3300022062: Marine viral communities from the oligotrophic San Pedro Time Series (SPOT) site, San Pedro Channel, CA, USA ? 35 SPOT_SRF_2012-08-15 (v2)

Overview

Basic Information

• IMG/M Taxon OID: 3300022062
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0127565 | Gp0198093 | Ga0224901
• Sample Name: Marine viral communities from the oligotrophic San Pedro Time Series (SPOT) site, San Pedro Channel, CA, USA ? 35 SPOT_SRF_2012-08-15 (v2)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 6155730
• Sequencing Scaffolds: 22
• Novel Protein Genes: 25
• Associated Families: 25

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
unclassified Hyphomonas → Hyphomonas sp.	1
Not Available	13
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Mediterranean phage MEDS2 group	1
All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Pelagibacterales → Pelagibacteraceae → Candidatus Pelagibacter → unclassified Candidatus Pelagibacter → Candidatus Pelagibacter sp. TMED197	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Alphaproteobacteria incertae sedis → SAR116 cluster → Candidatus Puniceispirillum → unclassified Candidatus Puniceispirillum → Candidatus Puniceispirillum sp. TMED52	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → Viruses → Varidnaviria → Bamfordvirae → Nucleocytoviricota → Megaviricetes → Algavirales → Phycodnaviridae → Prasinovirus → unclassified Prasinovirus → Bathycoccus sp. RCC1105 virus BpV	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → Flavobacteriaceae → unclassified Flavobacteriaceae → Flavobacteriaceae bacterium	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Marine Viral Communities From The Oligotrophic San Pedro Time Series (Spot) Site, San Pedro Channel, Ca, Usa
• Type: Environmental
• Taxonomy: Environmental → Aquatic → Marine → Strait → Unclassified → Seawater → Marine Viral Communities From The Oligotrophic San Pedro Time Series (Spot) Site, San Pedro Channel, Ca, Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): marine biome → ocean strait → sea water
• Earth Microbiome Project Ontology (EMPO): Free-living → Saline → Water (saline)

Location Information

• Location: USA: California
• Coordinates
  • Lat. (^o): 33.55
  • Long. (^o): -118.4
  • Alt. (m): N/A
  • Depth (m): 5

Associated Families

Family	Category	Number of Sequences	3D Structure?
F004493	Metagenome	436	Y
F005940	Metagenome / Metatranscriptome	386	N
F006217	Metagenome	378	Y
F009788	Metagenome / Metatranscriptome	313	Y
F010314	Metagenome / Metatranscriptome	305	Y
F011846	Metagenome / Metatranscriptome	286	Y
F015102	Metagenome / Metatranscriptome	257	Y
F018289	Metagenome	236	Y
F019231	Metagenome / Metatranscriptome	231	N
F020110	Metagenome	226	N
F020448	Metagenome / Metatranscriptome	224	Y
F021189	Metagenome / Metatranscriptome	220	Y
F023484	Metagenome	210	N
F035540	Metagenome / Metatranscriptome	172	Y
F038270	Metagenome / Metatranscriptome	166	Y
F040920	Metagenome	161	Y
F058925	Metagenome / Metatranscriptome	134	N
F063164	Metagenome / Metatranscriptome	130	N
F065684	Metagenome / Metatranscriptome	127	Y
F067110	Metagenome / Metatranscriptome	126	N
F081278	Metagenome / Metatranscriptome	114	Y
F086302	Metagenome / Metatranscriptome	111	Y
F088928	Metagenome / Metatranscriptome	109	N
F101213	Metagenome / Metatranscriptome	102	Y
F101901	Metagenome	102	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0224901_100103	unclassified Hyphomonas → Hyphomonas sp.	1941
Ga0224901_100306	Not Available	1191
Ga0224901_100374	Not Available	1083
Ga0224901_100482	Not Available	953
Ga0224901_100501	Not Available	936
Ga0224901_100560	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes → environmental samples → uncultured Mediterranean phage MEDS2 group	884
Ga0224901_100561	Not Available	884
Ga0224901_100586	All Organisms → Viruses → Duplodnaviria → Heunggongvirae → Uroviricota → Caudoviricetes	858
Ga0224901_100817	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Pelagibacterales → Pelagibacteraceae → Candidatus Pelagibacter → unclassified Candidatus Pelagibacter → Candidatus Pelagibacter sp. TMED197	742
Ga0224901_100834	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Alphaproteobacteria incertae sedis → SAR116 cluster → Candidatus Puniceispirillum → unclassified Candidatus Puniceispirillum → Candidatus Puniceispirillum sp. TMED52	734
Ga0224901_101207	Not Available	627
Ga0224901_101216	All Organisms → cellular organisms → Bacteria	624
Ga0224901_101258	All Organisms → Viruses → Varidnaviria → Bamfordvirae → Nucleocytoviricota → Megaviricetes → Algavirales → Phycodnaviridae → Prasinovirus → unclassified Prasinovirus → Bathycoccus sp. RCC1105 virus BpV	616
Ga0224901_101393	Not Available	592
Ga0224901_101490	Not Available	576
Ga0224901_101665	Not Available	551
Ga0224901_101745	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → Flavobacteriaceae → unclassified Flavobacteriaceae → Flavobacteriaceae bacterium	540
Ga0224901_101841	Not Available	530
Ga0224901_101979	All Organisms → cellular organisms → Bacteria	518
Ga0224901_102051	Not Available	510
Ga0224901_102052	Not Available	510
Ga0224901_102122	Not Available	503

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0224901_100103	Ga0224901_1001034	F010314	MEEVKIYSLNLIALAFSVSAINPILQAVSLLLAIGYTIISISQKLKK
Ga0224901_100306	Ga0224901_1003062	F086302	MNEKNNINPDTHWLATDKIQAKLVNLMFAVEDTKKQLRTGIYGGVTKEEMEMVLDSEIREKEIYEYILDALDNKND
Ga0224901_100374	Ga0224901_1003743	F019231	MTYKVNILRADNSPAEMHSFEKKPTYDEIKALLNHRVFDIVDGRYVDHNSGASVKVEIWCDDEGLMVNNPQRNHRASMLRWNHFKRMEKQLTDDWEDWAHIYGDAIFVFKENDRVKQNG
Ga0224901_100482	Ga0224901_1004821	F015102	MESDDDAEDTNTPFDDVTHWVGNLPRKGTDSDERTNKRNTRRKTKSNFLRKKLGLEEKQ
Ga0224901_100482	Ga0224901_1004824	F006217	YCMSKHDHWTGRAACVQELRHAPRKMEVEALREFLKANPHYKYPGMALPNGRIKPLDVCWGSDKTYYIGTDKVKKEKC
Ga0224901_100501	Ga0224901_1005012	F004493	MRNSVTKNNALDFTNDEWSQLIEGNGLLLMWFIEWNKGDKQGVDIQDFFKLKYRQSAGGDPWPMKNAKISLDGKFVSEGDDDLEPYFLINTDDGVGYIYPYAFVALPKKSGGHHIVRMD
Ga0224901_100501	Ga0224901_1005013	F018289	MTQFTRPMLSNLRSVLQSTLDKADFDNMTIDVGNCSYTGGEATFKVKCILKGAKTREQIDLEYYADLHGIDTTAIAKLQGEDMSIIGYKSRARKKPWILQRLRDGAEFVCDDNLAKKFFKKREEINAE
Ga0224901_100560	Ga0224901_1005602	F011846	VKLSAGFIQSLEQENDGSSSKDNYLGYTKLEQGKPANFALLEQDPLEYWLVWAEAKASGSMKPFRFMGQPSSDEIDLELGSEFVQSMNYDKTAIRKPQQCLTWPVYNWDMNRVQVLEVSHISLARQFAKYGLNKKYSKNLLDWDFELSKIKADMVRYELLIVPRDEDEHNETQMEKAWLQVQKGGFDLNRMVTGDDPFSES
Ga0224901_100561	Ga0224901_1005612	F101901	KIYCDMITDKGFGNDTAYSTNFIPDISAPSCWGTFELTADLTEISGTAFRASTDKYRADATQI
Ga0224901_100586	Ga0224901_1005861	F023484	MNINTKTGELLIATLGRYTSKTEKIIFFKTRAGSLVSSYYISTFNSIKEGDGLMLSNSCDPDQVLDADQVAKCKTFIRNHS
Ga0224901_100586	Ga0224901_1005863	F020110	MSTQLEVQARLSYTRAMLERGIRTASVATMVSAKFCVSRSTAYNDIQAAQAEIDLSDDGPSLEESSEPINTSSVLAMLQHRLEVSVATGDDKAVCSLIKAMNQAKQWNGYNTQSVSPFA
Ga0224901_100817	Ga0224901_1008174	F088928	MTELTPKHFEVIDKNKAKAHEDKKQMRDEVAFFTLNCNSYELQRMYAEFKRLR
Ga0224901_100834	Ga0224901_1008341	F065684	MAYIGASPTYGVFDRQVLAGDGTTTSYNLDHMAVPTSLLVVLDGVVQEPEYSYSTNLTAGQPKITFSEAPDSGGRISIVYLGNEVLTATPATSSTHIDEFNGNGSTTVFTLTRTPAANNAHNYVV
Ga0224901_101207	Ga0224901_1012072	F005940	NISDQVERPFRKALRVNGQGDLIYQALRNKEGQNVQLEIFRPDTLLRGIIENVSSPIEEISPRGSVTQYCLVRFRGSKVIATSASGEGLAIGLLGVERLG
Ga0224901_101216	Ga0224901_1012163	F040920	LFSMKSRPRYYKPEKTGFLVSIVVGLLFSTATFVTLQSVFNQQQITHCEQGWQRACASLP
Ga0224901_101258	Ga0224901_1012581	F021189	FMRKPKKVETAPAALIVAADLKDMKYQILNSPKTEMYRSGDSTSHTIAGTILEQAIDIIVAVLERPEVVKFGNTLIASKEDADNVATMIEEVGKDAVASITNLSEEQVSKGPDSTYPLLISEMKTSLKDEVDKSDIWFPIVQRFLEAHGSKAPFNMNDRQREEVKNASPDRINESRDMIKNSIDEFMVEQRGPPSAPPT
Ga0224901_101393	Ga0224901_1013932	F035540	MAWVLVALFIFNGEPLIMSDNILYENREKCNAAVSARTKYLEATRPESMWEADYWVWCTQIPQEV
Ga0224901_101490	Ga0224901_1014902	F063164	SLLVVVINLSYLMFCVVIATPDNMQVKLYGEKEWLSKCHVAVTEHGFNNPKDRCFCVKMDDKDT
Ga0224901_101665	Ga0224901_1016652	F101213	MKYNWNEETVQHFKFESFYESREKIEQRIKEFVEIDCIPEDGETEEELVDDLIDAVFAN
Ga0224901_101745	Ga0224901_1017452	F038270	MKKLLSLLILTGTLFAQANNVFTLNPSVNSAGMGNVGIANADVKNVFHNPAFAGLRESHQEVSYVDWLPNLTDDMGYQSILYTSDL
Ga0224901_101841	Ga0224901_1018411	F067110	MKGLLQTIVGEAVKRGYYYGIDCGEGYEFTSEYFFQHPTQDLDLLCNQKPEDEYIGLDNLDEGHIFFFTKEQADRLNNAVGKVKFDHEIWKSEEEEDNGDYYEGWILWSNWNDGVERVCDYTTNLDNLIGLRETTDKWEEMVTEFT
Ga0224901_101979	Ga0224901_1019791	F020448	LMVYYDLVKEKQDNHKGSFAEAVRYLMLPELILHEEKIEDRTILRDEENGKPRNWGTKREWRDYMVSKGYNTHNTKLNYVDHASIPGDLLTALNTLPIKHPVFSINIQPPGSVVPAHEDTWRIWYDKNPELAKKYTFEDTAFFIVFLTPQEIGHSFQCGTTNIKWGAGDVVQ
Ga0224901_102051	Ga0224901_1020511	F081278	MIRRNATAADFQNWETLAAEMTDAELLYAAMDCRKVESLWRHHDPMVEGFYSDQASTFGTVLNRRRLSH
Ga0224901_102052	Ga0224901_1020522	F058925	MKITGKQEVQIEISEGQRHLIAIDYISEVFGWDSDYFIEDGWVIKREIAHTSHSFEMKNKVRKADKQDQYLYDIFKTLKRRVV
Ga0224901_102122	Ga0224901_1021222	F009788	AVVGFFNTKMDIIEKDTTNYVYCNISNEVENTYYTMSIQSAEYEVNATLAAPIGVNNRYVKFTLIEGTQDLANATIELPNNGDYPYKIVNATTLGGTEGIEIHRGILRLKQPQETVYSYTDEQSTYIYE