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= 0535.0006.p
         (119 letters)

Database: pfamseq 
           9,421,015 sequences; 3,060,696,203 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

C4IH78.1 C4IH78_CLOBU Regulatory protein VanR                         194   2e-48
B1QXZ9.1 B1QXZ9_CLOBU Regulatory protein VanR                         194   2e-48
C5EK34.1 C5EK34_9FIRM Two-component response regulator                157   4e-37
C3RGY6.1 C3RGY6_9MOLU Two-component system response regulator         154   4e-36
B0N158.1 B0N158_9FIRM Putative uncharacterized protein                154   4e-36

>C4IH78.1 C4IH78_CLOBU Regulatory protein VanR
          Length = 229

 Score =  194 bits (493), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 90/119 (75%), Positives = 104/119 (87%)

Query: 1   VKALLRRYYVYKGKDSAPSSDTIHIHDLSINTASNEVTMAQQEITLTETEYQILLLLAQN 60
           VKALLRRYY+YKGK++  SSD+I I+ L IN  SNEV++  +EI LTE EY++LLL+A N
Sbjct: 111 VKALLRRYYIYKGKEAPESSDSIDINGLKINKTSNEVSIDNEEIILTEIEYRLLLLMASN 170

Query: 61  RMKIFSAQNLYESVWNEPYFYSCNNTVMVHIRNLRSKLEADPQNPEYIKTVWGKGYRID 119
           R KIFSAQNLYESVWNEPYFY+ NNTVMVHIRNLRSKLE DPQNP+YIKTVWGKGYRI+
Sbjct: 171 RSKIFSAQNLYESVWNEPYFYTNNNTVMVHIRNLRSKLECDPQNPKYIKTVWGKGYRIE 229


>B1QXZ9.1 B1QXZ9_CLOBU Regulatory protein VanR
          Length = 229

 Score =  194 bits (493), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 90/119 (75%), Positives = 104/119 (87%)

Query: 1   VKALLRRYYVYKGKDSAPSSDTIHIHDLSINTASNEVTMAQQEITLTETEYQILLLLAQN 60
           VKALLRRYY+YKGK++  SSD+I I+ L IN  SNEV++  +EI LTE EY++LLL+A N
Sbjct: 111 VKALLRRYYIYKGKEAPESSDSIDINGLKINKTSNEVSIDNEEIILTEIEYRLLLLMASN 170

Query: 61  RMKIFSAQNLYESVWNEPYFYSCNNTVMVHIRNLRSKLEADPQNPEYIKTVWGKGYRID 119
           R KIFSAQNLYESVWNEPYFY+ NNTVMVHIRNLRSKLE DPQNP+YIKTVWGKGYRI+
Sbjct: 171 RSKIFSAQNLYESVWNEPYFYTNNNTVMVHIRNLRSKLECDPQNPKYIKTVWGKGYRIE 229


>C5EK34.1 C5EK34_9FIRM Two-component response regulator
          Length = 243

 Score =  157 bits (396), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 73/119 (61%), Positives = 92/119 (77%), Gaps = 1/119 (0%)

Query: 1   VKALLRRYYVYKGKDSAPSSDTIHIHDLSINTASNEVTMAQQEITLTETEYQILLLLAQN 60
           VKA++RRY++YKGK+     ++I + DL I  + NEV     EI LT+ EY+ILLLLA N
Sbjct: 126 VKAMIRRYHIYKGKEE-DGEESIAVKDLVIQKSFNEVMKNGGEILLTDLEYRILLLLASN 184

Query: 61  RMKIFSAQNLYESVWNEPYFYSCNNTVMVHIRNLRSKLEADPQNPEYIKTVWGKGYRID 119
           R K+F+ +N+YESVW E Y+YS NNTVMVHIRNLR KLEADP+NP+YI  VWGKGYRI+
Sbjct: 185 RGKLFTIENIYESVWGEAYYYSANNTVMVHIRNLRKKLEADPKNPKYIVNVWGKGYRIE 243


>C3RGY6.1 C3RGY6_9MOLU Two-component system response regulator
          Length = 233

 Score =  154 bits (388), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 74/121 (61%), Positives = 91/121 (75%), Gaps = 2/121 (1%)

Query: 1   VKALLRRYYVYKGK--DSAPSSDTIHIHDLSINTASNEVTMAQQEITLTETEYQILLLLA 58
           VKALLRRYYVY+GK      + D I  ++++IN  S  V +  ++I LT  EYQIL LL 
Sbjct: 113 VKALLRRYYVYQGKMEKEENNDDNIVYNNITINPNSEAVYLNGEQIELTYLEYQILYLLL 172

Query: 59  QNRMKIFSAQNLYESVWNEPYFYSCNNTVMVHIRNLRSKLEADPQNPEYIKTVWGKGYRI 118
            NR +IFS Q LYES+WNEPY+YS NNT+MVHIRNLR K+E+DPQNP+ IKT+WGKGYR 
Sbjct: 173 SNRKRIFSTQTLYESIWNEPYYYSANNTIMVHIRNLRKKIESDPQNPKIIKTIWGKGYRC 232

Query: 119 D 119
           D
Sbjct: 233 D 233


>B0N158.1 B0N158_9FIRM Putative uncharacterized protein
          Length = 233

 Score =  154 bits (388), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 74/121 (61%), Positives = 91/121 (75%), Gaps = 2/121 (1%)

Query: 1   VKALLRRYYVYKGK--DSAPSSDTIHIHDLSINTASNEVTMAQQEITLTETEYQILLLLA 58
           VKALLRRYYVY+GK      + D I  ++++IN  S  V +  ++I LT  EYQIL LL 
Sbjct: 113 VKALLRRYYVYQGKMEKEENNDDNIVYNNITINPNSEAVYLNGEQIELTYLEYQILYLLL 172

Query: 59  QNRMKIFSAQNLYESVWNEPYFYSCNNTVMVHIRNLRSKLEADPQNPEYIKTVWGKGYRI 118
            NR +IFS Q LYES+WNEPY+YS NNT+MVHIRNLR K+E+DPQNP+ IKT+WGKGYR 
Sbjct: 173 SNRKRIFSTQTLYESIWNEPYYYSANNTIMVHIRNLRKKIESDPQNPKIIKTIWGKGYRC 232

Query: 119 D 119
           D
Sbjct: 233 D 233


  Database: pfamseq
    Posted date:  Aug 5, 2010  3:22 PM
  Number of letters in database: 3,060,696,203
  Number of sequences in database:  9,421,015
  
Lambda     K      H
   0.317    0.131    0.382 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 9421015
Number of Hits to DB: 663,165,195
Number of extensions: 20856117
Number of successful extensions: 79481
Number of sequences better than 1.0e-05: 7032
Number of HSP's gapped: 80135
Number of HSP's successfully gapped: 7032
Length of query: 119
Length of database: 3,060,696,203
Length adjustment: 85
Effective length of query: 34
Effective length of database: 2,259,909,928
Effective search space: 76836937552
Effective search space used: 76836937552
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: 126 (53.1 bits)