1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
|
BLASTP 2.2.21 [Jun-14-2009]
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= gi|3298468|dbj|BAA31520.1| SAMIPF
(472 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
from WGS projects
8,994,603 sequences; 3,078,807,967 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
pdb|1JLX|A Chain A, Agglutinin In Complex With T-Disaccharide >g... 640 0.0
gb|AAQ03084.1|AF401479_1 agglutinin [Amaranthus caudatus] 630 e-179
gb|AAL05954.1| agglutinin [Amaranthus caudatus] 627 e-178
gb|AAD33922.1|AF143954_1 agglutinin [Amaranthus hypochondriacus]... 625 e-177
gb|AAM09540.1|AF491291_1 seed protein AmA1 [Amaranthus hypochond... 624 e-177
ref|XP_002264858.1| PREDICTED: hypothetical protein [Vitis vinif... 245 6e-63
ref|XP_002264911.1| PREDICTED: hypothetical protein [Vitis vinif... 244 1e-62
emb|CAN71829.1| hypothetical protein [Vitis vinifera] 239 5e-61
ref|XP_002264098.1| PREDICTED: hypothetical protein [Vitis vinif... 237 2e-60
ref|XP_002264775.1| PREDICTED: hypothetical protein [Vitis vinif... 231 9e-59
>pdb|1JLX|A Chain A, Agglutinin In Complex With T-Disaccharide
pdb|1JLX|B Chain B, Agglutinin In Complex With T-Disaccharide
pdb|1JLY|A Chain A, Crystal Structure Of Amaranthus Caudatus Agglutinin
pdb|1JLY|B Chain B, Crystal Structure Of Amaranthus Caudatus Agglutinin
Length = 303
Score = 640 bits (1652), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 303/303 (100%), Positives = 303/303 (100%)
Query: 170 AGLPVIMCLKSNNHQKYLRYQSDNIQQYGLLQFSADKILDPLAQFEVEPSKTYDGLVHIK 229
AGLPVIMCLKSNNHQKYLRYQSDNIQQYGLLQFSADKILDPLAQFEVEPSKTYDGLVHIK
Sbjct: 1 AGLPVIMCLKSNNHQKYLRYQSDNIQQYGLLQFSADKILDPLAQFEVEPSKTYDGLVHIK 60
Query: 230 SRYTNKYLVRWSPNHYWITASANEPDENKSNWACTLFKPLYVEEGNMKKVRLLHVQLGHY 289
SRYTNKYLVRWSPNHYWITASANEPDENKSNWACTLFKPLYVEEGNMKKVRLLHVQLGHY
Sbjct: 61 SRYTNKYLVRWSPNHYWITASANEPDENKSNWACTLFKPLYVEEGNMKKVRLLHVQLGHY 120
Query: 290 TQNYTVGGSFVSYLFAESSQIDTGSKDVFHVIDWKSIFQFPKGYVTFKGNNGKYLGVITI 349
TQNYTVGGSFVSYLFAESSQIDTGSKDVFHVIDWKSIFQFPKGYVTFKGNNGKYLGVITI
Sbjct: 121 TQNYTVGGSFVSYLFAESSQIDTGSKDVFHVIDWKSIFQFPKGYVTFKGNNGKYLGVITI 180
Query: 350 NQLPCLQFGYDNLNDPKVAHQMFVTSNGTICIKSNYMNKFWRLSTDDWILVDGNDPRETN 409
NQLPCLQFGYDNLNDPKVAHQMFVTSNGTICIKSNYMNKFWRLSTDDWILVDGNDPRETN
Sbjct: 181 NQLPCLQFGYDNLNDPKVAHQMFVTSNGTICIKSNYMNKFWRLSTDDWILVDGNDPRETN 240
Query: 410 EAAALFRSDVHDFNVISLLNMQKTWFIKRFTSGKPGFINCMNAATQNVDETAILEIIELG 469
EAAALFRSDVHDFNVISLLNMQKTWFIKRFTSGKPGFINCMNAATQNVDETAILEIIELG
Sbjct: 241 EAAALFRSDVHDFNVISLLNMQKTWFIKRFTSGKPGFINCMNAATQNVDETAILEIIELG 300
Query: 470 QNN 472
QNN
Sbjct: 301 QNN 303
BLASTP 2.2.21 [Jun-14-2009]
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= gi|4959044|gb|AAD34209.1|AF069992_1 LIM domain interacting RING
finger protein
(600 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
from WGS projects
8,994,603 sequences; 3,078,807,967 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
sp|Q9WTV7.1|RNF12_MOUSE RecName: Full=E3 ubiquitin-protein ligas... 684 0.0
ref|NP_035406.3| ring finger protein, LIM domain interacting [Mu... 676 0.0
dbj|BAB28712.1| unnamed protein product [Mus musculus] 674 0.0
dbj|BAC26379.1| unnamed protein product [Mus musculus] 672 0.0
ref|NP_001020063.1| ring finger protein, LIM domain interacting ... 620 e-175
ref|NP_057204.2| ring finger protein, LIM domain interacting [Ho... 606 e-171
ref|XP_001141975.1| PREDICTED: ring finger protein 12 isoform 1 ... 605 e-171
ref|XP_001096367.1| PREDICTED: similar to ring finger protein 12... 605 e-171
dbj|BAA91632.1| unnamed protein product [Homo sapiens] 604 e-170
ref|XP_001505028.1| PREDICTED: similar to E3 ubiquitin-protein l... 602 e-170
>sp|Q9WTV7.1|RNF12_MOUSE RecName: Full=E3 ubiquitin-protein ligase RNF12; AltName: Full=RING
finger protein 12; AltName: Full=LIM domain-interacting
RING finger protein; AltName: Full=RING finger LIM
domain-binding protein; Short=R-LIM
gb|AAD34209.1|AF069992_1 LIM domain interacting RING finger protein [Mus musculus]
Length = 600
Score = 684 bits (1765), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 353/414 (85%), Positives = 353/414 (85%)
Query: 1 MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTE 60
MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTE
Sbjct: 1 MENSDSNDKGSDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGESTE 60
Query: 61 EELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDWLNSVRQTGNTTRSRQRGNQS 120
EELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDWLNSVRQTGNTTRSRQRGNQS
Sbjct: 61 EELLRRLQQIKEGPPPQSPDENRAGESSDDVTNSDSIIDWLNSVRQTGNTTRSRQRGNQS 120
Query: 121 WRAVSRTNPNSGDFRFSLEINVNRNNGSQTSENESEPSTRRLSVENMESSSQRQMXXXXX 180
WRAVSRTNPNSGDFRFSLEINVNRNNGSQTSENESEPSTRRLSVENMESSSQRQM
Sbjct: 121 WRAVSRTNPNSGDFRFSLEINVNRNNGSQTSENESEPSTRRLSVENMESSSQRQMENSAS 180
Query: 181 XXXXXXXXXXXXXXTEAVTEVXXXXXXXXXXXXXXXXXXXXXXXERSMSPLQPTSEIPRR 240
TEAVTEV ERSMSPLQPTSEIPRR
Sbjct: 181 ESASARPSRAERNSTEAVTEVPTTRAQRRARSRSPEHRRTRARAERSMSPLQPTSEIPRR 240
Query: 241 APTLEQSSENEPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPXXXXXXXXXXXXX 300
APTLEQSSENEPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNP
Sbjct: 241 APTLEQSSENEPEGSSRTRHHVTLRQQISGPELLGRGLFAASGSRNPSQGTSSSDTGSNS 300
Query: 301 XXXXXXQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYESERGGFRRTF 360
QRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYESERGGFRRTF
Sbjct: 301 ESSGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQAPNNTVTYESERGGFRRTF 360
Query: 361 SRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFMY 414
SRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFMY
Sbjct: 361 SRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFMY 414
Score = 258 bits (658), Expect = 2e-66, Method: Compositional matrix adjust.
Identities = 115/115 (100%), Positives = 115/115 (100%)
Query: 486 KDGRHRAPVTFDESGSLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKT 545
KDGRHRAPVTFDESGSLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKT
Sbjct: 486 KDGRHRAPVTFDESGSLPFFSLAQFFLLNEDDEDQPRGLTKEQIDNLAMRSFGENDALKT 545
Query: 546 CSVCITEYTEGDKLRKLPCSHEFHVHCIDRWLSENSTCPICRRAVLSSGNRESVV 600
CSVCITEYTEGDKLRKLPCSHEFHVHCIDRWLSENSTCPICRRAVLSSGNRESVV
Sbjct: 546 CSVCITEYTEGDKLRKLPCSHEFHVHCIDRWLSENSTCPICRRAVLSSGNRESVV 600
BLASTP 2.2.21 [Jun-14-2009]
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= gi|671626|emb|CAA85685.1| rubisco large subunit
(473 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
from WGS projects
8,994,603 sequences; 3,078,807,967 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
emb|CAA85685.1| rubisco large subunit [Rosmarinus officinalis] 947 0.0
emb|CAA85698.1| rubisco large subunit [Salvia sclarea] >gi|14192... 942 0.0
emb|CAA85688.1| rubisco large subunit [Salvia bucharica] >gi|141... 942 0.0
emb|CAA85670.1| rubisco large subunit [Monarda menthaefolia] 941 0.0
emb|CAA85667.1| rubisco large subunit [Mentha suaveolens] 941 0.0
emb|CAA85676.1| rubisco large subunit [Origanum laevigatum] >gi|... 941 0.0
emb|CAA85684.1| rubisco large subunit [Rosmarinus officinalis] 940 0.0
emb|CAA85687.1| rubisco large subunit [Salvia argentea] 939 0.0
emb|CAA85686.1| rubisco large subunit [Salvia aethiopis] 939 0.0
emb|CAA85718.1| rubisco large subunit [Thymus alsinoides] 939 0.0
>emb|CAA85685.1| rubisco large subunit [Rosmarinus officinalis]
Length = 473
Score = 947 bits (2449), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 458/473 (96%), Positives = 458/473 (96%)
Query: 1 MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQXXXXXXXXXXXXXXX 60
MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQ
Sbjct: 1 MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAE 60
Query: 61 SSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEKDQCICYVAYPLDLFEEGSVTNMFTSI 120
SSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEKDQCICYVAYPLDLFEEGSVTNMFTSI
Sbjct: 61 SSTGTWTTVWTDGLTSLDRYKGRCYHIEPVPGEKDQCICYVAYPLDLFEEGSVTNMFTSI 120
Query: 121 VGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 180
VGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL
Sbjct: 121 VGNVFGFKALRALRLEDLRIPVAYVKTFQGPPHGIQVERDKLNKYGRPLLGCTIKPKLGL 180
Query: 181 SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYL 240
SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYL
Sbjct: 181 SAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFCAEAIYKAQAETGEIKGHYL 240
Query: 241 NATAGTCEEMIKRAIFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAV 300
NATAGTCEEMIKRAIFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAV
Sbjct: 241 NATAGTCEEMIKRAIFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAV 300
Query: 301 IDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSR 360
IDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSR
Sbjct: 301 IDRQKNHGMHFRVLAKALRLSGGDHIHSGTVVGKLEGERDITLGFVDLLRDDFIEKDRSR 360
Query: 361 GIYFTQDWVSLPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVAN 420
GIYFTQDWVSLPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVAN
Sbjct: 361 GIYFTQDWVSLPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGGGTLGHPWGNAPGAVAN 420
Query: 421 RVAVEACVKARNEGRDLAAEGNAIIREACKWSPELAAACEVWKEIKFEFPAMD 473
RVAVEACVKARNEGRDLAAEGNAIIREACKWSPELAAACEVWKEIKFEFPAMD
Sbjct: 421 RVAVEACVKARNEGRDLAAEGNAIIREACKWSPELAAACEVWKEIKFEFPAMD 473
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
from WGS projects
Posted date: Jun 4, 2009 5:40 PM
Number of letters in database: 3,078,807,967
Number of sequences in database: 8,994,603
Lambda K H
0.325 0.138 0.426
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 8994603
Number of Hits to DB: 8,456,431,703
Number of extensions: 350268212
Number of successful extensions: 843324
Number of sequences better than 1.0e-05: 30452
Number of HSP's gapped: 835403
Number of HSP's successfully gapped: 30847
Length of database: 3,078,807,967
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 133 (55.8 bits)
|
