1 | x | 2/27/2024 10:54:38 | (auto-updated) | ||||
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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 | |||||||
10 | portal protein | head to tail connector | TM4_5 | ||||
11 | |||||||
12 | |||||||
13 | scaffolding protein | Scaffold | D29_gp16 | ||||
14 | 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 | |||
15 | major capsid protein | capsid | Sisi_6 | ||||
16 | major capsid pentamer protein | Rosebush gp16 | experimental evidence | ||||
17 | major capsid hexamer protein | Rosebush gp15 | experimental evidence | ||||
18 | capsid decoration protein | head decoration protein | Patience_gp29, Rosebush_gp17 | experimental evidence | |||
19 | minor capsid protein | Patience_gp15, Myrna_gp98 | experimental evidence | ||||
20 | Hypothetical Protein | MuF-like minor capsid protein | If an HHPred alignment to gp15 of phage D29, see capsid maturation protease | 6/16/21 | |||
21 | 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 | |||
22 | |||||||
23 | Capsid maturation protease and VIP2-like ADP-ribosyltransferase toxin | Adolin_4 | |||||
24 | 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 | ||||
25 | head fiber protein | Briton15_18 | |||||
26 | 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. | |
27 | 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. | ||
28 | 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. | ||
29 | 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 | |||
30 | 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 | ||
31 | Hypothetical Protein | tail assembly chaperone | do not call TAC when there is NO evidence | cluster EA1 | |||
32 | tape measure protein | Tape Measure, tmp, tapemeasure | TM4_17 | ||||
33 | 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 | |||
34 | minor tail protein, D-ala-D-ala carboxypeptidase | must include "minor tail" as part of the functional assingment | Sisi_19 | ||||
35 | tail sheath protein | found in contractile tailed phages | Alice_120 | ||||
36 | tail fiber | ||||||
37 | 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 | ||||
38 | 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/ | |||
39 | baseplate J protein | Alice_133 | |||||
40 | tail tube protein | found in contractile tailed phages | RosiePosie_19 | ||||
41 | baseplate wedge protein | RosiePosie_38 | |||||
42 | |||||||
43 | Hypothetical Protein | HK97_gp10 | Hendrix lab (studiers of HK(& and capsid construction) never id'd a function for this gene | ||||
44 | 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 | ||
45 | 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 | ||||
46 | lysin A, protease M23 domain | if not a Mycobacteriophage, must have a lysin B, otherwise it is endolysin, protease M23 domain | |||||
47 | 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 | ||||
48 | 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 | ||||
49 | 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 | ||||
50 | 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 | ||||
51 | 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 | |||
52 | |||||||
53 | lysin B | LysB, endolysin B | Sisi_31 | ||||
54 | 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. | ||||
55 | endolysin, N-acetylmuramoyl-L-alanine amidase domain | 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 | ||||
64 | ParB-like nuclease domain | does not have to have a ParA partner | |||||
65 | 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 | ||||
66 | RepA-like replication initiator | Rachaly_36 | |||||
67 | immunity repressor | Repressor | likely to have an HHPred match to C1 protein in lambda | Sisi_45 | |||
68 | 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 | |||
69 | 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 | |
70 | 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 | ||
71 | recombination directionality factor | RDF | RedRock_58 | ||||
72 | 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 | ||||
73 | WhiB family transcription factor | Jasmine_32 | |||||
74 | antirepressor | Sisi_47 | |||||
75 | DnaE-like DNA polymerase III (alpha) | Spud_203 | |||||
76 | DNA polymerase I | Luchador_50 | |||||
77 | DNA polymerase III sliding clamp (Beta) | Corndog_84 | |||||
78 | DnaC-like helicase loader | Alice_189 | |||||
79 | helicase loader | Samman98_70 | |||||
80 | DNA helicase | ATP-dependent helicase | Chah_54 | ||||
81 | DnaB-like dsDNA helicase | RedRock_68 | |||||
82 | RepA-like helicase | Sour_52 | |||||
83 | DNA primase | Spud_199 | |||||
84 | DNA primase/helicase | make sure it has both parts | Schubert_31 | ||||
85 | DNA primase/polymerase | make sure it has both parts | Rosebush_54 | ||||
86 | DNA primase/polymerase/helicase | make sure it has all three parts | GreenHearts_47 | ||||
87 | DnaQ-like (DNA polymerase III subunit) | DNAQ is the exonuclease of Pol III (epsilon subunit) | Sisi_35 | ||||
88 | nucleotidyl transferase | Spud_3 | |||||
89 | FIC domain nucleotidyl transferase | MUST contain HPFxxGNGR motif | Bradissa_34 | ||||
90 | polynucleotide kinase | pnk | Spud_250 | ||||
91 | Lsr2-like DNA bridging protein | Lsr2 | Omega_61 | ||||
92 | RecA-like DNA recombinase | See link to identify requirements | Spud_205 | https://seaphages.org/forums/topic/5567/ | |||
93 | ASCE ATPase | AAA ATPase, RecA superfamily ATPase | Apiary_64 | https://seaphages.org/forums/topic/5567/ | |||
94 | AAA-ATPase | This call has been used inappropraitely. Be sure that you identify what type of ATPase you have before you call it. otherwise see ASCE ATPase entry | Corndog_96 | ||||
95 | RecB-like exonuclease/helicase | If both a helicase and nuclease domain are present, the RecB label should be used. | |||||
96 | |||||||
97 | host nuclease inhibitor | Laroye_83 | |||||
98 | VRR-Nuc domain protein | Zeina_89 | |||||
99 | Cas4 exonuclease | This 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 | ||||
100 | Ku-like dsDNA break-binding protein | Ku | Omega_206 | ||||
101 | MRE11 double-strand break endo/exonuclease | ||||||
102 | DprA-like DNA processing chain A | CherryBlossom_70 | |||||
103 | DprA-like ssDNA binding protein | ||||||
104 | RNA ligase | Cjw1_93 | |||||
105 | rtcB-like RNA ligase | Anaya_88 | |||||
106 | DNA ligase | Benedict_29 | |||||
107 | RNaseE | ||||||
108 | excise | WhiB | Sisi_55,57 | ||||
109 | DNA binding protein | RNA polymerase sigma factor | A misinterpretation of crystal structure chains lead to the mis-assignment of Zetzy1847 gene 42 as DNA directed RNA polymerase. | if an HTH is identified, cal it helix-turn-helix DNA binding domain | Nerujay_52 , Zeta1847 gp42 | ||
110 | rIIA-like protein | rIIA-like protein and rIIB-like protein are found by using the UniProt-SwissProt-viral database at HHPred | Cross_217 | ||||
111 | rIIB-like protein | Cross_218 | |||||
112 | ASC-1 transciption coactivator | Zombie_38 | |||||
113 | |||||||
114 | ribonucleotide reductase | RedRock_53 | |||||
115 | SprT-like protease | Peaches_79 | |||||
116 | cysteine protease | Saguaro_69 | |||||
117 | pyrimidine deaminase | DaVinci_40 | |||||
118 | nucleoside deaminase | Peaches_35 | |||||
119 | deoxycytidylate deaminase | dCMP deaminase | Muddy_45 | ||||
120 | nucleoside deoxyribosyltransferase | EniyanLRS_84 | |||||
121 | ThyX-like thymidylate synthase | ThyX | RedRock_51 | ||||
122 | thymidylate synthase | when you can't determine if it is ThyX or ThyA | Dismas_55 | ||||
123 | dUTPase | deoxyuridine triphosphatase | Muddy_48, Joann_53 | this call needs further investigation | |||
124 | |||||||
125 | lipoyl synthase | Mufasa8_95 | |||||
126 | lipid binding protein | Iter_49 | |||||
127 | dihydrofolate reductase | see forum post about ThyX vs DR | BubbaBear_56 | ||||
128 | MazG-like nucleotide pyrophosphohydrolase | MazG | Che12_gp40 | ||||
129 | phosphoribosyl pyrophosphate transferase | Do not use PRPP or ribose-phosphate pyrophosphokinase | Rose5_72 | ||||
130 | phosphoribosyltransferase | Bosnia_40 and Phelipe_64 | |||||
131 | MutT-like nucleotide pyrophosphohydrolase | ||||||
132 | glycoside hydrolase | ||||||
133 | peptidyl tRNA hydrolase | Spud_156 | |||||
134 | DNA methyltransferase | DNA methylase | 1-8-21 DNA methyltransferase and DNA mthylase are equivalent terms. We decided that DNA methyltransferase was a more informative term and more widely used. | Madiba_67 | |||
135 | 5' nucleotidase | Zooman_205 | |||||
136 | acetyltransferase | Hank144_74 | |||||
137 | O-acetyltransferase | OatA | to call this, the N-terminus should contain an acyltransferase domain and the C-terminus should contain a SGNH domain. it also has 9-11 transmembrane domains. | LonelyBoi_31 | |||
138 | methyltransferase | Optimus_14 | |||||
139 | O-methyltransferase | Send513_63 | |||||
140 | tRNA-methyltransferase | SPB78_36 | |||||
141 | helix-turn-helix DNA binding domain, MerR-like | Be cautious as you call this, use the forums to show the relevant data to support the call. if you cannot do that, make the call a helix-turn-helix DNA binding domain for now | Ciao_64 | https://seaphages.org/forums/topic/5320/ | |||
142 | ribbon-helix-helix DNA binding domain | Be cautious as you call this, use the forums to show the relevant data to support the call. if you cannot do that, make the call a helix-turn-helix DNA binding domain for now | |||||
143 | helix-turn-helix DNA binding domain | Be sure to check the alignments of your protein hitting HTHs, that they indeed hit 2-3 alpha helices in the seqence separated by small spacer (turn) regions of 3-4 amino acids. | Che12_39, CaiB_41 | ||||
144 | hpothetical function or helix-turn-helix DNA binding domian | winged helix-turn-helix DNA binding domain | still trying figure out the feature needed to call it 'winged' | Cluster EE, gene 24 | |||
145 | DNA binding protein | MintFen_52 | |||||
146 | RuvC-like resolvase | Chah_6 | |||||
147 | RusA-like resolvase | Spud_209 | |||||
148 | NucT-like nuclease | Andrew_58 | |||||
149 | exonuclease | Trogglehumper_74 | |||||
150 | RecE-like exonuclease | RecE-like exonucleases are most likely to be called when upstream of a RecT-like ssDNA pairing protein. | Che9c_60 | ||||
151 | RecT-like DNA pairing protein | Che9c_61 | |||||
152 | ERF family DNA pairing protein | Erf | Cjw1_70 | ||||
153 | SSB protein | single stranded DNA binding protein, ssDNA binding protein | Rey_73 | May of these assignments are labeled as ssDNA binding proteins, but Dr. Hatful requested that they be designated SSB protein. that change will be coming.... | |||
154 | |||||||
155 | glycosylase | Barnyard_33 | |||||
156 | glycosyltransferase | Spud_232, Che8_109, Che8_110 | |||||
157 | glycosyltransferase/methylase | Che8_108 | |||||
158 | n-acetylglucosaminyltransferase | ||||||
159 | aGPT-Pplase1 domain-containing protein | Librie_53 | |||||
160 | glucosaminyl deacetylase | Baee_gp4 | |||||
161 | NAD-dependent deacetylase | Belfort_134 | |||||
162 | galactosyltransferase | Sisi_96 | |||||
163 | hydrolase | RedRock_64, Goose_60 | |||||
164 | peptidase | Omega_105 | |||||
165 | nicotinate ribosyltransferase | LeBron_72 | |||||
166 | PnuC-like Nicotinamide riboside transporter | PauloDiaboli_262 | |||||
167 | adenylyltransferase | PauloDiaboli_269 | |||||
168 | ClpP-like protease | Clp | Cjw1_103 | ||||
169 | Clp family protein, ATPase domain | Myrna_gp251 | |||||
170 | thioredoxin | Cjw1_37 | |||||
171 | NrdH-like glutaredoxin | NrdH | Bxb1_56 | ||||
172 | NrdI-like flavodoxin | PauloDiaboli_217 | |||||
173 | glutaredoxin | Zaria_30 | |||||
174 | HNH endonuclease | Must have H-N-H over a 30 aa span* | Sisi_99 and Arianna_54 | *See forum post for further information | |||
175 | G-I-Y Y-I-G endonuclease | Sisi_89 | |||||
176 | LAGLIDADG endonuclease | Wee_78 | |||||
177 | endonuclease VII | Bxb1_54 | |||||
178 | transposase | If the hit of the transposase is avspecific type, please ask if it is ok to add. | Omega_21 | Feyre_43, can be called IS110 family transposase | |||
179 | mycobacteriophage mobile element 1 (MPME 1) | Avrafan_57 | |||||
180 | mycobacteriophage mobile element 2 (MPME 2) | Fruitloop_71 | |||||
181 | lipase, LipC-like | LittleE_99 | |||||
182 | esterase | Rockstar_61 | |||||
183 | thioesterase | Pukovnik_62 | |||||
184 | carboxylesterase | Omega_105 | |||||
185 | lipoprotein | ||||||
186 | phosphoesterase | ||||||
187 | metalloprotease | Typically has HEXXH motif but other metalloprotease motifs (e.g. "ExnHxHx7Sx2D | Artemis2UCLA_2 | ||||
188 | metallophosphatase | Metallophosphatase - after the holin in K phages - this gene product has good matches to ?DNA polymerase II small subunit and to DNA double-strand break repair protein mre11; both belong to Metallophosphatase family; so until further notice call Metallophosphatase Typically has HEXXH motif but other metalloprotease motifs (e.g. "ExnHxHx7Sx2D | InvictusManeo_34 | Metallophosphoesterase is considered equivalent to metallophosphatase, use metallophophatase 2/27/24) | |||
189 | IrrE-like protein | this protein has both a HTH and a metalloprotease domain (Typically has HEXXH motif but other metalloprotease motifs (e.g. "ExnHxHx7Sx2D) | Finkle_42 | ||||
190 | phosphatase | ||||||
191 | |||||||
192 | ATP binding cassette-like protein | Quasar_51 | |||||
193 | serine/threonine kinase | LittleE_16 | |||||
194 | adenylate kinase | Altwerkus_1 | |||||
195 | ppGpp synthesis/degradation protein, SpoT-like | Phrann_29 | |||||
196 | dpdA-like tRNA-guanine transglycosylase | queuine tRNA-ribosyltransferase | Rosebush_2, Orion_20 | see article: https://pubmed.ncbi.nlm.nih.gov/31784519/ | See Case Study in BioInformatics Guide | ||
197 | PreQ0 pathway, queC-like | Rosebush_3 | see article: https://pubmed.ncbi.nlm.nih.gov/31784519/ | ||||
198 | PreQ0 pathway, queD-like | Rosebush_4 | see article: https://pubmed.ncbi.nlm.nih.gov/31784519/ | ||||
199 | PreQ0 pathway, queE-like | Rosebush_5 | see article: https://pubmed.ncbi.nlm.nih.gov/31784519/ | ||||
200 | PreQ0 pathway, queF-like | 7-cyano-7-deazaguanine reductase | Funsized_2 | see article: https://pubmed.ncbi.nlm.nih.gov/31784519/ | |||
201 | folE-like GTP cyclohydrolase I | Rosebush_6 | see article: https://pubmed.ncbi.nlm.nih.gov/31784519/ | ||||
202 | the following genes are part of a thymine hyper modification system: look for all parts before calling them: | https://www.researchgate.net/publication/279940129_The_TETJBP_Family_of_Nucleic_Acid_Base-Modifying_2-Oxoglutarate_and_Iron-Dependent_Dioxygenases | |||||
203 | ParB-like nuclease domain | Wooper_1 | |||||
204 | Tet-like J-binding protein | Wooper_2 | |||||
205 | aGPT-Pplase2 domain protein | Wooper_3 | |||||
206 | 5-hmU DNA kinase | Wooper_4 | |||||
207 | Hypothetical Protein | Wooper_5 | you may want to call this an oxidoreductase, but there is not enough evidence. But we are on the look out for it. | ||||
208 | RF-1 peptide chain release factor | Spud_204 | |||||
209 | Ro-like RNA binding protein | TROVE domain, Ro | Spud_226; Archie_55 | ||||
210 | RNA binding protein | EniyanLRS_128 | |||||
211 | membrane protein, Band-7 –like | Bxz1_29 | |||||
212 | PE/PPE family protein | see forum post https://seaphages.org/forums/topic/5094/?page=1#post-8196 | Kayacho_88 | ||||
213 | adenylosuccinate synthetase, PurA-like | PurA | Spud_256 | ||||
214 | adenylosuccinate lyase, PurB-like | Ghobes_36 | |||||
215 | histidine triad nucleotide binding protein | HIT domain | Catera_17 | ||||
216 | pentapeptide repeat protein | Cjw1_59 | |||||
217 | dsDNA break-binding protein, AddA-like | Omega_123 | |||||
218 | FtsK-like DNA translocase | Omega_203 | |||||
219 | LysM-like peptidoglycan binding protein | Spud_96 | |||||
220 | CobT-like cobalamin biosynthesis protein | PBI1_57 | |||||
221 | toxin, VIP2-like | RedRock_2 | |||||
222 | VIP2-like ADP-ribosyltransferase toxin | Goodman, gp5 | |||||
223 | protease | Wildcat_13 | |||||
224 | serine protease | Shagrat_109 | |||||
225 | tRNA nucleotidyltransferase | Myrna_28 | |||||
226 | chaperonin, DnaJ-like | Myrna_190 | |||||
227 | adenylate kinase | gene 1 of B1s | |||||
228 | PTPc tyrosine phosphatase | PTPc | Bongo_83 | ||||
229 | antirestriction protein, ArdA-like | Airmid_82 | |||||
230 | antirestriction protein, OCR-like | Saftant_68 | |||||
231 | aminotransferase | Spud_193 | |||||
232 | deoxyuridine triphosphatase | Joann__53 | |||||
233 | ADP-ribosyltransferase | do not call the MuF-like part | JustBecause 252 | ||||
234 | ADP-ribosyl glycohydrolase | Settecandela_212 | |||||
235 | antitoxin, VbhA-like | Gaia_133 | |||||
236 | antitoxin in toxin/antitoxin system, RelB-like | Fruitloop_42 | |||||
237 | toxin in toxin/antitoxin system, RelE-like | Fruitloop_41 | |||||
238 | toxin in toxin/antitoxin system, BrnT-like | PhrostedPhlake_39 | |||||
239 | antitoxin in toxin/antitoxin system, BrnA-like | SoSeph_draft_89 (57457-57888 ) | BrnT-like toxin is SoSeph_draft_8 | ||||
240 | antitoxin in toxin/antitoxin system, HicB-like | Xeno_30 | |||||
241 | toxin in toxin/antitoxin system, HicA-like | Xeno_32 | |||||
242 | toxin, VapBC family toxin/antitoxin system | Adora_40 | |||||
243 | antitoxin, VapBC family toxin/antitoxin system | Adora_41 | |||||
244 | antitoxin in toxin/antitoxin system | Must have a toxin pair to call | use only when the toxin/antitoxin system cannot be identified | Moosehead_39 | |||
245 | toxin in toxin/antitoxin system | Must have an antitoxin pair to call | use only when the toxin/antitoxin system cannot be identified | Moosehead_40 | |||
246 | RexA family abortive infection protein | Sidious_40 | |||||
247 | RexB family abortive infection protein | Sidious_41 | |||||
248 | |||||||
249 | |||||||
250 | |||||||
251 | PAPS reductase-like domain | this enzyme is involved in reducing phosphoadenosine | |||||
252 | purple acid phosphatase | PAP | ArMaWen_44 | this enzyme is involved in reducing phosphoadenosine | |||
253 | thymidylate kinase | Erdmann_199 | |||||
254 | deoxynucleoside monophosphate kinase | Aaronocolus_57 | |||||
255 | |||||||
256 | membrane protein | should not override more specific functions that happen to contain membrane domains; Use DeepTMHMM to call membrane proteins.https://dtu.biolib.com/DeepTMHMM. | |||||
257 | glutamine amidotransferase domain | Tesla_109 | |||||
258 | carboxylate amine ligase | Tesla_108 | |||||
259 | DNA binding, HU-like domain | Crosby and BH phages | |||||
260 | UDP-glucose dehydrogenase | Metamorphoo_86 | |||||
261 | arsenate reductase | Zeta1847 gp37 | |||||
262 | FabG-like reductase | Gumball gp65 | |||||
263 | oxidoreductase | Onyinye_78 | |||||
264 | phage membrane DNA delivery | This is restricted to members of the tectiviridae, like PRD1, that are phages that contain membranes. | Forthebois 22, 28 | ||||
265 | tellurium resistance protein D family | FlowerPower_76 | |||||
266 | |||||||
267 | |||||||
268 | GENERAL TERMS | ||||||
269 | It is OK to use the following general functional assignments if it is impossible to distinguish between specific instances | ||||||
270 | helicase | ||||||
271 | DNA polymerase | ||||||
272 | nuclease | ||||||
273 | methylase | ||||||
274 | hydrolase | ||||||
275 | protease | ||||||
276 | Holliday junction resolvase | if not RusA or RuvC | Note that "Holliday" is capitalized (it is named after Robin Holliday) | ||||
277 | nucleotide pyrophosphohydrolase | if not MazG or MutT | |||||
278 | kinase | ||||||
279 | histidine kinase | Shawty_53 |