ABCDEFGHIJKLMNOPQRSTUVWXY
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x2/27/2024 10:54:38(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), AT genomes (2-28-2020), and DT genomes (7-4-20). AS genomes appear to have a gene 1 with some alignment to the large subunit, but it is unclear if the domains are intact. (10-21-19, 2-21-2020)also applies to cluster GD genomesAuxilium_gp2
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terminase, large subunit (nuclease domain) Only applicable to Cluster AY genomes (8-21-18), AT genomes (2-28-2020) and DT genomes (7-4-20). AS genomes appear to have a gene 1 with some alignment to the large subunit, but it is unclear if the domains are intact. (10-21-19, 2-21-2020)also applies to cluster GD genomesAuxilium_gp3
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DNA packaging ATPase protein
for tectiviridae onlyBadulia_12
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portal proteinhead to tail connectorTM4_5
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scaffolding proteinScaffoldD29_gp16
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capsid maturation proteasewe are no longer using "capsid morphogenesis protein"sometimes the CMP hits to ClpP proteases. If so, look for a serine-type endopeptidase activity. A significant hit to the CMP of D29 and L5 is sufficient evidence.
Langerak_gp4 and D29_gp15
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major capsid proteincapsidSisi_6
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major capsid pentamer proteinRosebush gp16experimental evidence
https://pubmed.ncbi.nlm.nih.gov/32182721/
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major capsid hexamer proteinRosebush gp15experimental evidence
https://pubmed.ncbi.nlm.nih.gov/32182721/
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capsid decoration proteinhead decoration proteinPatience_gp29, Rosebush_gp17experimental evidence
https://pubmed.ncbi.nlm.nih.gov/32182721/
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minor capsid proteinPatience_gp15, Myrna_gp98experimental evidence
https://pubmed.ncbi.nlm.nih.gov/32182721/
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Hypothetical ProteinMuF-like minor capsid proteinIf an HHPred alignment to gp15 of phage D29, see capsid maturation protease6/16/21
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capsid decoration protein, LamD-likelook for the several beta strands and 2 alpha heiices pf PBD's 1C%E_A (lamdba)Turuncu_32https://www.nature.com/articles/nsb0300_230.pdf
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Capsid maturation protease and VIP2-like ADP-ribosyltransferase toxinAdolin_4
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major capsid and protease fusion proteinin this case, the scaffolding function is also part of the fusion, but we don't explicitly write it in the function nameCluster AN arthrobacter phages, EE microbacterium phages
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head fiber proteinBriton15_18
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head-to-tail adaptorwe are no longer calling "head-to-tail connector" or "head-to-tail connector complex protein" 3-6-19must have an HHPRED alignment to one of the following crystal structures: SPP1 15 (5A21 chain C or D in the macromolecular complex) OR must have an HHPRED alignment to one of the following crystal structures: HK97 gp6 or or Bacillus protein yqbG GageAP_19 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/33/8/1/23. The prescribe hits (namely the hits to PDB5A21) are not as likely to show up as they did when this function was added to the approved function list. You can now hit other head-to-tail adaptor calls that were based on this original data. I can include some example genes, but if there is a need for more let me know.
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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) or Bacillus protein yqbHGageAP_20 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/33/8/1/23. The prescribe hits (namely the hits to PDB5A21) are not as likely to show up as they did when this function was added to the approved function list. You can now hit other head-to-tail stopper calls that were based on this original data. I can include some example genes, but if there is a need for more let me know.
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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_chains A through F)GageAP_22 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/33/8/1/23. The prescribe hits (namely the hits to PDB5A21) are not as likely to show up as they did when this function was added to the approved function list. You can now hit other tail terminator calls that were based on this original data. I can include some example genes, but if there is a need for more let me know.
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major tail proteinmajor tail subunit; tail tube proteinSisi_11If you have a siphovirirdae but less than stellar hits to major tail, or tail tube proteins, you can use syntey to help make this call. example: Magritte
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tail assembly chaperoneTail scaffolding proteinEvidence needed to call TAC: Please see Bioinformatics Guide for what evidence is neededTM4_15; 16https://seaphagesbioinformatics.helpdocsonline.com/article-54
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Hypothetical Proteintail assembly chaperonedo not call TAC when there is NO evidencecluster EA1
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tape measure proteinTape Measure, tmp, tapemeasureTM4_17
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minor tail proteintail fiber-like protein, collagen-like, glycine richIf you have significant hits to either collagen-like or glycine-rich proteins, and are in the syntenic region of minor tail proteins, you can call them minor tail proteins.Sisi_15-18, Nebs_gp4
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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 proteinonly assign to a podo- or myo-viridae genomeno good example is availble yethttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2713385/ https://pubmed.ncbi.nlm.nih.gov/36292999/ https://pubmed.ncbi.nlm.nih.gov/29209037/
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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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Hypothetical ProteinHK97_gp10Hendrix lab (studiers of HK(& and capsid construction) never id'd a function for this gene
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lysin ALysA, endolysin Aonly appropriate for Mycobacteriophages; or for Actino phage in which you can identify a lysin b. if you only have one gene to call a lysin or endolysin, do not add a domain. if not a Mycobacteriophage, must have a lysin B, otherwise it is endolysinSisi_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.if not a Mycobacteriophage, must have a lysin B, otherwise it is endolysin, protease M15 domain
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lysin A, protease M23 domainif not a Mycobacteriophage, must have a lysin B, otherwise it is endolysin, protease M23 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.if not a Mycobacteriophage, must have a lysin B, otherwise it is endolysin, protease C39 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.if not a Mycobacteriophage, must have a lysin B, otherwise it is endolysin, glycosyl hydrolase domain
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lysin A, L-Ala-D-Glu peptidase domaindo not assign domains unless you can find genes that house the other needed domainsif not a Mycobacteriophage, must have a lysin B, otherwise it is endolysin, L-Ala-D-Glu peptidase domain
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lysin A, N-acetylmuramoyl-L-alanine amidase domaindo not assign domains unless you can find genes that house the other needed domainsif not a Mycobacteriophage, must have a lysin B, otherwise it is endolysin, N-acetylmuramoyl-L-alanine amidase 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., do not assign domains unless you can find genes that house the other needed domainsif not a Mycobacteriophage, must have a lysin B, otherwise it is endolysin, protease domain
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lysin BLysB, endolysin BSisi_31
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endolysinsome arthrobacter and streptomyces phages have a single endolysin with domains not found in the Mycobacteriophages (like the CHAP domain). use "endolysin" rather than lysin A if the phage does not infect Mycobacterium and no lysin b can be identified.if you only have one gene to call a lysin or endolysin, do not add a domain.
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endolysin, N-acetylmuramoyl-L-alanine amidase domain
if you only have one gene to call a lysin or endolysin, do not add a domain.
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serine hydrolaselysin B has 2 domains, peptidoglycan binding domain and a serine hydrolase domain. This protein only has the serine hydrolase domainDekHockey33_70
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holinevidence needed to call a holin can include biochemical data (1), seqeunce similarity to genes with biochemical data (2), at least 2 transmembrane domians found and the gene be adjacent to the endolysins (s), conderved domain hits (4), and the abscence of additional transmembrane domains in the area. The literature suggests that some phages have more than one holin, for now when we seem multiple possibilities for a holin gene, let's call them membrane proteins.D29_11
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serine integraseBxb1_35
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tyrosine integrasetyrosine homologous recombinaseSisi_43
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serine homologous recombinase
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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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ParB-N-terminal-like domain methyltransferase
at present (7-5-22), this is an orpham. It is big gene (becuase it contains the methyltransferase. Do not confuse with the hits to the DNA binding portion of the ParB.Evaa_gp2
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RepA-like replication initiator
Rachaly_36
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immunity repressorRepressorlikely to have an HHPred match to C1 protein in lambdaSisi_45
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Imm-like superinfection immunity proteinthis is not this phage's immunity repressorthis a pfam hit to T4's superinfection immunity protein: significance was an e-value of 10e-14.Niza_72
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hetero-immunity repressorimmunity repressor (Cluster A)to be used when there is a second immunity repressor that is NOT associated with the own phage's immunity casette (system).This assignment shares a pham with Cluster A immunity repressor. However these phages are not in cluster A; so far we see members in Clusters C, K, and F.LRRHood_44, SamScheppers_83, Rialto_43https://seaphages.org/forums/topic/5583/?page=1#post-10410
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exciseExcisionase, Xis, only one per phage;check to see if CRODo not call a protein excise unless you can identify a tyrosine integrase and the immunity repressor in the phage. A more general "helix-turn-helix DNA binding protein" might be more appropriate if you can't distinguish otherwise.Excision occurs differently in a phage with a serine recombinase. Instead of excise (which it will not have), you may be able to find a RDF (recombination directionality factor) that does the same task.D29_36
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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 and the immunity repressor in the phage. Cro will be present with both the serine and tyrosine integrases. When you have mutliple HTH hits in this region and cannot differentiate which one is the immunity repressor and which is the Cro, consider using the HTH designation.Che9c_47
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WhiB family transcription factor
Jasmine_32
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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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helicase loaderSamman98_70
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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_52
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DNA primaseSpud_199
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DNA primase/helicasemake sure it has both partsSchubert_31
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DNA primase/polymerasemake sure it has both partsRosebush_54
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DNA primase/polymerase/helicasemake sure it has all three partsGreenHearts_47
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DnaQ-like (DNA polymerase III subunit)DNAQ is the exonuclease of Pol III (epsilon subunit)Sisi_35
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nucleotidyl transferaseSpud_3
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FIC domain nucleotidyl transferaseMUST contain HPFxxGNGR motifBradissa_34
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polynucleotide kinasepnkSpud_250
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Lsr2-like DNA bridging proteinLsr2Omega_61
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RecA-like DNA recombinaseSee link to identify requirements Spud_205https://seaphages.org/forums/topic/5567/
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ASCE ATPaseAAA ATPase, RecA superfamily ATPaseApiary_64https://seaphages.org/forums/topic/5567/
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AAA-ATPaseThis call has been used inappropraitely. Be sure that you identify what type of ATPase you have before you call it. otherwise see ASCE ATPase entryCorndog_96
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RecB-like exonuclease/helicaseIf both a helicase and nuclease domain are present, the RecB label should be used.
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host nuclease inhibitorLaroye_83
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VRR-Nuc domain proteinZeina_89
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Cas4 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. Cas4 family nucleases tend to have alignments to the crystal structure 4R5Q_A, 41C1_A and to the PD-(D/E)XK nuclease superfamily (PF12705.7, among others).BiteSize_gp54
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Ku-like dsDNA break-binding proteinKuOmega_206