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1 | function | 2/12/2025 19:27:50 | (auto-updated) | ||||||||||||||||||||||
2 | USE | Do NOT use | Notes | Example | |||||||||||||||||||||
3 | terminase, small subunit | TerS | Sisi_1 | ||||||||||||||||||||||
4 | terminase | If there are not two obvious large and small terminase genes in the same genome, just assign the function "terminase". | TM4_4 | ||||||||||||||||||||||
5 | terminase, large subunit | TerL | Sisi_2 | ||||||||||||||||||||||
6 | 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 genomes | Auxilium_gp2 | |||||||||||||||||||||
7 | 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 genomes | Auxilium_gp3 | |||||||||||||||||||||
8 | DNA packaging ATPase protein | for tectiviridae only | Badulia_12 | ||||||||||||||||||||||
9 | DNA terminal protein | for podovirus only | PineapplePizza_gp4 | ||||||||||||||||||||||
10 | |||||||||||||||||||||||||
11 | portal protein | head to tail connector | TM4_5 | ||||||||||||||||||||||
12 | |||||||||||||||||||||||||
13 | |||||||||||||||||||||||||
14 | scaffolding protein | Scaffold | D29_gp16 | ||||||||||||||||||||||
15 | capsid maturation protease | we 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 | |||||||||||||||||||||
16 | major capsid protein | capsid | Sisi_6 | ||||||||||||||||||||||
17 | major capsid pentamer protein | Rosebush gp16 | experimental evidence | https://pubmed.ncbi.nlm.nih.gov/32182721/ | |||||||||||||||||||||
18 | major capsid hexamer protein | Rosebush gp15 | experimental evidence | https://pubmed.ncbi.nlm.nih.gov/32182721/ | |||||||||||||||||||||
19 | capsid decoration protein | head decoration protein | Patience_gp29, Rosebush_gp17 | experimental evidence | https://pubmed.ncbi.nlm.nih.gov/32182721/ | ||||||||||||||||||||
20 | minor capsid protein | Patience_gp15, Myrna_gp98 | experimental evidence | https://pubmed.ncbi.nlm.nih.gov/32182721/ | |||||||||||||||||||||
21 | Hypothetical Protein | MuF-like minor capsid protein | If an HHPred alignment to gp15 of phage D29, see capsid maturation protease | 6/16/21 | |||||||||||||||||||||
22 | capsid decoration protein, LamD-like | look for the several beta strands and 2 alpha heiices pf PBD's 1C%E_A (lamdba) | Turuncu_32 | https://www.nature.com/articles/nsb0300_230.pdf | |||||||||||||||||||||
23 | |||||||||||||||||||||||||
24 | Capsid maturation protease and VIP2-like ADP-ribosyltransferase toxin | Adolin_4 | |||||||||||||||||||||||
25 | major capsid and protease fusion protein | in this case, the scaffolding function is also part of the fusion, but we don't explicitly write it in the function name | Cluster AN arthrobacter phages, EE microbacterium phages | ||||||||||||||||||||||
26 | head fiber protein | Briton15_18 | |||||||||||||||||||||||
27 | head-to-tail adaptor | we are no longer calling "head-to-tail connector" or "head-to-tail connector complex protein" 3-6-19 | must 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. | |||||||||||||||||||
28 | head-to-tail stopper | must 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 yqbH | GageAP_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. | ||||||||||||||||||||
29 | tail terminator | must 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. | ||||||||||||||||||||
30 | major tail protein | major tail subunit; tail tube protein | Sisi_11 | If 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 | |||||||||||||||||||||
31 | tail assembly chaperone | Tail scaffolding protein | Evidence needed to call TAC: Please see Bioinformatics Guide for what evidence is needed | TM4_15; 16 | https://seaphagesbioinformatics.helpdocsonline.com/article-54 | ||||||||||||||||||||
32 | Hypothetical Protein | tail assembly chaperone | do not call TAC when there is NO evidence | cluster EA1 | |||||||||||||||||||||
33 | tape measure protein | Tape Measure, tmp, tapemeasure | TM4_17 | ||||||||||||||||||||||
34 | minor tail protein | tail fiber-like protein, collagen-like, glycine rich | If 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 | |||||||||||||||||||||
35 | minor tail protein, D-ala-D-ala carboxypeptidase | must include "minor tail" as part of the functional assingment | Sisi_19 | ||||||||||||||||||||||
36 | tail sheath protein | found in contractile tailed phages | Alice_120 | ||||||||||||||||||||||
37 | |||||||||||||||||||||||||
38 | tailspike protein | tailspike 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 | ||||||||||||||||||||||
39 | tail needle protein | only assign to a podo- or myo-viridae genome | no good example is availble yet | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2713385/ https://pubmed.ncbi.nlm.nih.gov/36292999/ https://pubmed.ncbi.nlm.nih.gov/29209037/ | |||||||||||||||||||||
40 | baseplate J protein | Alice_133 | |||||||||||||||||||||||
41 | tail tube protein | found in contractile tailed phages | RosiePosie_19 | ||||||||||||||||||||||
42 | baseplate wedge protein | RosiePosie_38 | |||||||||||||||||||||||
43 | |||||||||||||||||||||||||
44 | Hypothetical Protein | HK97_gp10 | Hendrix lab (studiers of HK(& and capsid construction) never id'd a function for this gene | ||||||||||||||||||||||
45 | lysin A | LysA, endolysin A | only 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 endolysin | Sisi_30 | ||||||||||||||||||||
46 | lysin A, protease M15 domain | some 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 | ||||||||||||||||||||||
47 | lysin A, protease M23 domain | if not a Mycobacteriophage, must have a lysin B, otherwise it is endolysin, protease M23 domain | |||||||||||||||||||||||
48 | lysin A, protease C39 domain | some 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 | ||||||||||||||||||||||
49 | lysin A, glycosyl hydrolase domain | some 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 | ||||||||||||||||||||||
50 | lysin A, L-Ala-D-Glu peptidase domain | do not assign domains unless you can find genes that house the other needed domains | if not a Mycobacteriophage, must have a lysin B, otherwise it is endolysin, L-Ala-D-Glu peptidase domain | ||||||||||||||||||||||
51 | lysin A, N-acetylmuramoyl-L-alanine amidase domain | do not assign domains unless you can find genes that house the other needed domains | if not a Mycobacteriophage, must have a lysin B, otherwise it is endolysin, N-acetylmuramoyl-L-alanine amidase domain | ||||||||||||||||||||||
52 | lysin A, protease domain | if not obviously M15 or C39 | some 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 domains | if not a Mycobacteriophage, must have a lysin B, otherwise it is endolysin, protease domain | |||||||||||||||||||||
53 | |||||||||||||||||||||||||
54 | lysin B | LysB, endolysin B | Sisi_31 | ||||||||||||||||||||||
55 | endolysin | some 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. | ||||||||||||||||||||||
56 | serine hydrolase | lysin B has 2 domains, peptidoglycan binding domain and a serine hydrolase domain. This protein only has the serine hydrolase domain | DekHockey33_70 | ||||||||||||||||||||||
57 | |||||||||||||||||||||||||
58 | holin | evidence 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 | ||||||||||||||||||||||
59 | serine integrase | Bxb1_35 | |||||||||||||||||||||||
60 | tyrosine integrase | tyrosine homologous recombinase | Sisi_43 | ||||||||||||||||||||||
61 | serine homologous recombinase | ||||||||||||||||||||||||
62 | ParA-like dsDNA partitioning protein | RedRock_37 | |||||||||||||||||||||||
63 | ParB-like dsDNA partitioning protein | Do not label anything a ParB or having a ParB partitioning domain without the presence of a ParA partner in the genome | RedRock_38 | https://pubmed.ncbi.nlm.nih.gov/27146086/ | |||||||||||||||||||||
64 | ParB-like nuclease domain | does not have to have a ParA partner | |||||||||||||||||||||||
65 | ParB-N-terminal-like domain | ParB-like nuclease domain, does not have a ParA partner. | Yotsuba_48 | ||||||||||||||||||||||
66 | 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 | ||||||||||||||||||||||
67 | RepA-like replication initiator | Rachaly_36 | |||||||||||||||||||||||
68 | immunity repressor | Repressor | likely to have an HHPred match to C1 protein in lambda | Sisi_45 | |||||||||||||||||||||
69 | Imm-like superinfection immunity protein | this is not this phage's immunity repressor | this a pfam hit to T4's superinfection immunity protein: significance was an e-value of 10e-14. | Niza_72 | |||||||||||||||||||||
70 | hetero-immunity repressor | immunity 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_43 | https://seaphages.org/forums/topic/5583/?page=1#post-10410 | |||||||||||||||||||
71 | excise | Excisionase, Xis, only one per phage;check to see if CRO | Do 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 | ||||||||||||||||||||
72 | recombination directionality factor | RDF | RedRock_58 | ||||||||||||||||||||||
73 | 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 | ||||||||||||||||||||||
74 | WhiB family transcription factor | Jasmine_32 | |||||||||||||||||||||||
75 | antirepressor | Sisi_47 | |||||||||||||||||||||||
76 | DnaE-like DNA polymerase III (alpha) | Spud_203 | |||||||||||||||||||||||
77 | DNA polymerase I | Luchador_50 | |||||||||||||||||||||||
78 | DNA polymerase III sliding clamp (Beta) | Corndog_84 | |||||||||||||||||||||||
79 | DnaC-like helicase loader | Alice_189 | |||||||||||||||||||||||
80 | helicase loader | Samman98_70 | |||||||||||||||||||||||
81 | DNA helicase | ATP-dependent helicase | Chah_54 | ||||||||||||||||||||||
82 | DnaB-like dsDNA helicase | RedRock_68 | |||||||||||||||||||||||
83 | RepA-like helicase | Sour_52 | |||||||||||||||||||||||
84 | DNA primase | Spud_199 | |||||||||||||||||||||||
85 | DNA primase/helicase | make sure it has both parts | Schubert_31 | ||||||||||||||||||||||
86 | DNA primase/polymerase | make sure it has both parts | Rosebush_54 | ||||||||||||||||||||||
87 | DNA primase/polymerase/helicase | make sure it has all three parts | GreenHearts_47 | ||||||||||||||||||||||
88 | DNA topoisomerase | ||||||||||||||||||||||||
89 | DnaQ-like (DNA polymerase III subunit) | DNAQ is the exonuclease of Pol III (epsilon subunit) | Sisi_35 | ||||||||||||||||||||||
90 | nucleotidyl transferase | Spud_3 | |||||||||||||||||||||||
91 | FIC domain nucleotidyl transferase | MUST contain HPFxxGNGR motif | Bradissa_34 | ||||||||||||||||||||||
92 | polynucleotide kinase | pnk | Spud_250 | ||||||||||||||||||||||
93 | Lsr2-like DNA bridging protein | Lsr2 | Omega_61 | ||||||||||||||||||||||
94 | RecA-like DNA recombinase | See link to identify requirements | Spud_205 | https://seaphages.org/forums/topic/5567/ | |||||||||||||||||||||
95 | ASCE ATPase | AAA ATPase, RecA superfamily ATPase. This call has been used inappropraitely. Be sure that you identify what type of ATPase you have before you call it. otherwise call ASCE ATPase entry | Apiary_64 | https://seaphages.org/forums/topic/5567/ | |||||||||||||||||||||
96 | RecB-like exonuclease/helicase | If both a helicase and nuclease domain are present, the RecB label should be used. | |||||||||||||||||||||||
97 | |||||||||||||||||||||||||
98 | host nuclease inhibitor | Laroye_83 | |||||||||||||||||||||||
99 | cyclic nucleotide sequestering protein | see forum post before calling this function | Wolfstar gp30 | for good info, examples about this function see forum post https://seaphages.org/forums/topic/5687/?page=1#post-11125 | |||||||||||||||||||||
100 | VRR-Nuc domain protein | Zeina_89 |