File: test_001.xml

package info (click to toggle)
python-biopython 1.78%2Bdfsg-4
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 65,756 kB
  • sloc: python: 221,141; xml: 178,777; ansic: 13,369; sql: 1,208; makefile: 131; sh: 70
file content (214 lines) | stat: -rw-r--r-- 14,659 bytes parent folder | download | duplicates (4)
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
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<protein-matches xmlns="http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5" interproscan-version="5.26-65.0">
    <protein>
        <sequence md5="fd17e73db0deb5f461347ec2eda4e559">MDPMDIVGKSKEDASLPKATMTKIIKEMLPPDVRVARDAQDLLIECCVEFINLVSSESNDVCNKEDKRTIAPEHVLKALQVLGFGEYIEEVYAAYEQHKYETMDTQRSVKWNPGAQMTEEEAAAEQQRMFAEARARMNGGVSVPQPEHPETDQRSPQS</sequence>
        <xref id="AT5G23090.4" name="pacid=19665592 transcript=AT5G23090.4 locus=AT5G23090 ID=AT5G23090.4.TAIR10 annot-version=TAIR10"/>
        <matches>
            <hmmer3-match evalue="5.7E-22" score="77.7">
                <signature ac="PF00808" desc="Histone-like transcription factor (CBF/NF-Y) and archaeal histone" name="CBFD_NFYB_HMF">
                    <entry ac="IPR003958" desc="Transcription factor CBF/NF-Y/archaeal histone domain" name="CBFA_NFYB_domain" type="DOMAIN">
                        <go-xref category="MOLECULAR_FUNCTION" db="GO" id="GO:0050660" name="flavin adenine dinucleotide binding"/>
                        <go-xref category="BIOLOGICAL_PROCESS" db="GO" id="GO:0055114" name="oxidation-reduction process"/>
                        <go-xref category="MOLECULAR_FUNCTION" db="GO" id="GO:0016627" name="oxidoreductase activity, acting on the CH-CH group of donors"/>
                        <go-xref category="BIOLOGICAL_PROCESS" db="GO" id="GO:0006099" name="tricarboxylic acid cycle"/>
                        <pathway-xref db="KEGG" id="00720+1.3.5.1" name="Carbon fixation pathways in prokaryotes"/>
                        <pathway-xref db="MetaCyc" id="PWY-7279" name="Aerobic respiration II (cytochrome c) (yeast)"/>
                        <pathway-xref db="KEGG" id="00020+1.3.5.1" name="Citrate cycle (TCA cycle)"/>
                        <pathway-xref db="MetaCyc" id="PWY-4302" name="Aerobic respiration III (alternative oxidase pathway)"/>
                        <pathway-xref db="MetaCyc" id="PWY-7254" name="TCA cycle VII (acetate-producers)"/>
                        <pathway-xref db="MetaCyc" id="PWY-6728" name="Methylaspartate cycle"/>
                        <pathway-xref db="MetaCyc" id="PWY-561" name="Superpathway of glyoxylate cycle and fatty acid degradation"/>
                        <pathway-xref db="Reactome" id="R-HSA-71403" name="Citric acid cycle (TCA cycle)"/>
                        <pathway-xref db="KEGG" id="00190+1.3.5.1" name="Oxidative phosphorylation"/>
                        <pathway-xref db="MetaCyc" id="PWY-5690" name="TCA cycle II (plants and fungi)"/>
                        <pathway-xref db="KEGG" id="00650+1.3.5.1" name="Butanoate metabolism"/>
                        <pathway-xref db="MetaCyc" id="PWY-6969" name="TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)"/>
                        <pathway-xref db="Reactome" id="R-HSA-611105" name="Respiratory electron transport"/>
                        <pathway-xref db="MetaCyc" id="PWY-3781" name="Aerobic respiration I (cytochrome c)"/>
                    </entry>
                    <models>
                        <model ac="PF00808" desc="Histone-like transcription factor (CBF/NF-Y) and archaeal histone" name="CBFD_NFYB_HMF"/>
                    </models>
                    <signature-library-release library="PFAM" version="31.0"/>
                </signature>
                <locations>
                    <hmmer3-location env-end="79" env-start="14" score="76.7" evalue="1.1E-21" hmm-start="1" hmm-end="65" start="14" end="79"/>
                    <hmmer3-location env-end="89" env-start="24" score="76.7" evalue="1.1E-21" hmm-start="11" hmm-end="75" start="24" end="89"/>
                </locations>
            </hmmer3-match>
            <hmmer3-match evalue="2.4E-25" score="88.4">
                <signature ac="G3DSA:1.10.20.10">
                    <models>
                        <model ac="4g92B00"/>
                        <model ac="1f1eA00"/>
                        <model ac="1wwiA00"/>
                        <model ac="4khaB00"/>
                        <model ac="3v9rA00"/>
                        <model ac="1b67A00"/>
                        <model ac="3nqjA00"/>
                        <model ac="1tzyF00"/>
                        <model ac="1bh9B00"/>
                        <model ac="1bh9A00"/>
                        <model ac="1q9cA01"/>
                        <model ac="1h3oA00"/>
                        <model ac="1tzyC00"/>
                        <model ac="4drbA00"/>
                        <model ac="2nqbG00"/>
                        <model ac="4ne3A00"/>
                        <model ac="2bykD00"/>
                        <model ac="1ulyA02"/>
                        <model ac="1tafB00"/>
                        <model ac="1tzyE00"/>
                        <model ac="1h3oB00"/>
                        <model ac="1eqzH00"/>
                        <model ac="1n1jB00"/>
                        <model ac="2hueC00"/>
                        <model ac="3b0dB00"/>
                        <model ac="4cayA00"/>
                        <model ac="4cayB00"/>
                        <model ac="1tafA00"/>
                        <model ac="1jfiB00"/>
                        <model ac="2bykA00"/>
                        <model ac="2hueB00"/>
                        <model ac="1kx5A00"/>
                        <model ac="1kx5D00"/>
                        <model ac="1kx5B00"/>
                        <model ac="1r4vA00"/>
                        <model ac="4m6bA00"/>
                        <model ac="1jfiA00"/>
                        <model ac="3b0dC00"/>
                    </models>
                    <signature-library-release library="GENE3D" version="4.1.0"/>
                </signature>
                <locations>
                    <hmmer3-location env-end="143" env-start="7" score="88.0" evalue="3.1E-25" hmm-start="9" hmm-end="137" start="7" end="143"/>
                </locations>
            </hmmer3-match>
            <mobidblite-match>
                <signature ac="mobidb-lite" desc="consensus disorder prediction" name="disorder_prediction">
                    <signature-library-release library="MOBIDB_LITE" version="1.0"/>
                </signature>
                <locations>
                    <mobidblite-location start="136" end="158"/>
                </locations>
            </mobidblite-match>
            <mobidblite-match>
                <signature ac="mobidb-lite" desc="consensus disorder prediction" name="disorder_prediction">
                    <signature-library-release library="MOBIDB_LITE" version="1.0"/>
                </signature>
                <locations>
                    <mobidblite-location start="36" end="58"/>
                </locations>
            </mobidblite-match>
            <superfamilyhmmer3-match evalue="2.48E-35">
                <signature ac="SSF47113" name="Histone-fold">
                    <entry ac="IPR009072" desc="Histone-fold" name="Histone-fold" type="HOMOLOGOUS_SUPERFAMILY">
                        <go-xref category="MOLECULAR_FUNCTION" db="GO" id="GO:0046982" name="protein heterodimerization activity"/>
                    </entry>
                    <models>
                        <model ac="0035368" name="Histone-fold"/>
                        <model ac="0047349" name="Histone-fold"/>
                        <model ac="0047348" name="Histone-fold"/>
                        <model ac="0034938" name="Histone-fold"/>
                        <model ac="0040265" name="Histone-fold"/>
                        <model ac="0042675" name="Histone-fold"/>
                        <model ac="0038404" name="Histone-fold"/>
                        <model ac="0054243" name="Histone-fold"/>
                        <model ac="0040304" name="Histone-fold"/>
                        <model ac="0049583" name="Histone-fold"/>
                        <model ac="0037139" name="Histone-fold"/>
                        <model ac="0047574" name="Histone-fold"/>
                        <model ac="0049584" name="Histone-fold"/>
                        <model ac="0037328" name="Histone-fold"/>
                        <model ac="0049779" name="Histone-fold"/>
                        <model ac="0038979" name="Histone-fold"/>
                        <model ac="0041190" name="Histone-fold"/>
                        <model ac="0039520" name="Histone-fold"/>
                        <model ac="0040306" name="Histone-fold"/>
                        <model ac="0043120" name="Histone-fold"/>
                        <model ac="0047118" name="Histone-fold"/>
                        <model ac="0035550" name="Histone-fold"/>
                        <model ac="0041191" name="Histone-fold"/>
                        <model ac="0047904" name="Histone-fold"/>
                        <model ac="0038978" name="Histone-fold"/>
                        <model ac="0052079" name="Histone-fold"/>
                        <model ac="0035549" name="Histone-fold"/>
                        <model ac="0052078" name="Histone-fold"/>
                        <model ac="0037410" name="Histone-fold"/>
                        <model ac="0050728" name="Histone-fold"/>
                        <model ac="0047903" name="Histone-fold"/>
                        <model ac="0046611" name="Histone-fold"/>
                    </models>
                    <signature-library-release library="SUPERFAMILY" version="1.75"/>
                </signature>
                <locations>
                    <superfamilyhmmer3-location start="12" end="141"/>
                </locations>
            </superfamilyhmmer3-match>
        </matches>
    </protein>
    <protein>
        <sequence md5="f09fabef7feaf88b2964da0045856024">MASTSIMLSSFFSFFFLTFFVTYAQQNVTVHTICYYDGGNFTSNTSYSLNLNRLISSLPDLTPTINGFYNISINGEVNAIALCRGDVKPNQDCISCITTAAKQLVESCPNIIEANIWLEKCMFRYTSRIILGQMEPVPFSYTSSNVSVTDKEGFSKGLGDLLDSLGAKIDAANETKEVKFAAGVKGTIYALAQCTPDLSESDCRICLAQIFAGVPTCCDGKTGGWWTNPSCYFRFEVYPFFDLSVTSEQKQPLSSHNNNTRRSDQGKSKDRSKTLIFAVVPIVAIILGLVFLFIYLKRRRKKKTLKENAENEFESTDSLHFDFETIRVATDDFSLTNKIGEGGFGVVYKGHLPDGLEIAVKRLSIHSGQGNAEFKTEVLLMTKLQHKNLVKLFGFSIKESERLLVYEFIPNTSLDRFLFDPIKQKQLDWEKRYNIIVGVSRGLLYLHEGSEFPIIHRDLKSSNVLLDEQMLPKISDFGMARQFDFDNTQAVTRRVVGTYGYMAPEYAMHGRFSVKTDVYSFGVLVLEIITGKRNSGLGLGEGTDLPTFAWQNWIEGTSMELIDPVLLQTHDKKESMQCLEIALSCVQENPTKRPTMDSVVSMLSSDSESRQLPKPSQPGFFRRSASFSISLNDVSLTDLSAR</sequence>
        <xref id="AT4G21230.1" name="pacid=19647625 transcript=AT4G21230.1 locus=AT4G21230 ID=AT4G21230.1.TAIR10 annot-version=TAIR10"/>
        <matches>
            <coils-match>
                <signature ac="Coil" name="Coil">
                    <signature-library-release library="COILS" version="2.2.1"/>
                </signature>
                <locations>
                    <coils-location start="636" end="642"/>
                </locations>
            </coils-match>
            <hmmer2-match evalue="8.4E-35" score="131.6">
                <signature ac="SM00220" name="serkin_6">
                    <entry ac="IPR000719" desc="Protein kinase domain" name="Prot_kinase_dom" type="DOMAIN">
                        <go-xref category="MOLECULAR_FUNCTION" db="GO" id="GO:0004672" name="protein kinase activity"/>
                        <go-xref category="BIOLOGICAL_PROCESS" db="GO" id="GO:0006468" name="protein phosphorylation"/>
                        <go-xref category="MOLECULAR_FUNCTION" db="GO" id="GO:0005524" name="ATP binding"/>
                    </entry>
                    <models>
                        <model ac="SM00220" name="serkin_6"/>
                    </models>
                    <signature-library-release library="SMART" version="7.1"/>
                </signature>
                <locations>
                    <hmmer2-location score="131.6" evalue="8.4E-35" hmm-start="1" hmm-end="231" start="333" end="603"/>
                </locations>
            </hmmer2-match>
            <hmmer3-match evalue="2.5E-50" score="171.1">
                <signature ac="PF07714" desc="Protein tyrosine kinase" name="Pkinase_Tyr">
                    <entry ac="IPR001245" desc="Serine-threonine/tyrosine-protein kinase, catalytic domain" name="Ser-Thr/Tyr_kinase_cat_dom" type="DOMAIN">
                        <go-xref category="MOLECULAR_FUNCTION" db="GO" id="GO:0004672" name="protein kinase activity"/>
                        <go-xref category="BIOLOGICAL_PROCESS" db="GO" id="GO:0006468" name="protein phosphorylation"/>
                    </entry>
                    <signature-library-release library="PFAM" version="31.0"/>
                </signature>
                <locations>
                    <hmmer3-location env-end="603" env-start="333" score="170.6" evalue="3.5E-50" hmm-start="2" hmm-end="260" start="334" end="603"/>
                </locations>
            </hmmer3-match>
        </matches>
    </protein>
    <protein>
        <sequence md5="ebc9372577bb293872fd313988a7bc82">MKNLSIFLFVVGLCMISDVYGKKSTITVKNELNPKNKNILKVHCKSKNNDIGVKYLKIGEVMSFSFKTNFWGTTEFWCNLYKGPDYKRYRGITAYQAIGLFAKDGSSYNWLARDDGIYFHKDSLPSYYKTYWL</sequence>
        <xref id="AT3G26880.1" name="pacid=19659241 transcript=AT3G26880.1 locus=AT3G26880 ID=AT3G26880.1.TAIR10 annot-version=TAIR10"/>
        <matches>
            <hmmer3-match evalue="1.4E-26" score="92.9">
                <signature ac="PF05938" desc="Plant self-incompatibility protein S1" name="Self-incomp_S1">
                    <models>
                        <model ac="PF05938" desc="Plant self-incompatibility protein S1" name="Self-incomp_S1"/>
                    </models>
                    <signature-library-release library="PFAM" version="31.0"/>
                </signature>
                <locations>
                    <hmmer3-location env-end="132" env-start="25" score="92.7" evalue="1.6E-26" hmm-start="1" hmm-end="102" start="25" end="131"/>
                </locations>
            </hmmer3-match>
        </matches>
    </protein>
    <protein>
        <sequence md5="532b059748db0acbd94e31c6ea953223">MLKIKRVPTVVSNYQKDDGAEDPVGCGRNCLGACCLNGARLPLYACKNLVKSGEKLVISHEAIEPPVAFLESLVLGEWEDRFQRGLFRYDVTACETKVIPGKYGFVAQLNEGRHLKKRPTEFRVDKVLQSFDGSKFNFTKVGQEELLFQFEAGEDAQVQFFPCMPIDPENSPSVVAINVSPIEYGHVLLIPRVLDCLPQRIDHKSLLLAVHMAAEAANPYFRLGYNSLGAFATINHLHFQAYYLAMPFPLEKAPTKKITTTVSGVKISELLSYPVRSLLFEGGSSMQELSDTVSDCCVCLQNNNIPFNILISDCGRQIFLMPQCYAEKQALGEVSPEVLETQVNPAVWEISGHMVLKRKEDYEGASEDNAWRLLAEASLSEERFKEVTALAFEAIGCSNQEEDLEGTIVHQQNSSGNVNQKSNRTHGGPITNGTAAECLVLQ</sequence>
        <xref id="AT4G26850.1" name="pacid=19647214 transcript=AT4G26850.1 locus=AT4G26850 ID=AT4G26850.1.TAIR10 annot-version=TAIR10"/>
        <matches/>
    </protein>
</protein-matches>