+ IR+ +   T P+V
Sbjct: 295 MASWQGHFDRPIFLAFVKALGIYPIGSIVKLQSGRTALVIRQNHVDLTKPVV 346


>gi|300314021|ref|YP_003778113.1| HD-GYP domain-containing protein
           [Herbaspirillum seropedicae SmR1]
          Length = 401

 Score = 56.6 bits (135), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 51/95 (53%), Gaps = 5/95 (5%)

Query: 18  QHHESPDGRGYPYGTKRE-LSELSQMIRFADIFTAKYSARKTRASMPPRQAAQSVYLVSD 76
            HHE  DG GYP+  K + +S +++M    D++ A  S R  +A   P ++ + +   S 
Sbjct: 250 HHHEKIDGSGYPFNLKADSISIMAKMGAVCDVYDAITSNRPYKAGWDPARSIRHMA-ASA 308

Query: 77  GH--PIA-SALLKEFGIYPPGCFVLLKSGETAVTI 108
           GH  PI   A +K  GIYP G  V+L+SG   V +
Sbjct: 309 GHFDPITMQAFVKAIGIYPTGSCVMLQSGRLGVVV 343


  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
   0.318    0.134    0.390 

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: 551,874
Number of extensions: 21196
Number of successful extensions: 80
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 82
Number of HSP's successfully gapped: 3
Length of query: 169
Length of database: 1,619,870
Length adjustment: 79
Effective length of query: 90
Effective length of database: 1,245,805
Effective search space: 112122450
Effective search space used: 112122450
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 127 (53.5 bits)