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= 0168.0060.p
         (376 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310193|ref|YP_003774285.1| transcription termination facto...   709   0.0  
gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase...    65   6e-12

>gi|300310193|ref|YP_003774285.1| transcription termination factor
           Rho protein [Herbaspirillum seropedicae SmR1]
          Length = 420

 Score =  709 bits (1831), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 352/374 (94%), Positives = 358/374 (95%), Gaps = 10/374 (2%)

Query: 1   VLPDGFGFLRSPDASYMASTDDIYISPSQIRRFNLHTGDSIEGEVRTPKDGERYFALVKV 60
           VLPDGFGFLRSPDASYMASTDDIYISPSQIRRFNLHTGDSIEGEVRTPKDGERYFALVKV
Sbjct: 57  VLPDGFGFLRSPDASYMASTDDIYISPSQIRRFNLHTGDSIEGEVRTPKDGERYFALVKV 116

Query: 61  DKVNGEAPEASKHRILFENLTPLHPNKIMQLEREMRGEENITGRIIDXMRGEENITGGQR 120
           DKVNGE PEASKHRILFENLTPLHPNK++QLER+MRGEENITGRIID +     +  GQR
Sbjct: 117 DKVNGEPPEASKHRILFENLTPLHPNKLLQLERDMRGEENITGRIIDLI---APVGRGQR 173

Query: 121 GLLVASPKSGKSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGEVVASTFD 180
           GLLVASPKSGKSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGEVVASTFD
Sbjct: 174 GLLVASPKSGKSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGEVVASTFD 233

Query: 181 EPATRHVQVAEMVLEKAKRLVEMKKDVVILLDSITRLAREKGATRRAYNTVIPASGKVLT 240
           EPATRHVQVAEMVLEKAKRLVEMKKDVVILLDSITRLAR       AYNTVIPASGKVLT
Sbjct: 234 EPATRHVQVAEMVLEKAKRLVEMKKDVVILLDSITRLAR-------AYNTVIPASGKVLT 286

Query: 241 GGVDANALQRPKRFFGAARNVEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLE 300
           GGVDANALQRPKRFFGAARNVEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLE
Sbjct: 287 GGVDANALQRPKRFFGAARNVEEGGSLTIIATALIETGSRMDDVIYEEFKGTGNMEVHLE 346

Query: 301 RRLAEKRVYPAINLSKSGTRREELLIKPDQLQKIWVLRKLMYDMDEIEAMEFILDKMKST 360
           RRLAEKRVYPAINLSKSGTRREELLIKPDQLQKIWVLRKLMYDMDEIEAMEFILDKMKST
Sbjct: 347 RRLAEKRVYPAINLSKSGTRREELLIKPDQLQKIWVLRKLMYDMDEIEAMEFILDKMKST 406

Query: 361 KNNAEFFDMMRRGS 374
           KNNAEFFDMMRRG+
Sbjct: 407 KNNAEFFDMMRRGN 420


>gi|300311372|ref|YP_003775464.1| flagellum-specific ATP synthase
           [Herbaspirillum seropedicae SmR1]
          Length = 468

 Score = 65.5 bits (158), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 66/210 (31%), Positives = 95/210 (45%), Gaps = 17/210 (8%)

Query: 118 GQRGLLVASPKSGKSVMLQHIAHAITTNHPDTVMIVLLIDERPEEVTEMQRSVRGE---- 173
           GQR  L A    GKSV+L  +A   + +    V++V LI ER  EV E    + G     
Sbjct: 189 GQRMGLFAGSGVGKSVLLGMMARYTSAD----VIVVGLIGERGREVKEFIEQILGAEGLA 244

Query: 174 ---VVASTFDEPATRHVQVAEMVLEKAKRLVEMKKDVVILLDSITRLAREKGATRRAYNT 230
              VVA+  D P    +Q A      A+   +  KDV++++DS+TR A  +     A   
Sbjct: 245 RSVVVAAPADTPPLMRLQGAAYCTSIAEYFRDQGKDVLLIMDSLTRYAMAQREIALAIGE 304

Query: 231 VIPASGKVLTGGVDANALQRPKRFFGAARNVEEGGSLTIIATALIETGSRMDDVIYEEFK 290
             P + K     V A   + P     A    E GGS+T   T L E G    D I +  +
Sbjct: 305 --PPATKGYPPSVFA---KLPALVERAGNGDEGGGSITAFYTVLTE-GDDQQDPIADAAR 358

Query: 291 GTGNMEVHLERRLAEKRVYPAINLSKSGTR 320
              +  + L R+LAE   YPAI++ +S +R
Sbjct: 359 AILDGHIVLNRQLAEAGHYPAIDIEQSISR 388


  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    0.134    0.372 

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: 1,141,209
Number of extensions: 46211
Number of successful extensions: 130
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 127
Number of HSP's successfully gapped: 2
Length of query: 376
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 289
Effective length of database: 1,207,925
Effective search space: 349090325
Effective search space used: 349090325
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: 131 (55.1 bits)