BLASTP 2.2.17 [Aug-26-2007]


Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
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 composition-based statistics:
Schäffer, Alejandro A., L. Aravind, Thomas L. Madden, 
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= TDE1929 
         (285 letters)

Database: nr 
           5,470,121 sequences; 1,894,087,724 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|42527434|ref|NP_972532.1|  hypothetical protein TDE1929 [...   540   e-152
gi|15639769|ref|NP_219219.1|  hypothetical protein TP0782 [T...    97   8e-19
gi|15639768|ref|NP_219218.1|  hypothetical protein TP0781 [T...    75   3e-12

>gi|42527434|ref|NP_972532.1| hypothetical protein TDE1929 [Treponema denticola ATCC 35405]
 gi|41818019|gb|AAS12443.1| conserved hypothetical protein [Treponema denticola ATCC 35405]
          Length = 285

 Score =  540 bits (1391), Expect = e-152,   Method: Composition-based stats.
 Identities = 285/285 (100%), Positives = 285/285 (100%)

Query: 1   MKKNLYIFLFFMTFLYSYSFEWPVENPSLLRLFAQRNDAFVSRSLVFKEVDTVRASGYGK 60
           MKKNLYIFLFFMTFLYSYSFEWPVENPSLLRLFAQRNDAFVSRSLVFKEVDTVRASGYGK
Sbjct: 1   MKKNLYIFLFFMTFLYSYSFEWPVENPSLLRLFAQRNDAFVSRSLVFKEVDTVRASGYGK 60

Query: 61  HIISIEEKNSTRFFPSTLGNAMIFIDDEGLQSIYANLSDTDLFTSRKETEAGSILGYAGK 120
           HIISIEEKNSTRFFPSTLGNAMIFIDDEGLQSIYANLSDTDLFTSRKETEAGSILGYAGK
Sbjct: 61  HIISIEEKNSTRFFPSTLGNAMIFIDDEGLQSIYANLSDTDLFTSRKETEAGSILGYAGK 120

Query: 121 SAWTEEKSLIFQVADTRNNVLINPLLFMPAIEEKTEPQIQNTVLINGDKQTISLETVKKI 180
           SAWTEEKSLIFQVADTRNNVLINPLLFMPAIEEKTEPQIQNTVLINGDKQTISLETVKKI
Sbjct: 121 SAWTEEKSLIFQVADTRNNVLINPLLFMPAIEEKTEPQIQNTVLINGDKQTISLETVKKI 180

Query: 181 KQGSYDLYSSISDSTEKGGPQLAPFRITVSINGMNISDLPFEVLSSDGKDLYLQNKKSSL 240
           KQGSYDLYSSISDSTEKGGPQLAPFRITVSINGMNISDLPFEVLSSDGKDLYLQNKKSSL
Sbjct: 181 KQGSYDLYSSISDSTEKGGPQLAPFRITVSINGMNISDLPFEVLSSDGKDLYLQNKKSSL 240

Query: 241 SLLYEKEGTMHLGKINLPAGKIELIITVLDKSGNQKKASFIFQVE 285
           SLLYEKEGTMHLGKINLPAGKIELIITVLDKSGNQKKASFIFQVE
Sbjct: 241 SLLYEKEGTMHLGKINLPAGKIELIITVLDKSGNQKKASFIFQVE 285



>gi|15639769|ref|NP_219219.1| hypothetical protein TP0782 [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|14285935|sp|O83761|Y782_TREPA Uncharacterized protein TP_0782 precursor
 gi|3323093|gb|AAC65752.1| predicted coding region TP0782 [Treponema pallidum subsp. pallidum
           str. Nichols]
          Length = 147

 Score = 97.4 bits (241), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 48/124 (38%), Positives = 70/124 (56%), Gaps = 11/124 (8%)

Query: 19  SFEWPVENPSLLRLFAQRNDA-FVSRSLVFKEVDT-------VRASGYGKHIISIEEKNS 70
           + EWPV+ P  L LF Q   A  + + L+F   D+       VR +GYG+ ++ +++   
Sbjct: 21  ALEWPVDKPKFLSLFGQSVGAGLLQQGLIFDGADSAGERGYAVRTAGYGRCVMRLQKHRR 80

Query: 71  TRFFPSTLGNAMIFIDDEGLQSIYANL---SDTDLFTSRKETEAGSILGYAGKSAWTEEK 127
            R FP  LGNA+IF  ++GLQ++YANL    +   F S  E E+G  +GYAG SAW    
Sbjct: 81  ARVFPGALGNALIFAHEDGLQTVYANLREAKNAQDFGSTAEAESGVTVGYAGSSAWAPPN 140

Query: 128 SLIF 131
           S +F
Sbjct: 141 SFVF 144



>gi|15639768|ref|NP_219218.1| hypothetical protein TP0781 [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|14285934|sp|O83760|Y781_TREPA Uncharacterized protein TP_0781
 gi|3323092|gb|AAC65751.1| predicted coding region TP0781 [Treponema pallidum subsp. pallidum
           str. Nichols]
          Length = 153

 Score = 75.5 bits (184), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 37/108 (34%), Positives = 60/108 (55%)

Query: 178 KKIKQGSYDLYSSISDSTEKGGPQLAPFRITVSINGMNISDLPFEVLSSDGKDLYLQNKK 237
           +++ QG+Y LY++++D  E G     PF++ V +NG  +S + FE++ +      L    
Sbjct: 46  RRVTQGTYRLYAAVADVLEHGTQTFTPFQVHVVVNGSEVSAVSFELIVAKDSQACLSGSL 105

Query: 238 SSLSLLYEKEGTMHLGKINLPAGKIELIITVLDKSGNQKKASFIFQVE 285
            +  LLYE +G + LG + L  G  EL I+  D SGN++   F  QVE
Sbjct: 106 LNERLLYEMKGRVFLGSVVLTRGTAELAISARDISGNERTEVFFLQVE 153



  Database: nr
    Posted date:  Sep 17, 2007 11:41 AM
  Number of letters in database: 999,999,834
  Number of sequences in database:  2,976,859
  
  Database: /nucleus1/users/jsaw/ncbi/db/nr.01
    Posted date:  Sep 17, 2007 11:48 AM
  Number of letters in database: 894,087,890
  Number of sequences in database:  2,493,262
  
Lambda     K      H
   0.316    0.134    0.371 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 985,856,645
Number of Sequences: 5470121
Number of extensions: 40453615
Number of successful extensions: 107689
Number of sequences better than 1.0e-05: 3
Number of HSP's better than  0.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 107685
Number of HSP's gapped (non-prelim): 3
length of query: 285
length of database: 1,894,087,724
effective HSP length: 131
effective length of query: 154
effective length of database: 1,177,501,873
effective search space: 181335288442
effective search space used: 181335288442
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 129 (54.3 bits)