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= 0002.0622.p
         (204 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313520|ref|YP_003777612.1| transcription regulator protein...   150   1e-37
gi|300310732|ref|YP_003774824.1| hypothetical protein Hsero_1400...   135   3e-33
gi|300312368|ref|YP_003776460.1| GntR family transcription regul...    69   2e-13
gi|300312446|ref|YP_003776538.1| GntR family transcription regul...    59   2e-10

>gi|300313520|ref|YP_003777612.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 233

 Score =  150 bits (378), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 76/90 (84%), Positives = 84/90 (93%)

Query: 1   VVREALSRLKHEGLVEPRQGSGVFVTEQAGIKPLRIDYTEVSSPEAVLQIVELRRAIEAE 60
           VVREA++RLKHEG+VEPRQGSGVFVTEQAGIKPLRIDYTEVSSPEAVLQIVELRRAIEAE
Sbjct: 49  VVREAIARLKHEGVVEPRQGSGVFVTEQAGIKPLRIDYTEVSSPEAVLQIVELRRAIEAE 108

Query: 61  VAAQAAKRRTDADMAAIDAALARXDADMAA 90
           VAAQAAKRR+  D+ AI+AALA+   D+AA
Sbjct: 109 VAAQAAKRRSAEDLQAIEAALAQIGVDVAA 138


>gi|300310732|ref|YP_003774824.1| hypothetical protein Hsero_1400
           [Herbaspirillum seropedicae SmR1]
          Length = 365

 Score =  135 bits (340), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 62/77 (80%), Positives = 70/77 (90%)

Query: 104 TPEQSALRVLTAQQDRLYNVAAPLLTANAQLCRGNARNLLGFTAKNKYSYPSEFADAAQS 163
           TP+Q  L+ L AQQDRLY VAAPLLT+NAQLCRGNARNLLGFTAKN+YS+P E+AD A+S
Sbjct: 58  TPQQQQLQELIAQQDRLYRVAAPLLTSNAQLCRGNARNLLGFTAKNRYSFPIEYADTARS 117

Query: 164 LGFDDRLQVTGVLPGSG 180
           LG+DDRLQVTGVLPGSG
Sbjct: 118 LGYDDRLQVTGVLPGSG 134


>gi|300312368|ref|YP_003776460.1| GntR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 278

 Score = 69.3 bits (168), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 55/134 (41%), Positives = 70/134 (52%), Gaps = 14/134 (10%)

Query: 1   VVREALSRLKHEGLVEPRQGSGVFVTEQAGIKPLRIDYT---EVSSPEAVLQIVELRRAI 57
           V+REA+SRLK EGLV  R+GSG  V       P R+D        S +AVL+++ELRR +
Sbjct: 69  VIREAISRLKSEGLVGSRRGSGTVVLPANPATPFRLDLDVDDGRDSIQAVLRVIELRRGV 128

Query: 58  EAEVAAQAAKRRTDADMAAIDAALARXDADMAAIDAAPVAVKAQVLTPEQSALR--VLTA 115
           E E+AA AA+RRT A   AI  AL        AID A  A +  V  PE  A    +  A
Sbjct: 129 EGEMAALAAQRRTSAQNLAIQQAL-------QAIDEAAAAGRDGV--PEDFAFHAAISNA 179

Query: 116 QQDRLYNVAAPLLT 129
             + LY      L+
Sbjct: 180 SHNPLYTSLVQFLS 193


>gi|300312446|ref|YP_003776538.1| GntR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 255

 Score = 59.3 bits (142), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 48/81 (59%)

Query: 1   VVREALSRLKHEGLVEPRQGSGVFVTEQAGIKPLRIDYTEVSSPEAVLQIVELRRAIEAE 60
           VVREA+SRL+  GLVE R G G FV E      + ID   +++   +L ++ELR ++E E
Sbjct: 59  VVREAISRLQAAGLVETRHGIGTFVLEAKKGGNINIDPATITTMRDLLALLELRISLETE 118

Query: 61  VAAQAAKRRTDADMAAIDAAL 81
            A  AA RRT+  +  I  AL
Sbjct: 119 TAGLAAARRTEEQLQEIREAL 139


  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
   0.317    0.131    0.362 

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: 494,438
Number of extensions: 16415
Number of successful extensions: 89
Number of sequences better than 1.0e-08: 5
Number of HSP's gapped: 90
Number of HSP's successfully gapped: 5
Length of query: 204
Length of database: 1,619,870
Length adjustment: 81
Effective length of query: 123
Effective length of database: 1,236,335
Effective search space: 152069205
Effective search space used: 152069205
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: 128 (53.9 bits)