1 <?xml version="1.0" encoding="UTF-8"?>
2 <VamsasDocument xmlns="http://www.vamsas.ac.uk/vamsasDocument"
3 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
4 xsi:schemaLocation="http://www.vamsas.ac.uk/vamsasDocument file:vamsasDocument.xsd">
5 <Version>alpha</Version>
6 <LockFile>some kind of resolvable session reference.</LockFile>
7 <Provenance xmlns="http://www.vamsas.org">
11 <Action>updated the xml schema</Action>
12 <Date>2006-01-17</Date>
15 <VAMSAS xmlns="http://www.vamsas.org"></VAMSAS>
16 <VAMSAS xmlns="http://www.vamsas.org" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.vamsas.org
19 <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554296">
20 <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLNINVIAVQGDISNYKECEKIIKAALDKFNGIDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
23 <Sequence start="1" end="168" dictionary="vamsas:aa" id="a1127235554297">
24 <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDELRKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWLGNIGQANYSAAKAGVIGFTKTLAREL</sequence>
27 <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554298">
28 <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKLKALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGRIDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
31 <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554299">
32 <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALGFKFYVAEGDVSDFESCKAMVAKIEADLGPVDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
33 <name>NODG_AZOBR</name>
35 <Sequence start="1" end="166" dictionary="vamsas:aa" id="a1127235554300">
36 <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDIRETARMVEKEGRKALPVSTDIRVEEDVENMISEAVDAFGRIDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
39 <Sequence start="1" end="167" dictionary="vamsas:aa" id="a1127235554301">
40 <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMGVKAKGYASNAANFEDTAKVVEEIHKDFGRIDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
43 <Sequence start="1" end="164" dictionary="vamsas:aa" id="a1127235554302">
44 <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKLAKVAAQLKGAEHLIRATDVADLTDVEALFKEVAERFGRLDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD</sequence>
47 <Sequence start="1" end="164" dictionary="vamsas:aa" id="a1127235554303">
48 <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQLAIVIEQFDSARVYAQKVDVSDPEQVQALVRKTVERFGRLDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD</sequence>
51 <Sequence start="1" end="163" dictionary="vamsas:aa" id="a1127235554304">
52 <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGAAAISEYLGENGKGLALNVTDVESIEATLKAINDEFGAIDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
55 <Alignment gapChar="-">
56 <AlignmentAnnotation type="recombinationbreakpoint" graph="false">
57 <seg start="1" end="163" inclusive="false"/>
58 <annotationElement position="50" after="true">
59 <description>Topali Breakpoint</description>
60 <glyph dict="utf8">?</glyph>
66 <Action>added-by hand</Action>
67 <Date>2006-09-11</Date>
70 </AlignmentAnnotation>
71 <alignmentSequence start="1" end="167" refid="a1127235554296">
72 <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLN--INVIAVQGDISNYKECEKIIKAALDKFNG--IDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
75 <alignmentSequence start="1" end="168" refid="a1127235554297">
76 <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDEL--RKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWL-GNIGQANYSAAKAGVIGFTKTLAREL</sequence>
79 <alignmentSequence start="1" end="167" refid="a1127235554298">
80 <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKL--KALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGR--IDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
83 <alignmentSequence start="1" end="167" refid="a1127235554299">
84 <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALG--FKFYVAEGDVSDFESCKAMVAKIEADLGP--VDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
85 <name>NODG_AZOBR</name>
87 <alignmentSequence start="1" end="166" refid="a1127235554300">
88 <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDI--RETARMVEKEG-RKALPVSTDIRVEEDVENMISEAVDAFGR--IDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
91 <alignmentSequence start="1" end="167" refid="a1127235554301">
92 <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMG--VKAKGYASNAANFEDTAKVVEEIHKDFGR--IDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
95 <alignmentSequence start="1" end="164" refid="a1127235554302">
96 <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKL--AKVAAQLKG---AEHLIRATDVADLTDVEALFKEVAERFGR--LDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD-</sequence>
99 <alignmentSequence start="1" end="164" refid="a1127235554303">
100 <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQL--AIVIEQFDS---ARVYAQKVDVSDPEQVQALVRKTVERFGR--LDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD-</sequence>
103 <alignmentSequence start="1" end="163" refid="a1127235554304">
104 <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGA--AAISEYLG----ENGKGLALNVTDVESIEATLKAINDEFGA--IDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
111 <Action>edited</Action>
112 <Date>2005-12-21</Date>
120 <Action>edited</Action>
121 <Date>2005-11-21</Date>
126 <ApplicationData xmlns="http://www.vamsas.org" version="" name="">
127 <dataReference>name of accompanying jar entry containing data</dataReference> <!-- alternative is base64 encoded string in <data></data> -->
128 <User fullname="a user" organization="probably very little">
129 <dataReference>another accompanying jar entry or the data tag with embedded data.</dataReference>
131 <Common><dataReference>another bogus reference</dataReference></Common>
133 <ApplicationData xmlns="http://www.vamsas.org" version="alpha" name="hmm">
134 <data>somedata</data>
135 <Instance urn="hmm://myInstancetype"><dataReference>some reference</dataReference></Instance>
137 <Attachment xmlns="http://www.vamsas.org" type="HMMER2/HMM" objectref="a1127235554304" compressed="false">