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|
# /opt/fasta/fasta34 -m 10 -y 10 -X "-13 -17" -Q -d 2 NC_002127.faa NC_002695.faa
FASTA searches a protein or DNA sequence data bank
version 34.26 January 12, 2007
Please cite:
W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448
Query library NC_002127.faa vs NC_002695.faa library
searching NC_002695.faa library
1>>>gi|10955263|ref|NP_052604.1| plasmid mobilization [Escherichia coli O157:H7 s 107 aa - 107 aa
vs NC_002695.faa library
opt E()
< 20 1 0:=
22 0 0: one = represents 8 library sequences
24 0 0:
26 0 0:
28 1 1:*
30 4 7:*
32 32 28:===*
34 87 76:=========*=
36 180 156:===================*===
38 308 258:================================*======
40 354 359:============================================*
42 471 439:======================================================*====
44 458 484:========================================================== *
46 412 493:==================================================== *
48 450 472:========================================================= *
50 430 431:=====================================================*
52 380 379:===============================================*
54 301 324:====================================== *
56 272 270:=================================*
58 218 222:===========================*
60 191 180:======================*=
62 152 144:=================*=
64 133 115:==============*==
66 99 91:===========*=
68 84 71:========*==
70 53 56:======*
72 54 44:=====*=
74 27 34:====*
76 20 26:===*
78 24 21:==*
80 15 16:=*
82 6 12:=*
84 11 10:=*
86 5 7:*
88 4 6:* inset = represents 1 library sequences
90 2 4:*
92 8 3:* :==*=====
94 2 3:* :==*
96 1 2:* :=*
98 2 2:* :=*
100 0 1:* :*
102 0 1:* :*
104 0 1:* :*
106 0 1:* :*
108 0 0: *
110 1 0:= *=
112 0 0: *
114 0 0: *
116 0 0: *
118 0 0: *
>120 0 0: *
1578204 residues in 5253 sequences
Expectation_n fit: rho(ln(x))= 4.3805+/-0.00127; mu= 8.3307+/- 0.071
mean_var=55.5989+/-11.432, 0's: 1 Z-trim: 1 B-trim: 0 in 0/43
Lambda= 0.172005
Kolmogorov-Smirnov statistic: 0.0215 (N=29) at 42
FASTA (3.5 Sept 2006) function [optimized, BL50 matrix (15:-5)] ktup: 2
join: 36, opt: 24, open/ext: -10/-2, width: 10
Scan time: 0.200
The best scores are: opt bits E(5253)
gi|162139799|ref|NP_309634.2| 23S rRNA pseudouridi ( 207) 77 26.5 1.2
gi|15831859|ref|NP_310632.1| trehalose-6-phosphate ( 266) 69 24.6 5.8
gi|15832986|ref|NP_311759.1| EivE [Escherichia col ( 381) 70 25.0 6.4
gi|15829430|ref|NP_308203.1| undecaprenyl pyrophos ( 253) 67 24.1 7.9
gi|15832380|ref|NP_311153.1| sn-glycerol-3-phospha ( 542) 69 24.9 9.9
>>>gi|10955263|ref|NP_052604.1|, 107 aa vs NC_002695.faa library
; pg_name: /opt/fasta/fasta34
; pg_ver: 34.26
; pg_argv: /opt/fasta/fasta34 -m 10 -y 10 -X -13 -17 -Q -d 2 NC_002127.faa NC_002695.faa
; pg_name: FASTA
; pg_ver: 3.5 Sept 2006
; pg_matrix: BL50 (15:-5)
; pg_open-ext: -10 -2
; pg_ktup: 2
; pg_optcut: 24
; pg_cgap: 36
; mp_extrap: 60000 5253
; mp_stats: Expectation_n fit: rho(ln(x))= 4.3805+/-0.00127; mu= 8.3307+/- 0.071 mean_var=55.5989+/-11.432, 0's: 1 Z-trim: 1 B-trim: 0 in 0/43 Lambda= 0.172005
; mp_KS: 0.0215 (N=29) at 42
>>gi|162139799|ref|NP_309634.2| 23S rRNA pseudouridine synthase E [Escherichia coli O157:H7 str. Sakai]
; fa_frame: f
; fa_initn: 55
; fa_init1: 55
; fa_opt: 77
; fa_z-score: 110.8
; fa_bits: 26.5
; fa_expect: 1.2
; sw_score: 77
; sw_ident: 0.284
; sw_sim: 0.545
; sw_overlap: 88
>gi|10955263| ..
; sq_len: 107
; sq_offset: 1
; sq_type: p
; al_start: 5
; al_stop: 89
; al_display_start: 1
-----------MTKRSGSNTRRRAISRPVR--LTAEEDQEIRKRAAECG-
KTVSGFLRAAALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREY
AEVLIAITEYHRALLSRLMAD
>gi|162139799|ref|NP_309634.2| ..
; sq_len: 207
; sq_type: p
; al_start: 16
; al_stop: 103
; al_display_start: 1
MQKTSFRNHQVKRFSSQRSTRRKPENQPTRVILFNKPYDVLPQFTDEAGR
KTLKEFIPVQGVYAAGRLDRDSEGLLVLTNNGALQARLTQPGKRTGKIYY
VQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRER
KSIPTSWLKITLYEGRNRQVRRMTAHVGFP
>>gi|15831859|ref|NP_310632.1| trehalose-6-phosphate phosphatase [Escherichia coli O157:H7 str. Sakai]
; fa_frame: f
; fa_initn: 43
; fa_init1: 43
; fa_opt: 69
; fa_z-score: 98.6
; fa_bits: 24.6
; fa_expect: 5.8
; sw_score: 69
; sw_ident: 0.283
; sw_sim: 0.660
; sw_overlap: 53
>gi|10955263| ..
; sq_len: 107
; sq_offset: 1
; sq_type: p
; al_start: 27
; al_stop: 74
; al_display_start: 1
----MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAA
A-LGKKV----NSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLI
AITEYHRALLSRLMAD
>gi|15831859|ref|NP_310632.1| ..
; sq_len: 266
; sq_type: p
; al_start: 167
; al_stop: 219
; al_display_start: 137
PQHEDALMTLAQRITQIWPQMALQQGKCVVEIKPRGTSKGEAIAAFMQEA
PFIGRTPVFLGDDLTDESGFAVVNRLGGMSVKIGTGATQASWRLAGVPDV
WSWLEMITTALQQKRENNRS
2>>>gi|10955264|ref|NP_052605.1| hypothetical protein pOSAK1_02 [Escherichia coli O157:H7 s 126 aa - 126 aa
vs NC_002695.faa library
opt E()
< 20 0 0:
22 0 0: one = represents 9 library sequences
24 0 0:
26 0 0:
28 0 1:*
30 3 7:*
32 10 28:== *
34 57 76:======= *
36 184 156:=================*===
38 286 258:============================*===
40 413 359:=======================================*======
42 455 439:================================================*==
44 512 484:=====================================================*===
46 456 493:=================================================== *
48 451 472:=================================================== *
50 400 431:============================================= *
52 333 379:===================================== *
54 341 324:===================================*==
56 289 270:=============================*===
58 191 222:====================== *
60 178 180:===================*
62 153 144:===============*=
64 102 115:============*
66 95 91:==========*
68 71 71:=======*
70 45 56:===== *
72 58 44:====*==
74 46 34:===*==
76 33 26:==*=
78 21 21:==*
80 21 16:=*=
82 14 12:=*
84 5 10:=*
86 6 7:*
88 2 6:* inset = represents 1 library sequences
90 3 4:*
92 6 3:* :==*===
94 5 3:* :==*==
96 2 2:* :=*
98 2 2:* :=*
100 1 1:* :*
102 1 1:* :*
104 1 1:* :*
106 1 1:* :*
108 0 0: *
110 0 0: *
112 0 0: *
114 0 0: *
116 0 0: *
118 0 0: *
>120 0 0: *
1578204 residues in 5253 sequences
Expectation_n fit: rho(ln(x))= 3.9868+/-0.00133; mu= 9.5505+/- 0.074
mean_var=58.9770+/-12.363, 0's: 0 Z-trim: 0 B-trim: 194 in 1/42
Lambda= 0.167006
Kolmogorov-Smirnov statistic: 0.0212 (N=29) at 44
FASTA (3.5 Sept 2006) function [optimized, BL50 matrix (15:-5)] ktup: 2
join: 36, opt: 24, open/ext: -10/-2, width: 10
Scan time: 0.180
The best scores are: opt bits E(5253)
gi|15829419|ref|NP_308192.1| serine endoprotease [ ( 474) 77 27.0 2.3
gi|15832592|ref|NP_311365.1| phosphoribosylaminoim ( 237) 74 26.0 2.4
gi|15833483|ref|NP_312256.1| DNA adenine methylase ( 278) 72 25.6 3.7
gi|15831563|ref|NP_310336.1| NAD(P) transhydrogena ( 510) 73 26.1 4.7
gi|15834523|ref|NP_313296.1| hypothetical protein ( 404) 71 25.5 5.6
gi|15829964|ref|NP_308737.1| glutaminyl-tRNA synth ( 554) 72 25.9 5.8
gi|15831153|ref|NP_309926.1| putative LACI-type tr ( 332) 69 24.9 6.9
gi|15832760|ref|NP_311533.1| hypothetical lipoprot ( 131) 65 23.5 7.2
gi|15830381|ref|NP_309154.1| hypothetical protein ( 60) 61 22.2 8.4
gi|15831794|ref|NP_310567.1| carboxy-terminal prot ( 682) 70 25.5 9.4
gi|15830925|ref|NP_309698.1| hypothetical protein ( 122) 63 23.0 9.6
>>>gi|10955264|ref|NP_052605.1|, 126 aa vs NC_002695.faa library
; pg_name: /opt/fasta/fasta34
; pg_ver: 34.26
; pg_argv: /opt/fasta/fasta34 -m 10 -y 10 -X -13 -17 -Q -d 2 NC_002127.faa NC_002695.faa
; pg_name: FASTA
; pg_ver: 3.5 Sept 2006
; pg_matrix: BL50 (15:-5)
; pg_open-ext: -10 -2
; pg_ktup: 2
; pg_optcut: 24
; pg_cgap: 36
; mp_extrap: 60000 5253
; mp_stats: Expectation_n fit: rho(ln(x))= 3.9868+/-0.00133; mu= 9.5505+/- 0.074 mean_var=58.9770+/-12.363, 0's: 0 Z-trim: 0 B-trim: 194 in 1/42 Lambda= 0.167006
; mp_KS: 0.0212 (N=29) at 44
>>gi|15829419|ref|NP_308192.1| serine endoprotease [Escherichia coli O157:H7 str. Sakai]
; fa_frame: f
; fa_initn: 64
; fa_init1: 40
; fa_opt: 77
; fa_z-score: 105.8
; fa_bits: 27.0
; fa_expect: 2.3
; sw_score: 77
; sw_ident: 0.250
; sw_sim: 0.620
; sw_overlap: 92
>gi|10955264| ..
; sq_len: 126
; sq_offset: 1
; sq_type: p
; al_start: 31
; al_stop: 117
; al_display_start: 1
MKKDKKYQIEAIKNKDKTLFIVYATDIYSPSEFFSKIESDLKKKKSKGDV
FFDLIIPNG-----GKKDRYVYTSFNGEKFSSYTLNKVTKTDEYNDLSEL
SASFFKKNFDKINVNLLSKATSFALKKGIPI
>gi|15829419|ref|NP_308192.1| ..
; sq_len: 474
; sq_type: p
; al_start: 296
; al_stop: 384
; al_display_start: 266
FAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRG-A
FVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRA-QVGTMPVGSKL
TLGLLRDG-KQVNVNLELQQSSQNQVDSSSIFNGIEGAEMSNKGKDQGVV
VNNVKTGTPAAQIGLKKGDVIIGANQQAVK
>>gi|15832592|ref|NP_311365.1| phosphoribosylaminoimidazole-succinocarboxamide synthase [Escherichia coli O157:H7 str. Sakai]
; fa_frame: f
; fa_initn: 73
; fa_init1: 45
; fa_opt: 74
; fa_z-score: 105.5
; fa_bits: 26.0
; fa_expect: 2.4
; sw_score: 74
; sw_ident: 0.274
; sw_sim: 0.589
; sw_overlap: 73
>gi|10955264| ..
; sq_len: 126
; sq_offset: 1
; sq_type: p
; al_start: 51
; al_stop: 123
; al_display_start: 21
IVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSF
NGEKFSSYTLNKVTKTDEYNDLSELSASFFKKNFDKINVNLLSKATSFAL
KKGIPI
>gi|15832592|ref|NP_311365.1| ..
; sq_len: 237
; sq_type: p
; al_start: 117
; al_stop: 185
; al_display_start: 87
VPVECVVRNRAAGSLVKRLGIEEGIELNPPLFDLFLKNDAMHDPMVNESY
C-ETFGWVSKENLARMKE---LTYKANDVLKKLFDDAGLILVDFKLEFGL
YKGEVVLGDEFSPDGSRLWDKETLEKMDKDRFRQSLGGLIEAYEAVARRL
GVQLD
3>>>gi|10955265|ref|NP_052606.1| hypothetical protein pOSAK1_03 [Escherichia coli O157:H7 s 346 aa - 346 aa
vs NC_002695.faa library
opt E()
< 20 0 0:
22 0 0: one = represents 9 library sequences
24 0 0:
26 0 0:
28 0 1:*
30 8 7:*
32 20 28:===*
34 81 76:========*
36 147 156:=================*
38 283 258:============================*===
40 380 359:=======================================*===
42 450 439:================================================*=
44 480 484:=====================================================*
46 496 493:======================================================*=
48 467 472:====================================================*
50 444 431:===============================================*==
52 370 379:==========================================*
54 315 324:===================================*
56 271 270:=============================*=
58 218 222:========================*
60 154 180:================== *
62 143 144:===============*
64 114 115:============*
66 83 91:==========*
68 77 71:=======*=
70 51 56:======*
72 55 44:====*==
74 28 34:===*
76 27 26:==*
78 21 21:==*
80 13 16:=*
82 15 12:=*
84 7 10:=*
86 6 7:*
88 7 6:* inset = represents 1 library sequences
90 3 4:*
92 3 3:* :==*
94 2 3:* :==*
96 1 2:* :=*
98 3 2:* :=*=
100 0 1:* :*
102 3 1:* :*==
104 1 1:* :*
106 2 1:* :*=
108 0 0: *
110 2 0:= *==
112 1 0:= *=
114 0 0: *
116 1 0:= *=
118 0 0: *
>120 0 0: *
1578204 residues in 5253 sequences
Expectation_n fit: rho(ln(x))= 4.3951+/-0.00131; mu= 12.1593+/- 0.073
mean_var=61.9743+/-12.803, 0's: 0 Z-trim: 1 B-trim: 15 in 1/42
Lambda= 0.162918
Kolmogorov-Smirnov statistic: 0.0096 (N=29) at 50
FASTA (3.5 Sept 2006) function [optimized, BL50 matrix (15:-5)] ktup: 2
join: 37, opt: 25, open/ext: -10/-2, width: 10
Scan time: 0.350
The best scores are: opt bits E(5253)
gi|38704138|ref|NP_311957.2| hypothetical protein ( 111) 86 28.6 0.51
gi|15833861|ref|NP_312634.1| hypothetical protein ( 330) 87 29.2 0.95
gi|15830902|ref|NP_309675.1| host specificity prot (1132) 90 30.4 1.4
gi|15830597|ref|NP_309370.1| TerW [Escherichia col ( 155) 81 27.5 1.5
gi|15830637|ref|NP_309410.1| hypothetical protein ( 171) 80 27.3 1.9
gi|15832101|ref|NP_310874.1| putative UDP-galactos ( 331) 82 28.1 2.2
gi|15830086|ref|NP_308859.1| putative minor tail p ( 192) 79 27.1 2.4
gi|15833543|ref|NP_312316.1| putative regulator [E ( 345) 80 27.6 3.1
gi|15833652|ref|NP_312425.1| putative cytochrome C ( 465) 81 28.0 3.2
gi|15830726|ref|NP_309499.1| acyl carrier protein ( 78) 72 25.1 3.9
gi|15832800|ref|NP_311573.1| transcriptional repre ( 176) 74 25.9 5
gi|15830949|ref|NP_309722.1| hypothetical protein ( 93) 70 24.7 6.1
gi|15831415|ref|NP_310188.1| putative host specifi (1159) 81 28.3 6.2
gi|15831371|ref|NP_310144.1| predicted lipoprotein (1343) 81 28.4 6.9
gi|15831965|ref|NP_310738.1| hypothetical protein ( 216) 71 25.3 9.5
>>>gi|10955265|ref|NP_052606.1|, 346 aa vs NC_002695.faa library
; pg_name: /opt/fasta/fasta34
; pg_ver: 34.26
; pg_argv: /opt/fasta/fasta34 -m 10 -y 10 -X -13 -17 -Q -d 2 NC_002127.faa NC_002695.faa
; pg_name: FASTA
; pg_ver: 3.5 Sept 2006
; pg_matrix: BL50 (15:-5)
; pg_open-ext: -10 -2
; pg_ktup: 2
; pg_optcut: 25
; pg_cgap: 37
; mp_extrap: 60000 5253
; mp_stats: Expectation_n fit: rho(ln(x))= 4.3951+/-0.00131; mu= 12.1593+/- 0.073 mean_var=61.9743+/-12.803, 0's: 0 Z-trim: 1 B-trim: 15 in 1/42 Lambda= 0.162918
; mp_KS: 0.0096 (N=29) at 50
>>gi|38704138|ref|NP_311957.2| hypothetical protein ECs3930 [Escherichia coli O157:H7 str. Sakai]
; fa_frame: f
; fa_initn: 50
; fa_init1: 50
; fa_opt: 86
; fa_z-score: 117.5
; fa_bits: 28.6
; fa_expect: 0.51
; sw_score: 86
; sw_ident: 0.302
; sw_sim: 0.635
; sw_overlap: 63
>gi|10955265| ..
; sq_len: 346
; sq_offset: 1
; sq_type: p
; al_start: 188
; al_stop: 246
; al_display_start: 158
YLQIASLINDFMCSILNMKEIVEQKNKEFNVDIKK-ETIESELHSKLPKS
IDKIHEDIKKQLSCSLI--MKKID-VEMEDYSTYCFSALRAIEGFIYQIL
NDVCNPSSSKNLGEYFTENKPKYIIREIHQETINGEIAEVLCECYTYWHE
NRHGLFHMKPGIADTKTINKLESIAIIDTV
>gi|38704138|ref|NP_311957.2| ..
; sq_len: 111
; sq_type: p
; al_start: 14
; al_stop: 76
; al_display_start: 1
-----------------MALNTYQYRETTMIDPKKIEQIARQVHESMPKG
IREFGEDVEKKIRQTLQAQLTRLDLVSREEFDVQTQVLLRTREKLALLEQ
RSSELEARNNSVADLQSPPAIPPIDKAE
>>gi|15833861|ref|NP_312634.1| hypothetical protein ECs4607 [Escherichia coli O157:H7 str. Sakai]
; fa_frame: f
; fa_initn: 32
; fa_init1: 32
; fa_opt: 87
; fa_z-score: 112.7
; fa_bits: 29.2
; fa_expect: 0.95
; sw_score: 87
; sw_ident: 0.210
; sw_sim: 0.580
; sw_overlap: 157
>gi|10955265| ..
; sq_len: 346
; sq_offset: 1
; sq_type: p
; al_start: 131
; al_stop: 281
; al_display_start: 101
DDDRANLFEFLSEEGITITEDNNNDPNCKHQYIMTTSNGDRVRAKIYKRG
SIQFQGKYLQIASLINDFMCSILNMKEIVEQKNKEFNVDI---KKETI-E
SELHSKLPKSIDKIHEDIKKQLSCSLIMKKIDV-EMEDYSTYCFSALRA-
IEGFIYQILNDVCNPSSSKNLGEYFTENKPKYIIREIHQETINGEIAEVL
CECYTYWHENRHGLFHMKPGIADTKTINKLESIAIIDTVC
>gi|15833861|ref|NP_312634.1| ..
; sq_len: 330
; sq_type: p
; al_start: 10
; al_stop: 155
; al_display_start: 1
---------------------MDFSGRNVKEFIRLLSDHDQFEKDQISEL
TVAANALKLEVAK--NNY-----NMKYSFDTQTERRMIELIREQKDLIPE
KYLHQSGIKKL-KLHED---EFSSLLVDAERQVLEGSSFVLCCGEKINST
ISELLSKKITDLTHPTESFTLSEYFSYDVYEEIFKKVVFTPGECDLVRDS
LVQDGIKPEKIAKIISCLSSRTGIRNLFYACSQAFHVAND
>>><<<
579 residues in 3 query sequences
1578204 residues in 5253 library sequences
Scomplib [34.26]
start: Fri May 23 14:05:39 2008 done: Fri May 23 14:05:40 2008
Total Scan time: 0.730 Total Display time: 0.000
Function used was FASTA [version 34.26 January 12, 2007]
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