SEA-PHAGES FUNCTIONAL ASSIGNMENTS
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Last modified:1/9/2019 11:37:58(auto-updated)
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USEDo NOT useNotesExample
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terminase, small subunitTerSSisi_1
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terminaseIf there are not two obvious large and small terminase genes in the same genome, just assign the function "terminase".TM4_4
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terminase, large subunitTerLSisi_2
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terminase, large subunit (ATPase domain) Only applicable to Cluster AY genomes (8-21-18)Auxilium_gp2
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terminase, large subunit (nuclease domain) Only applicable to Cluster AY genomes (8-21-18)Auxilium_gp3
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portal proteinhead to tail connectorTM4_5
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portal and MuF-like fusion proteincluster AK arthrobacter phages
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scaffolding proteinScaffoldSisi_5
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capsid maturation proteaseSisi_4
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major capsid proteincapsidSisi_6
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minor capsid proteinother than the MuF minor capsid protein and LamD decoration protein
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MuF-like minor capsid protein
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capsid decoration protein, LamD-likeTuruncu_32
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capsid maturation protease and MuF-like fusion proteinSchubert_gp3
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major capsid and protease fusion proteinCluster AN arthrobacter phages
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capsid morphogenesis protein
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head-to-tail connector complex proteinhead-to-tail connector this is NOT a portal.must have an HHPRED alignment to one of the following crystal structures: HK97 gp6 or or Bacillus protein yqbG Please see the portal and head-to-tail connector case study at the links provided. Note: SPP1 gp17 and 17.1 are NOT h-t connectors (they are the tail terminator and major tail subunit.https://seaphages.org/meetings/33/
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head-to-tail adaptormust have an HHPRED alignment to one of the following crystal structures: SPP1 15 (5A21 chain C or D in the macromolecular complex)Please see the portal and head-to-tail connector case study at the links provided. Note: SPP1 gp17 and 17.1 are NOT h-t connectors (they are the tail terminator and major tail subunit.https://seaphages.org/meetings/33/
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head-to-tail stoppermust have an HHPRED alignment to one of the following crystal structures: SPP1 16 (5A21 chain E or F in the macromolecular complex)Please see the portal and head-to-tail connector case study at the links provided. Note: SPP1 gp17 and 17.1 are NOT h-t connectors (they are the tail terminator and major tail subunit.https://seaphages.org/meetings/33/
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tail terminatormust have an HHPRED alignment to one of the following: SPP1 17 (5A21 chain G in the macromolecular complex) or Lambda U (3FZ2_F)Please see the portal and head-to-tail connector case study at the links provided. Note: SPP1 gp17 and 17.1 are NOT h-t connectors (they are the tail terminator and major tail subunit.)https://seaphages.org/meetings/33/
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major tail proteinmajor tail subunitSisi_11
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tail assembly chaperoneTail scaffolding proteinTM4_15; 16
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tape measure proteinTape Measure, tmp, tapemeasureTM4_17
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minor tail proteintail fiber-like proteinSisi_15-18
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minor tail protein, D-ala-D-ala carboxypeptidasemust include "minor tail" as part of the functional assingmentSisi_19
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tail sheath proteinfound in contractile tailed phagesAlice_120
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tail fiber
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tailspike proteintailspike has triple beta coils. make sure you are matching the spike part of the protein and not the N-terminal tail tip binding domain.Turuncu_23
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tail needle proteinZeta1847_gp20
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baseplate J proteinAlice_133
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tail tube proteinfound in contractile tailed phagesRosiePosie_19
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baseplate wedge proteinRosiePosie_38
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capsid decoration proteinhead decoration proteinmatches LamD, for exampleAlice_107, Alice_232
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lysin ALysA, endolysin ASisi_30
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lysin A, protease M15 domainsome Gordonia phages have lysin A split into two genes. make sure to label each domain.
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lysin A, protease C39 domainsome Gordonia phages have lysin A split into two genes. make sure to label each domain.
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lysin A, glycosyl hydrolase domainsome Gordonia phages have lysin A split into two genes. make sure to label each domain.
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lysin A, L-Ala-D-Glu peptidase domain
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lysin A, protease domainif not obviously M15 or C39some actinobacteriophages (not yet seen in the mycobacteriophages) have lysin A split into two genes. make sure to label each domain.
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lysin BLysB, endolysin BSisi_31
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holinmust be adjacent to lysins and have mutliple transmembrane domainsSisi_32
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integrase, (S-int)Bxb1_35
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integrase, (Y-int)Sisi_43
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ParA-like dsDNA partitioning proteinRedRock_37
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ParB-like dsDNA partitioning proteinDo not label anything a ParB or having a ParB partitioning domain without the presence of a ParA partner in the genomeRedRock_38
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ParB-like nuclease domaindoes not have to have a ParA partner
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immunity repressorRepressorlikely to have an HHPred match to C1 protein in lambdaSisi_45
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T4 Imm-like proteinImmunity repressorZeeculate_69
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exciseExcisionase, Xis, only one per phage;check to see if CRODo not call a protein excise unless you can identify the integrase and the immunity repressor in the phage.BPs_34
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recombination directionality factorRDFRedRock_58
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Cro (control of repressor’s operator)Do not call a protein Cro unless you can identify the integrase, excise, and the immunity repressor in the phage.Che9c_47
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antirepressorSisi_47
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DnaE-like DNA polymerase III (alpha)Spud_203
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DNA polymerase ILuchador_50
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DNA polymerase III sliding clamp (Beta)Corndog_84
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DnaC-like helicase loaderAlice_189
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DNA helicaseATP-dependent helicaseChah_54
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DnaB-like dsDNA helicaseRedRock_68
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RepA-like helicaseSour_51
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DNA primasemake sure it has both partsSpud_199
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DNA primase/helicaseSchubert_31
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DNA primase/polymeraseRosebush_54
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DnaQ-like (DNA polymerase III subunit)Sisi_35
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Nucleotidyl transferaseSpud_3
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polynucleotide kinasepnkSpud_250
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Lsr2-like DNA bridging proteinLsr2Omega_61
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RecA-like DNA recombinaseSpud_205
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RecB-like exonuclease/helicaseIf both a helicase and nuclease domain are present, the RecB label should be used.RedRock_72
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Cas4 family exonucleaseThis family of exonucleases is similar to the exonuclease domain of RecB. The Cas4 label should be used if the gene includes only the exonuclease region. IF the gene also includes a helicase domain, the RecB label should be used.Baby16_68
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Ku-like dsDNA break-binding proteinKuOmega_206
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MRE11 double-strand break endo/exonuclease
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DprA-like DNA processing chain A
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RNA ligaseCjw1_93
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rtcB-like RNA ligaseAnaya_88
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DNA ligaseBenedict_29
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RNaseE
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WhiB family transcription factorWhiBSisi_55,57
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RNA polymerase sigma factorNerujay_52
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ASC-1 transciption coactivator
Zombie_38
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DNA-directed RNA polymerase subunit alpha
Zeta1847 gp42
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ribonucleotide reductaseRedRock_53
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SprT-like proteasePeaches_79
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cysteine proteaseSaguaro_6
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pyrimidine deaminaseDaVinci_40
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nucleoside deaminasePeaches_35
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deoxycytidylate deaminasedCMP deaminase
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ThyX-like thymidylate synthaseThyXRedRock_51
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thymidylate synthasewhen you can't determine if it is ThyX or ThyADismas_55
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MazG-like nucleotide pyrophosphohydrolaseMazGChe12_gp40
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MutT-like nucleotide pyrophosphohydrolase
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glycoside hydrolaseBonray_180
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peptidyl tRNA hydrolaseSpud_156
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DNA methylaseSisi_69
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acetyltransferaseHank144_74
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methyltransferaseOptimus_14
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