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= 0001.2960.p
         (312 letters)

Database: BlastDatabases/690/690 
           3295 sequences; 1,000,347 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|134094523|ref|YP_001099598.1| flagellar motor protein MotB [H...   457   e-130
gi|134094541|ref|YP_001099616.1| flagellar motor protein MotD [H...    75   4e-15

>gi|134094523|ref|YP_001099598.1| flagellar motor protein MotB
           [Herminiimonas arsenicoxydans]
          Length = 327

 Score =  457 bits (1176), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 227/298 (76%), Positives = 263/298 (88%)

Query: 1   MADEGLRPIIVKRIKKGGGGHHGGAWKIAYADFVTAMMAFFLLMWLLGSTAKGDLNGIAE 60
           MADEGLRPIIVKRIKK GGGHHGGAWKIAYADFVTAMMAFFLLMWLLGST KG+L GIA+
Sbjct: 1   MADEGLRPIIVKRIKKSGGGHHGGAWKIAYADFVTAMMAFFLLMWLLGSTTKGNLQGIAD 60

Query: 61  YFKTPLKVAMAGGSGSGDANTVLPGGGKDLTRQDGQLRKGENDIVSRKQSLKQAQQELER 120
           YF TPLKVAMAGGSGSGDA +V+ GGGKD+TR DGQ +KGEN   ++  +LK A+ ELER
Sbjct: 61  YFSTPLKVAMAGGSGSGDATSVIKGGGKDMTRIDGQQKKGENLTPTKSLNLKDAEAELER 120

Query: 121 AERTRLEELKTRLEKAIDSNPTLKQFKNQLLIDITTEGLRIQIVDEKNRPMFALASAQLQ 180
            E  RL+ LK R+E+AIDS P+L+Q+KNQLL+DIT+EGLRIQIVDEKNRPMFAL+ A LQ
Sbjct: 121 QEMNRLKSLKERIEEAIDSIPSLRQYKNQLLLDITSEGLRIQIVDEKNRPMFALSKADLQ 180

Query: 181 PYTKEILHEIGRTLNDVPNKISLSGHTDATPYSQGEKGYSNWELSADRANASRRELIAGG 240
           PYTK ILHEI +TLND+PN+ISLSGHTDATPYS GEK YSNWELS+DRANASRRELIAGG
Sbjct: 181 PYTKLILHEIAKTLNDIPNRISLSGHTDATPYSSGEKSYSNWELSSDRANASRRELIAGG 240

Query: 241 MDESKVLRVVGLSSAVLLDKEDPFNPINRRISIIVMNKKAEEMVEKDSGSLNVPTDAS 298
           M+E+K+LRVVGLSSAVL D++DP NPINRRISIIVMNKK E+ + K + +L+V ++A+
Sbjct: 241 MEEAKMLRVVGLSSAVLFDQKDPLNPINRRISIIVMNKKTEDSITKANRTLDVVSEAT 298


>gi|134094541|ref|YP_001099616.1| flagellar motor protein MotD
           [Herminiimonas arsenicoxydans]
          Length = 261

 Score = 75.1 bits (183), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 60/228 (26%), Positives = 106/228 (46%), Gaps = 34/228 (14%)

Query: 26  WKIAYADFVTAMMAFFLLMWLLGSTAKGDLN------GIAEYFKTPLKVAMAGGSGSGDA 79
           W ++YADF+T + AFF++M+ + S  +G         GIA    TP   A+   + S  +
Sbjct: 16  WLVSYADFITLLFAFFVVMYAISSVNEGKYRILSNSLGIAFSGITPKAPALKDPAPSSPS 75

Query: 80  NTVLPGGGKDLTRQDGQLRKGENDIVSRKQSLKQAQQELERAERTRLEELKTRLEKAIDS 139
              LP      +++        ND  +++             E+ R+  +   + KA+  
Sbjct: 76  ILPLPMPAHSPSQR-------ANDAATKR-------------EKARMTNIARDILKAMA- 114

Query: 140 NPTLKQFKNQLLIDITTEGLRIQIVDEKNRPMFALASAQLQPYTKEILHEIGRTLNDVPN 199
            P +++ K  + +  T  G+ ++I       +FA   A+L   +++ L  +   LN V N
Sbjct: 115 -PLIREGK--VRVTQTNRGVSVEI---NASVLFAPGEARLSAQSEKALRAVAEVLNKVDN 168

Query: 200 KISLSGHTDATPYSQGEKGYSNWELSADRANASRRELIAGGMDESKVL 247
            I + GHTD  P +      SNWELSA RA++  R  +  GM+E +++
Sbjct: 169 DIQVEGHTDNVPINNA-MFPSNWELSAVRASSVVRLFLESGMNEKRLV 215


  Database: BlastDatabases/690/690
    Posted date:  Apr 9, 2011  4:48 AM
  Number of letters in database: 1,000,347
  Number of sequences in database:  3295
  
Lambda     K      H
   0.313    0.132    0.371 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3295
Number of Hits to DB: 505,705
Number of extensions: 18074
Number of successful extensions: 56
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 56
Number of HSP's successfully gapped: 2
Length of query: 312
Length of database: 1,000,347
Length adjustment: 82
Effective length of query: 230
Effective length of database: 730,157
Effective search space: 167936110
Effective search space used: 167936110
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 128 (53.9 bits)