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 <alignmentSequence start="1" end="167" refid="a1127235554296">
57 <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLN--INVIAVQGDISNYKECEKIIKAALDKFNG--IDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
60 <alignmentSequence start="1" end="168" refid="a1127235554297">
61 <sequence>KIAIVTGASSGIGRAIAFKLASRGANLILGDVKIDEL--RKVAEEIAKETKVKVIPLYVNVGDFNSTKEFYNKGISELGVDYVDILVNNAGINRDALFVKMTYEQWDEVIKVDLYSMFNMTKQVVDMVKRNYGRIINISSLSWL-GNIGQANYSAAKAGVIGFTKTLAREL</sequence>
64 <alignmentSequence start="1" end="167" refid="a1127235554298">
65 <sequence>KVIVITGASSGIGEQVAMQVAEQGATPVLMARTEEKL--KALADKIKETYNTPCYYYVLDVSEETEVQSVFSKVLQEVGR--IDILVNNAGFGIFKTFEDASMDEVKDMFQVNVFGLVACTKAVLPYMVKRNGHIINIASLAGKIATPKSSAYAATKHAVLGFTNSLRMEL</sequence>
68 <alignmentSequence start="1" end="167" refid="a1127235554299">
69 <sequence>KIALVTGAMGGLGTAICQALAKDGCIVAANCLPNFEPAAAWLGQQEALG--FKFYVAEGDVSDFESCKAMVAKIEADLGP--VDILVNNAGITRDKFFAKMDKAQWDAVIATNLSSLFNVTQQVSPKMERGWGRIINISSVNGVKGQAGQTNYSAAKAGVIGFTKALAAEL</sequence>
70 <name>NODG_AZOBR</name>
72 <alignmentSequence start="1" end="166" refid="a1127235554300">
73 <sequence>QTAVVTGGGKGIGRAICLALAREGADIVIAARTEKDI--RETARMVEKEG-RKALPVSTDIRVEEDVENMISEAVDAFGR--IDILVNNAGVAYRKYMVETSTEEYDNIMDTNLKGMFFCTKYALPYLLKREGRIINISSGAGKHGIPKLSIYSASKFAVIGFTESIAYEI</sequence>
76 <alignmentSequence start="1" end="167" refid="a1127235554301">
77 <sequence>KTAIVTGAARGIGKAIALKFAAEGANIAFTDLVIDENAEKTRVELEAMG--VKAKGYASNAANFEDTAKVVEEIHKDFGR--IDILVNNAGITRDGLMMRMSEQQWDMVINVNLKSAFNFIHACTPMMRQKAGSIINMASVVGVHGNAGQANYAASKAGMIALAKSIAQEL</sequence>
80 <alignmentSequence start="1" end="164" refid="a1127235554302">
81 <sequence>KVVVVTGAGSGIGEATAKRFAHEGASVVLVGRNQEKL--AKVAAQLKG---AEHLIRATDVADLTDVEALFKEVAERFGR--LDVLVNNAGVVKSGKVTELGVEDWKAVMSVDLDGVFYCTRTAMPALIASKGNIINVSSVSGLGGDWGMSFYNAAKGAITNFTRALALD-</sequence>
84 <alignmentSequence start="1" end="164" refid="a1127235554303">
85 <sequence>KVALVTGAANGIGLAIAERLYQEGATLALADWNEEQL--AIVIEQFDS---ARVYAQKVDVSDPEQVQALVRKTVERFGR--LDILVNNAGIHIPGTVLECSVQDWRRIASVNIDGVVYCAMHALPELIKTRGCMVNTASVSGLGGDWGAAFYCATKGAVVNFTRALALD-</sequence>
88 <alignmentSequence start="1" end="163" refid="a1127235554304">
89 <sequence>KIALVTGASRGIGRAIAELLVERGATVIGTATSEGGA--AAISEYLG----ENGKGLALNVTDVESIEATLKAINDEFGA--IDILVNNAGITRDNLLMRMKDDEWNDIINTNLTPIYRMSKAVLRMMKKRAGRIINVGSVVGTMGNAGQTNYAAAKAGVIGFTKSMAREV</sequence>
96 <Action>edited</Action>
97 <Date>2005-12-21</Date>
105 <Action>edited</Action>
106 <Date>2005-11-21</Date>
111 <ApplicationData xmlns="http://www.vamsas.org" version="" name="">
112 <dataReference>name of accompanying jar entry containing data</dataReference> <!-- alternative is base64 encoded string in <data></data> -->
113 <User fullname="a user" organization="probably very little">
114 <dataReference>another accompanying jar entry or the data tag with embedded data.</dataReference>
116 <Common><dataReference>another bogus reference</dataReference></Common>
118 <ApplicationData xmlns="http://www.vamsas.org" version="alpha" name="hmm">
119 <data>somedata</data>
120 <Instance urn="hmm://myInstancetype"><dataReference>some reference</dataReference></Instance>
122 <Attachment xmlns="http://www.vamsas.org" type="HMMER2/HMM" objectref="a1127235554304" compressed="false">