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= 0012.0139.p
         (120 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310854|ref|YP_003774946.1| NodT family protein [Herbaspiri...   144   2e-36
gi|300311796|ref|YP_003775888.1| outer membrane channel lipoprot...    93   5e-21
gi|300309656|ref|YP_003773748.1| outer membrane drug efflux prot...    77   3e-16
gi|300313898|ref|YP_003777990.1| outer membrane drug efflux lipo...    67   6e-13

>gi|300310854|ref|YP_003774946.1| NodT family protein
           [Herbaspirillum seropedicae SmR1]
          Length = 507

 Score =  144 bits (363), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 73/102 (71%), Positives = 86/102 (84%)

Query: 1   VLDAQQQLLDDTVAAYQRSYQLTLNQYNAGVVAKSDVIQAQTQLKSAQAQALDNGVQRAQ 60
           VLDAQQQLL++TV AY+RS Q+  NQY AG+VAKSDVIQAQTQLKSAQA ALDNGV RAQ
Sbjct: 199 VLDAQQQLLEETVQAYERSLQVAQNQYAAGMVAKSDVIQAQTQLKSAQASALDNGVTRAQ 258

Query: 61  LEHAIALLVGQPASTFSITPSPLTAAAPPIPVALPSMLLERR 102
           +EHAIALLVG+  + F++  +PL A APP+P  +PSMLLERR
Sbjct: 259 VEHAIALLVGKTPAQFALPRAPLAAVAPPVPQGVPSMLLERR 300


>gi|300311796|ref|YP_003775888.1| outer membrane channel lipoprotein
           [Herbaspirillum seropedicae SmR1]
          Length = 510

 Score = 93.2 bits (230), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 56/117 (47%), Positives = 70/117 (59%), Gaps = 15/117 (12%)

Query: 1   VLDAQQQLLDDTVAAYQRSYQLTLNQYNAGVVAKSDVIQAQTQLKSAQAQALDNGVQRAQ 60
           V D Q+ L   TVAAY RS QL+ +QY AG   +SDV QA+TQL++AQAQ +D    R Q
Sbjct: 209 VTDLQKDLYRRTVAAYTRSLQLSTHQYEAGTALRSDVAQAETQLRAAQAQLIDLDDTRNQ 268

Query: 61  LEHAIALLVGQPASTFSITPSP---------------LTAAAPPIPVALPSMLLERR 102
           LEHAIA+L+G+  + FS+   P               L  + P IPV LPS LLERR
Sbjct: 269 LEHAIAMLIGKAPAQFSLPALPPAAASDSAIDANAARLQGSLPQIPVGLPSELLERR 325


>gi|300309656|ref|YP_003773748.1| outer membrane drug efflux protein
           [Herbaspirillum seropedicae SmR1]
          Length = 504

 Score = 77.4 bits (189), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 44/101 (43%), Positives = 63/101 (62%)

Query: 2   LDAQQQLLDDTVAAYQRSYQLTLNQYNAGVVAKSDVIQAQTQLKSAQAQALDNGVQRAQL 61
           LDA   L   TV   Q S +L   +++ G +++ DV +A+ +L SAQ++AL    QRA  
Sbjct: 211 LDAAAALYRGTVDLRQESLRLVQRRFDEGDISEVDVARARAELASAQSEALGIARQRATA 270

Query: 62  EHAIALLVGQPASTFSITPSPLTAAAPPIPVALPSMLLERR 102
           EHA+A+L+G+  + FS+ P PLT  A  +P  LPS LLERR
Sbjct: 271 EHALAILLGRTPAEFSLPPQPLTRLAVTVPPGLPSALLERR 311


>gi|300313898|ref|YP_003777990.1| outer membrane drug efflux
           lipoprotein [Herbaspirillum seropedicae SmR1]
          Length = 486

 Score = 66.6 bits (161), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 44/102 (43%), Positives = 59/102 (57%), Gaps = 2/102 (1%)

Query: 2   LDAQQQLLDDTVAAYQRSYQLTLNQYNAGVVAKSDVIQAQTQLKSAQAQALDNGVQRAQL 61
           LD +  ++   +A  +++ +L   +++ G  +  D+ Q Q  L S   Q    G QRAQ 
Sbjct: 191 LDVELDVVRRAIALQRQALELATARHDLGATSGLDMAQQQALLDSTLTQIDLLGRQRAQY 250

Query: 62  EHAIALLVGQPASTFSITPSPLTAAAPP-IPVALPSMLLERR 102
           EHAIA L G PA  FSITPS LT   PP IPV +PS +LERR
Sbjct: 251 EHAIATLTGTPAPAFSITPS-LTPITPPAIPVGVPSDVLERR 291


  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
   0.314    0.127    0.347 

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: 337,570
Number of extensions: 11856
Number of successful extensions: 113
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 114
Number of HSP's successfully gapped: 4
Length of query: 120
Length of database: 1,619,870
Length adjustment: 74
Effective length of query: 46
Effective length of database: 1,269,480
Effective search space: 58396080
Effective search space used: 58396080
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 (21.6 bits)
S2: 125 (52.8 bits)