# /Users/pjcock/Downloads/Software/fasta-35.3.6/ssearch35 -m 10 -q -E 0.5 -H NC_002127.faa NC_002128.faa
SSEARCH searches a sequence data bank
 version 35.03 Feb. 18, 2008
Please cite:
 T. F. Smith and M. S. Waterman, (1981) J. Mol. Biol. 147:195-197; 
 W.R. Pearson (1991) Genomics 11:635-650

Query: NC_002127.faa
  1>>>gi|10955263|ref|NP_052604.1| plasmid mobilization [Escherichia coli O157:H7 s 107 aa - 107 aa
Library: NC_002128.faa   24233 residues in    85 sequences

  24233 residues in    85 sequences
Statistics: (shuffled [500]) Expectation_n fit: rho(ln(x))= 5.2595+/-0.00883; mu= 8.9348+/- 0.464
 mean_var=48.7394+/-11.263, 0's: 0 Z-trim: 0  B-trim: 0 in 0/29
 Lambda= 0.183711
Algorithm: Smith-Waterman (SSE2, Michael Farrar 2006) (6.0 Mar 2007)
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 Scan time:  0.010
!! No sequences with E() < 0.500000
  2>>>gi|10955264|ref|NP_052605.1| hypothetical protein pOSAK1_02 [Escherichia coli O157:H7 s 126 aa - 126 aa
Library: NC_002128.faa   24233 residues in    85 sequences

  24233 residues in    85 sequences
Statistics: (shuffled [500]) Expectation_n fit: rho(ln(x))= 5.9214+/-0.00691; mu= 3.1033+/- 0.354
 mean_var=36.9389+/- 8.060, 0's: 0 Z-trim: 0  B-trim: 0 in 0/29
 Lambda= 0.211024
Algorithm: Smith-Waterman (SSE2, Michael Farrar 2006) (6.0 Mar 2007)
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 Scan time:  0.010

The best scores are:                                      s-w bits E(85)
gi|10955282|ref|NP_052623.1| hemolysin C [Escheric ( 163)   69 26.0   0.025

>>>gi|10955264|ref|NP_052605.1|, 126 aa vs NC_002128.faa library
; pg_name: /Users/pjcock/Downloads/Software/fasta-35.3.6/ssearch35
; pg_ver: 35.03
; pg_argv: /Users/pjcock/Downloads/Software/fasta-35.3.6/ssearch35 -m 10 -q -E 0.5 -H NC_002127.faa NC_002128.faa
; pg_name: Smith-Waterman (SSE2, Michael Farrar 2006)
; pg_ver: 6.0 Mar 2007
; pg_matrix: BL50 (15:-5)
; pg_open-ext: -10 -2
; mp_extrap: 60000 500
; mp_stats: (shuffled [500]) Expectation_n fit: rho(ln(x))= 5.9214+/-0.00691; mu= 3.1033+/- 0.354  mean_var=36.9389+/- 8.060, 0's: 0 Z-trim: 0  B-trim: 0 in 0/29  Lambda= 0.211024
; mp_KS: -0.0000 (N=0) at  20
; mp_Algorithm: Smith-Waterman (SSE2, Michael Farrar 2006) (6.0 Mar 2007)
; mp_Parameters: BL50 matrix (15:-5), open/ext: -10/-2
>>gi|10955282|ref|NP_052623.1| hemolysin C [Escherichia coli O157:H7 str. Sakai]
; sw_frame: f
; sw_s-w opt:  69
; sw_z-score: 108.8
; sw_bits: 26.0
; sw_expect:  0.025
; sw_score: 69
; sw_ident: 0.209
; sw_sim: 0.555
; sw_overlap: 110
>gi|10955264| ..
; sq_len: 126
; sq_offset: 1
; sq_type: p
; al_start: 12
; al_stop: 114
; al_display_start: 1
-------------------MKKDKKYQIEAIKNKDKTLFIVYAT-DIYSP
SEFFSKIESDLKKKKSKGDV--FFDLIIPNGGKKD--RYVYTSFNGEKFS
SYTLNKVTKTDEYNDL--SELSASFFKKNFDKINVNLLSKATSFALKKGI
PI
>gi|10955282|ref|NP_052623.1| ..
; sq_len: 163
; sq_offset: 1
; sq_type: p
; al_start: 39
; al_stop: 148
; al_display_start: 9
ACSPLHKKWPLSVFAINVIPAIQTNQFALLIKDELPVAFCSWASLDLECE
VKYINDVTSLYAKDWMSGERKWFIDWIAPFGHNMELYKYMRKKYPYELFR
AIRLDESSKTGKIAEFHGGGIDKKLASKIFRQYHHELMSEVKNRQDFNFN
IEKEN
  3>>>gi|10955265|ref|NP_052606.1| hypothetical protein pOSAK1_03 [Escherichia coli O157:H7 s 346 aa - 346 aa
Library: NC_002128.faa   24233 residues in    85 sequences

  24233 residues in    85 sequences
Statistics: (shuffled [500]) Expectation_n fit: rho(ln(x))= 6.4605+/-0.00918; mu= 7.4169+/- 0.474
 mean_var=67.9947+/-15.439, 0's: 0 Z-trim: 0  B-trim: 0 in 0/29
 Lambda= 0.155538
Algorithm: Smith-Waterman (SSE2, Michael Farrar 2006) (6.0 Mar 2007)
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 Scan time:  0.030
!! No sequences with E() < 0.500000
>>><<<


579 residues in 3 query   sequences
24233 residues in 85 library sequences
 Scomplib [35.03]
 start: Tue Jul 15 17:49:23 2008 done: Tue Jul 15 17:49:23 2008
 Total Scan time:  0.050 Total Display time:  0.000

Function used was SSEARCH [version 35.03 Feb. 18, 2008]
