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= 0017.0004.p
         (274 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312695|ref|YP_003776787.1| AraC family transcription regul...   568   e-163
gi|300310394|ref|YP_003774486.1| AraC family transcription regul...   258   5e-70
gi|300309661|ref|YP_003773753.1| AraC family transcription regul...    75   4e-15

>gi|300312695|ref|YP_003776787.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 293

 Score =  568 bits (1464), Expect = e-163,   Method: Compositional matrix adjust.
 Identities = 274/274 (100%), Positives = 274/274 (100%)

Query: 1   VHDYPHTVAKWHFHPEYEVHVITASSGKFFVGDFIGDFGPGNLVLTGPNLPHNWVSNLGA 60
           VHDYPHTVAKWHFHPEYEVHVITASSGKFFVGDFIGDFGPGNLVLTGPNLPHNWVSNLGA
Sbjct: 20  VHDYPHTVAKWHFHPEYEVHVITASSGKFFVGDFIGDFGPGNLVLTGPNLPHNWVSNLGA 79

Query: 61  HQQVPARDLVLQFSRPFAERVVGAIPELSPLQEMLDGAARGLQFPDALGASITPLMQELA 120
           HQQVPARDLVLQFSRPFAERVVGAIPELSPLQEMLDGAARGLQFPDALGASITPLMQELA
Sbjct: 80  HQQVPARDLVLQFSRPFAERVVGAIPELSPLQEMLDGAARGLQFPDALGASITPLMQELA 139

Query: 121 QASGARRVVLMMSVLERLASCPERKPLAGPGYDLNAQRHMSSTLNQVLSCIRQNLGGNLR 180
           QASGARRVVLMMSVLERLASCPERKPLAGPGYDLNAQRHMSSTLNQVLSCIRQNLGGNLR
Sbjct: 140 QASGARRVVLMMSVLERLASCPERKPLAGPGYDLNAQRHMSSTLNQVLSCIRQNLGGNLR 199

Query: 181 ETDLAELAGMSVSSFTRFFKRHTGCTFIQYQNGLRLNEACELLMCTELSVTEVCYRVGFN 240
           ETDLAELAGMSVSSFTRFFKRHTGCTFIQYQNGLRLNEACELLMCTELSVTEVCYRVGFN
Sbjct: 200 ETDLAELAGMSVSSFTRFFKRHTGCTFIQYQNGLRLNEACELLMCTELSVTEVCYRVGFN 259

Query: 241 NLSNFNRQFLASKGMPPSRFRSLHRLNDDVRAVA 274
           NLSNFNRQFLASKGMPPSRFRSLHRLNDDVRAVA
Sbjct: 260 NLSNFNRQFLASKGMPPSRFRSLHRLNDDVRAVA 293


>gi|300310394|ref|YP_003774486.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 294

 Score =  258 bits (658), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 118/263 (44%), Positives = 174/263 (66%), Gaps = 1/263 (0%)

Query: 1   VHDYPHTVAKWHFHPEYEVHVITASSGKFFVGDFIGDFGPGNLVLTGPNLPHNWVSNLGA 60
           +H YP    +WH+HPEYE+H++ A+SG+F+VGD IGDF PG LV+TGPNLP NW+S++ A
Sbjct: 20  MHGYPFRTVRWHYHPEYEIHLVVATSGRFYVGDHIGDFAPGQLVMTGPNLPQNWISDIAA 79

Query: 61  HQQVPARDLVLQFSRPFAERVVGAIPELSPLQEMLDGAARGLQFPDALGASITPLMQELA 120
            + VP R LV+QF     ++   +I E+  +  +L+ + RGL F  A   ++ PLMQ L 
Sbjct: 80  DEMVPVRSLVIQFPEQLVDQCAASIAEMEAIMPLLERSHRGLLFDAATSETVRPLMQRLI 139

Query: 121 QASGARRVVLMMSVLERLASCPERKPLAGPGYDLNAQRHMSSTLNQVLSCIRQNLGGNLR 180
              G +R+ L   +L+ LA+ PE + LA   Y L+     SS LN+ ++ +R++L  ++ 
Sbjct: 140 DQRGLKRLALFWELLDVLANAPEPEVLASLSYKLDLSGVNSSGLNRAIAYLREHLTDDIG 199

Query: 181 ETDLAELAGMSVSSFTRFFKRHTGCTFIQYQNGLRLNEAC-ELLMCTELSVTEVCYRVGF 239
           E DLA++ G ++SSF+R FKRHTG T ++Y+N LR++ AC  LL   +  +T++CY  GF
Sbjct: 200 EQDLADMVGQNLSSFSRAFKRHTGTTLVRYKNQLRVDLACLALLTRPQARITDICYETGF 259

Query: 240 NNLSNFNRQFLASKGMPPSRFRS 262
           +NLSNFNR F   KGM PS FR+
Sbjct: 260 SNLSNFNRHFHKIKGMSPSEFRN 282


>gi|300309661|ref|YP_003773753.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 338

 Score = 75.5 bits (184), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 111/253 (43%), Gaps = 29/253 (11%)

Query: 21  VITASSGKFFVGDFIGDFGPGNLVLTGPNLPHNWVSNLGAHQQVPARDLVLQFSRPFAER 80
           VI   S + FVGD I ++ P + ++   +LP      + +  + P   L L+        
Sbjct: 88  VIAQGSKRIFVGDEIYEYDPMHYLVASVDLPVVGKVMVTSPDE-PYLGLRLELDTQEIGE 146

Query: 81  VVGAIPELSPLQEMLDGAARGLQFPDALGASITPLMQELAQASGARRVVLMMSVLERLAS 140
           ++G    L    ++ +GAARGL         +  L  +L  A     V+ ++ + ER A 
Sbjct: 147 LIGD-ENLPAAAQVSEGAARGL--------YVNRLDVDLLDA-----VLRLLRLQERPAD 192

Query: 141 CPERKPLA-----------GPGYDLNAQRHMSSTLNQVLSCIR---QNLGGNLRETDLAE 186
            P   P+            G G  L       S +N+V   IR   +     LR  D+A 
Sbjct: 193 VPILAPMIRREILYRLLMNGQGALLRQTVLQDSQMNRVAKAIRLIKEGYDQALRIDDIAR 252

Query: 187 LAGMSVSSFTRFFKRHTGCTFIQYQNGLRLNEACELLMCTELSVTEVCYRVGFNNLSNFN 246
              MSVSS    FK  T  + +QYQ  LRL EA +L++  + SV    +RVG+ + S F+
Sbjct: 253 DVHMSVSSLHHHFKLVTAMSPLQYQKNLRLQEARKLILTADASVATAAHRVGYESSSQFS 312

Query: 247 RQFLASKGMPPSR 259
           R++    G PP R
Sbjct: 313 REYSRLFGAPPLR 325


  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
   0.323    0.137    0.417 

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: 870,140
Number of extensions: 35487
Number of successful extensions: 142
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 145
Number of HSP's successfully gapped: 3
Length of query: 274
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 190
Effective length of database: 1,222,130
Effective search space: 232204700
Effective search space used: 232204700
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 (22.0 bits)
S2: 130 (54.7 bits)