Basic pLAST usageο
Imports and configurationο
[1]:
import logging
from pathlib import Path
from threadpoolctl import threadpool_limits
import pandas as pd
from plast.data import PLASTData
from plast.plast import PLAST
from examples.configuration import config
Load configuration to PLASTData objectο
[2]:
pl_data = PLASTData(config)
Loading pLAST data...
Analyze sequence using MMseqs2 modelο
Initialize PLAST object - load config, choose model and add loggerο
[3]:
plast = PLAST(data=pl_data, model="mmseqs2_model")
Load example plasmid sequence from .fasta file and annotate with prodigalο
[4]:
plast = plast.load_nt_fasta(open("examples/NC_005000.1.fasta").read())
print("Plasmid of langth", plast.length, "has the following annotation:")
display(plast.parsed)
Plasmid of langth 24873 has the following annotation:
| locus_tag | start | end | strand | type | gene | product | translation | |
|---|---|---|---|---|---|---|---|---|
| 0 | NC_005000.1_1 | 1 | 291 | -1 | CDS | MSINTFVYSHPINVYIIKNLGITVEQFCELYAYPQGTVASWITRQR... | ||
| 1 | NC_005000.1_2 | 427 | 606 | -1 | CDS | MNIIQQYELKYITFDQLSEEIWGYGQRLINEVGVERFSFYVEAAAG... | ||
| 2 | NC_005000.1_3 | 603 | 980 | -1 | CDS | MRAEMGELKMIDYNDRGRLKWAGFYLSDHTEEIDADNEQRTSQNLA... | ||
| 3 | NC_005000.1_4 | 946 | 2271 | -1 | CDS | MMDYSKEPVNDYFLIDMKSFYASVECIERNLDPLTTELVVMSRADN... | ||
| 4 | NC_005000.1_5 | 2721 | 3335 | 1 | CDS | MRVAYIRVSSIDQNEQRQIEEMKKFGAERIFIEKQSGATITHRPVF... | ||
| 5 | NC_005000.1_6 | 3500 | 4504 | -1 | CDS | MEYKFNLNLKEVLPTQGTININGQDNDDDIVIKKIEFIDSDINVFF... | ||
| 6 | NC_005000.1_7 | 4963 | 5220 | -1 | CDS | MIKAWSDDAWDDYLYWHEQGNKSNIKKINKLIKDIDRSPFAGLGKP... | ||
| 7 | NC_005000.1_8 | 5213 | 5482 | -1 | CDS | MEAVAYSNFRQNLRSYMKQVNEDAETLIVTSKDVEDTVVVLSKRDY... | ||
| 8 | NC_005000.1_9 | 5620 | 6126 | 1 | CDS | MSAGTSNPAFSWAINKSNAIHIILDSLLPYFCFSCCNSFCLFSSNV... | ||
| 9 | NC_005000.1_10 | 6173 | 6868 | -1 | CDS | MQQNPTEDVSHFLTNKEHLNEVIRRIQKDFSCMEEMKYFIQRVEEQ... | ||
| 10 | NC_005000.1_11 | 6924 | 7571 | 1 | CDS | MTMNHFKGKQFQQDVIIVAVGYYLRYNLSYREVQEILYDRGINVSH... | ||
| 11 | NC_005000.1_12 | 7524 | 7763 | -1 | CDS | MDTETDQLQNQVLLDNFVDIMKEDSINTFVPENVLNLIKTFSSTYE... | ||
| 12 | NC_005000.1_13 | 7789 | 8130 | -1 | CDS | MRISPELKKLIEKYRCVKDTEGMSPAKVYKLVGENENLYLKMTDSR... | ||
| 13 | NC_005000.1_14 | 8232 | 8774 | -1 | CDS | MITEMKAGHLKDIDKPSEPFEVIGKIIPRYENENWTFTELLYEAPY... | ||
| 14 | NC_005000.1_15 | 8771 | 9679 | -1 | CDS | MRSEKEMMDLVLSLAEQDERIRIVTLEGSRANINIPKDEFQDYDIT... | ||
| 15 | NC_005000.1_16 | 9712 | 10446 | -1 | CDS | MKENKYDDNIFFQKYSQMSRSQKGLAGAGEWETLKKMLPDFKGKRV... | ||
| 16 | NC_005000.1_17 | 10427 | 11344 | -1 | CDS | MAWNFYSSESIKGACLMVDNIIKSVAEKLSSLSYIEGIVLGGSRAR... | ||
| 17 | NC_005000.1_18 | 11399 | 11644 | -1 | CDS | MIDVNELLEEAIRETENLNDGEVFLVKDLFKGYVGNRIPRKDRLLL... | ||
| 18 | NC_005000.1_19 | 11671 | 12345 | -1 | CDS | MYQNYTINQLCLPIDLEIKLEENDFAHAIVQFVDSIPDEVFLPYYQ... | ||
| 19 | NC_005000.1_20 | 12802 | 12993 | -1 | CDS | MSKYCLFLIVIYYLTGGNNSMSRFFKFGKLHVTKGNGDKLLDILLT... | ||
| 20 | NC_005000.1_21 | 12938 | 13675 | -1 | CDS | MNKNIKYSQNFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTK... | ||
| 21 | NC_005000.1_22 | 13904 | 14167 | -1 | CDS | MGNLGAQKEKRNDTPISAKKDIMGDKTVRVRADLHHIIKIETAKNG... | ||
| 22 | NC_005000.1_23 | 14564 | 15250 | 1 | CDS | MTMNHFKGKQFQQDVIIVAVGYYLRYNLSYREVQEILYDRGINVSH... | ||
| 23 | NC_005000.1_24 | 15306 | 15854 | 1 | CDS | MEDDGFTRLDLAFDFEDDLSDYYALSEKALKRTVFFGTTGKAETKY... | ||
| 24 | NC_005000.1_25 | 15987 | 17174 | 1 | CDS | MTQVHFTFESEEIQAIINESGANDTAKTLMTIMFNQLMEEQRNQYI... | ||
| 25 | NC_005000.1_26 | 17464 | 18111 | 1 | CDS | MTFNIINLETWDRKEYFNHYFNQQTTYSVTKELDITLLKSMIKDKG... | ||
| 26 | NC_005000.1_27 | 18098 | 18253 | 1 | CDS | MNGFKSKINFINLSNHDIYKFIATTFLVAFVLILNLVLNYEWLAFC... | ||
| 27 | NC_005000.1_28 | 18426 | 18824 | 1 | CDS | MSEHDNNLASDLSVGGNRKPNRKEPKQISFRVNEGEYEKLRSSAET... | ||
| 28 | NC_005000.1_29 | 18806 | 19192 | 1 | CDS | MATTKISSTKSTSRAINYAEKRAEEKSALNCDIDYAKSSFKATREM... | ||
| 29 | NC_005000.1_30 | 19240 | 19926 | 1 | CDS | MTMNHFKGKQFQQDVIIVAVGYYLRYNLSYREVQEILYDRGINVSH... | ||
| 30 | NC_005000.1_31 | 20542 | 21582 | -1 | CDS | MNDFNYYKSKEIYREKYYQMPKVFFTNEKYMDLSNDAKIAYMLLKD... | ||
| 31 | NC_005000.1_32 | 21931 | 22257 | -1 | CDS | MAEDNRSQAAVSRLLGNKNKKNFKSKEVEEIELTKKNISKVIKDQG... | ||
| 32 | NC_005000.1_33 | 22244 | 23047 | -1 | CDS | MGDILMARILSVANQKGGVSKTTTSVNLAACLKFVYGKNVLLVDID... | ||
| 33 | NC_005000.1_34 | 23471 | 24658 | -1 | CDS | MTQVHFTFESEEIQAIINESGANDTAKTLMTIMFNQLMEEQRNQYI... |
Assign cluster identifiers to the plasmid proteinsο
GPU usage is recommended
[5]:
plast = plast.assign_mmseqs_clusters(use_gpu=False, threads=16)
print("Number of assigned clusters:", len(plast.vector))
print("Assigned clusters:")
print(plast.vector)
Number of assigned clusters: 34
Assigned clusters:
['503696', '766345', '869197', '1937138', '978057', '383425', '945760', '589250', '690891', '1551360', '1281006', None, '1324730', '503880', '1456404', '465833', '1342390', '643142', '840054', '126491', '1148733', '112363', '1281006', '23491', '464026', '1559939', None, '645043', '1967057', '1281006', '1058438', '1180625', '1377695', '464026']
Pass data through pLAST model and receive embeddingsο
[6]:
plast = plast.encode()
print("Plasmid embedding:")
print(plast.embedding)
Plasmid embedding:
[ 0.1384209 -0.04938016 0.08050069 -0.28110254 -0.15616207 -0.07490253
0.16827418 -0.13507421 -0.23134972 0.17394237 0.03949427 0.14928077
0.0778301 -0.12385113 0.08690757 -0.0044575 0.12068866 -0.17245157
-0.05543656 -0.12488046 -0.06651291 -0.0363512 0.0564674 -0.05215054
0.13757774 -0.15772095 -0.08525286 0.01317535 0.01092703 -0.11166314
0.15189844 0.05494929 -0.0992474 0.1242907 -0.05032507 -0.02236419
0.05827509 0.08067824 -0.19969554 -0.24305034 0.1439417 -0.06540675
0.16099109 0.11031093 -0.12261283 -0.0014736 0.09187076 0.15333791
-0.11933523 -0.24098885 0.0586763 0.3031614 -0.01348991 -0.13698538
-0.02973128 -0.02080188 0.14846162 -0.08702841 -0.10383306 0.01379118
0.10749927 0.16289651 0.00122075 0.03645242]
Whole-plasmid comparison (global search)ο
get_most_similar() compares the embedding of the complete query plasmid against complete plasmid embeddings stored in the selected pLAST model.
[7]:
results = plast.get_most_similar(maxret=10)
[8]:
df = pd.DataFrame.from_dict(results, orient="index")
for c in ("pLAST_distance", "gc"):
if c in df.columns:
df[c] = pd.to_numeric(df[c], errors="coerce").round(6)
preferred = [
"pLAST_distance",
"length",
"gc",
"taxid",
"organism",
"definition",
"taxonomy",
"rep_type(s)",
"AMR",
"relaxase_type(s)",
"mpf_type",
"orit_type(s)",
"predicted_mobility",
]
cols = [c for c in preferred if c in df.columns] + [
c for c in df.columns if c not in preferred
]
display(df[cols])
| pLAST_distance | length | gc | taxid | organism | definition | taxonomy | rep_type(s) | AMR | relaxase_type(s) | mpf_type | orit_type(s) | predicted_mobility | accession | database | topology | primary_cluster_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| COMPASS_NC_005000.1 | 0.984177 | 24873 | 0.340329 | 1352.0 | -,Enterococcus faecium | Enterococcus faecium plasmid pRUM, complete se... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc1118,rc889 | - | MOBP | - | MOBP | mobilizable | COMPASS_NC_005000.1,GenBank_AF507977.1,IMGPR_p... | COMPASS,GenBank,IMG-PR,RefSeq | circular | AD100 |
| GenBank_GG692536.1 | 0.978578 | 22101 | 0.344378 | 565660.0 | Enterococcus faecium | Enterococcus faecium 1,231,410 map unlocalized... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc1968,rc889 | - | - | - | - | non-mobilizable | GenBank_GG692536.1,IMGPR_plasmid_647533149_000... | GenBank,IMG-PR,RefSeq | linear | AD100 |
| COMPASS_NZ_CP018131.1 | 0.975886 | 23736 | 0.348290 | 1352.0 | Enterococcus faecium | Enterococcus faecium strain A_020709_82 plasmi... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc1968,rc889 | - | - | - | - | non-mobilizable | COMPASS_NZ_CP018131.1,IMGPR_plasmid_2872254902... | COMPASS,IMG-PR,PLDSB,RefSeq | circular | AD100 |
| COMPASS_KP842560.1 | 0.974289 | 23269 | 0.341957 | 1352.0 | Enterococcus faecium | Enterococcus faecium strain 17i48 ST17 plasmid... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc889 | - | MOBP | - | MOBP | mobilizable | COMPASS_KP842560.1,GenBank_KP842560.1,RefSeq_N... | COMPASS,GenBank,RefSeq | circular | AD100 |
| PLSDB_NZ_LR135437.1 | 0.974187 | 19194 | 0.341252 | 1352.0 | Enterococcus faecium | Enterococcus faecium isolate E8691 plasmid 3 | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc889 | - | - | - | - | non-mobilizable | PLSDB_NZ_LR135437.1,RefSeq_NZ_LR135437.1 | PLDSB,RefSeq | linear | AD100 |
| EMBL_LN999989.1 | 0.973734 | 32402 | 0.345102 | 1352.0 | Enterococcus faecium | Enterococcus faecium isolate EFE11651 plasmid ... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc185,rc889 | - | MOBP | - | MOBP | mobilizable | EMBL_LN999989.1,IMGPR_plasmid_2875025650_00000... | ENA,IMG-PR,PLDSB,RefSeq | circular | AD100 |
| IMGPR_plasmid_647533152_000004 | 0.968064 | 25520 | 0.344262 | NaN | Enterococcus faecium | NaN | NaN | rc889 | AMK,AZM,BUT,CBM,CHL,CLI,CLR,CST,DAL,DIR,ERY,EV... | MOBV | - | - | mobilizable | IMGPR_plasmid_647533152_000004 | IMG-PR | linear | AD100 |
| GenBank_CP097025.1 | 0.965033 | 23514 | 0.341371 | 1352.0 | Enterococcus faecium | Enterococcus faecium strain AT45b plasmid pAT4... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc889 | - | MOBP | - | MOBP | mobilizable | GenBank_CP097025.1,PLSDB_NZ_CP097025.1,RefSeq_... | GenBank,PLDSB,RefSeq | circular | AD100 |
| GenBank_LPUE01000006.1 | 0.955718 | 45034 | 0.349336 | NaN | Enterococcus faecium | Enterococcus faecium C68 map unlocalized plasm... | NaN | rc889 | - | MOBV | - | - | mobilizable | GenBank_LPUE01000006.1,RefSeq_NZ_LPUE01000006.1 | GenBank,RefSeq | linear | AD100 |
| PLSDB_NZ_LR135446.1 | 0.955302 | 44438 | 0.353436 | 1352.0 | Enterococcus faecium | Enterococcus faecium isolate E7114 plasmid 4 | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc1763,rc889,rc943 | - | - | - | - | non-mobilizable | PLSDB_NZ_LR135446.1,RefSeq_NZ_LR135446.1 | PLDSB,RefSeq | linear | AB173 |
Local cassette/module searchο
module_search() looks for the query architecture as a sliding window inside database plasmids. The example below uses Tn1548_armA_pCTX_M3.fasta, a Tn1548/armA multidrug-resistance module from plasmid pCTX-M3. pLAST is well suited for finding such functional modules because it compares ordered protein-cluster architectures, not only complete plasmid-to-complete plasmid similarity.
[9]:
cassette = PLAST(data=pl_data, model="mmseqs2_model")
cassette = cassette.load_nt_fasta(Path("examples/Tn1548_armA_pCTX_M3.fasta").read_text())
print("Resistance module length:", cassette.length, "bp")
display(cassette.parsed)
Resistance module length: 13362 bp
| locus_tag | start | end | strand | type | gene | product | translation | |
|---|---|---|---|---|---|---|---|---|
| 0 | Tn1548_armA_pCTX_M3_1 | 1 | 705 | 1 | CDS | MNPFKGRHFQRDIILWAVRWYCKYGISYRELQEMLAERGVNVDHST... | ||
| 1 | Tn1548_armA_pCTX_M3_2 | 980 | 1993 | -1 | CDS | MKTATAPLPPLRSVKVLDQLRERIRYLHYSLPTEQAYVHWVRAFIR... | ||
| 2 | Tn1548_armA_pCTX_M3_3 | 2138 | 2635 | 1 | CDS | MNSESVRIYLVAAMGANRVIGNGPNIPWKIPGEQKIFRRLTEGKVV... | ||
| 3 | Tn1548_armA_pCTX_M3_4 | 3055 | 3834 | 1 | CDS | MTIEISNQLSEVLSVIERHLESTLLAVHLYGSAVDGGLKPYSDIDL... | ||
| 4 | Tn1548_armA_pCTX_M3_5 | 3998 | 4345 | 1 | CDS | MKGWLFLVIAIVGEVIATSALKSSEGFTKLAPSAVVIIGYGIAFYF... | ||
| 5 | Tn1548_armA_pCTX_M3_6 | 4339 | 5178 | 1 | CDS | MVTVFGILNLTEDSFFDESRRLDPAGAVTAAIEMLRVGSDVVDVGP... | ||
| 6 | Tn1548_armA_pCTX_M3_7 | 5583 | 7124 | 1 | CDS | MSLARNATASQSPTQTNGYERHQPDQTLLYQLVEQHYPAFKASLEA... | ||
| 7 | Tn1548_armA_pCTX_M3_8 | 7361 | 8197 | 1 | CDS | MDEQAIKQWHCLVHHGRRGRGFHYSDTAIETALMLKGLFKLPLRAL... | ||
| 8 | Tn1548_armA_pCTX_M3_9 | 8280 | 8372 | 1 | CDS | MASWGSYVFELCRINANQGLTAEMDWNYTS* | ||
| 9 | Tn1548_armA_pCTX_M3_10 | 8523 | 9296 | 1 | CDS | MDKNDVVKKILESKKYENLDSDIVEKVVSISEKKYKLKEVENYSKK... | ||
| 10 | Tn1548_armA_pCTX_M3_11 | 9778 | 9963 | -1 | CDS | MFPNQLTFYFNYRISGDTSGGLQLFGLIGLIYGPIIFALTMVLLRL... | ||
| 11 | Tn1548_armA_pCTX_M3_12 | 10021 | 11196 | 1 | CDS | MNVKAMLADFLTFVTPKSMHKARFSVLLDAVTALAKDACCTVTAIG... | ||
| 12 | Tn1548_armA_pCTX_M3_13 | 11595 | 13070 | 1 | CDS | MSLIIKARNIRLDYAGRDVLDIDELEIHSYDRIGLVGDNGAGKSSL... | ||
| 13 | Tn1548_armA_pCTX_M3_14 | 13126 | 13362 | 1 | CDS | MTIQDIQSLAEAHGLLLTDKMNFNEMGIDFKVVFALDTKGQQWLLR... |
[10]:
cassette = cassette.assign_mmseqs_clusters(use_gpu=False, threads=16)
print("Number of assigned cassette clusters:", len(cassette.vector))
print("Assigned cassette clusters:")
print(cassette.vector)
Number of assigned cassette clusters: 14
Assigned cassette clusters:
['1281006', '747980', '577471', '709541', '1403434', '1328189', '947673', '158253', '1504072', '1890956', '1289284', '854564', '592301', '718297']
[11]:
cassette = cassette.encode()
print("Cassette size:", len(cassette.vector), "protein clusters")
print("Cassette embedding:")
print(cassette.embedding)
Cassette size: 14 protein clusters
Cassette embedding:
[ 0.31502214 0.01017629 -0.2995464 -0.2074935 0.19848059 -0.02487027
0.14860755 -0.09596689 0.0591081 -0.00915496 -0.04902752 -0.04312475
0.10233568 -0.102058 0.07681113 0.09836045 0.09629957 -0.14701653
-0.09711459 -0.10175263 -0.03978896 -0.01350529 0.06437908 -0.10153474
-0.15441005 -0.08279423 -0.00678984 0.00929052 -0.19468668 -0.09421448
0.09613787 -0.00748611 0.22859618 0.1055662 -0.29159564 0.04676434
0.17769937 0.07126724 -0.08586723 0.12043469 -0.12860203 -0.15519026
0.09250353 0.1306932 -0.04544971 -0.01354803 -0.04920986 0.00072894
-0.21197118 -0.11548286 -0.02085261 0.09450696 -0.07827361 -0.06611867
-0.22803688 0.04948623 -0.04389391 -0.02406676 0.00620364 0.13520016
0.09837677 0.2118936 -0.06386898 0.07951403]
[12]:
if not hasattr(cassette, "module_search"):
print("module_search() is available in the current pLAST development version.")
cassette_results = {}
elif "gbfeatures" not in pl_data.config:
print(
"Local cassette search requires ordered database features. "
)
cassette_results = {}
else:
with threadpool_limits(limits=1):
cassette_results = cassette.module_search(
maxret=15,
window_size=len(cassette.vector),
)
[13]:
if cassette_results:
cassette_df = pd.DataFrame.from_dict(cassette_results, orient="index")
for c in ("pLAST_distance", "gc"):
if c in cassette_df.columns:
cassette_df[c] = pd.to_numeric(cassette_df[c], errors="coerce").round(6)
preferred = [
"pLAST_distance",
"window_start",
"window_end",
"window_size",
"window_wraps",
"target_orf_count",
"module_fallback_vectors",
"length",
"gc",
"taxid",
"organism",
"definition",
"taxonomy",
"rep_type(s)",
"AMR",
"relaxase_type(s)",
"mpf_type",
"orit_type(s)",
"predicted_mobility",
]
cols = [c for c in preferred if c in cassette_df.columns] + [
c for c in cassette_df.columns if c not in preferred
]
display(cassette_df[cols])
| pLAST_distance | window_start | window_end | window_size | window_wraps | target_orf_count | module_fallback_vectors | length | gc | taxid | ... | rep_type(s) | AMR | relaxase_type(s) | mpf_type | orit_type(s) | predicted_mobility | accession | database | topology | primary_cluster_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| COMPASS_AF550415.2 | 1.000000 | 84 | 97 | 14 | False | 111 | 0 | 89468 | 0.510305 | 546.0 | ... | IncL/M,rc1254 | - | MOBP | MPF_I | - | conjugative | COMPASS_AF550415.2,GenBank_AF550415.2,IMGPR_pl... | COMPASS,GenBank,IMG-PR,RefSeq | circular | AA002 |
| PLSDB_CP082393.1 | 0.991495 | 67 | 80 | 14 | False | 111 | 3 | 89721 | 0.504709 | NaN | ... | IncA,rc1254 | ABK,ACR,AMK,AMX,APR,ATM,AZD,AZM,BUT,CEF,CHL,CI... | MOBH | MPF_F | - | conjugative | PLSDB_CP082393.1 | PLDSB | circular | AA622 |
| DDBJ_LC744448.1 | 0.983330 | 158 | 171 | 14 | False | 280 | 0 | 257396 | 0.463916 | NaN | ... | IncFIB,IncHI1B | A201A,ABK,ACR,AMK,AMP,AMX,APR,AST,ATM,AZD,AZM,... | MOBH | MPF_F | - | conjugative | DDBJ_LC744448.1 | DDBJ | circular | AA405 |
| DDBJ_AP018143.1 | 0.983330 | 142 | 155 | 14 | False | 210 | 0 | 176026 | 0.506641 | 562.0 | ... | IncC,rc1254 | - | MOBH | MPF_F | MOBH | conjugative | DDBJ_AP018143.1,RefSeq_NZ_AP018143.1 | DDBJ,RefSeq | circular | AA860 |
| DDBJ_LC744445.1 | 0.983330 | 135 | 148 | 14 | False | 215 | 0 | 187175 | 0.508791 | NaN | ... | IncC,rc1254 | A201A,ABK,ACR,AMK,AMP,AMX,ATM,AZD,AZM,BCM,BCT,... | MOBH | MPF_F | MOBH | conjugative | DDBJ_LC744445.1 | DDBJ | circular | AA860 |
| DDBJ_LC508263.1 | 0.983330 | 80 | 93 | 14 | False | 103 | 0 | 86197 | 0.507547 | 573.0 | ... | IncL/M,rc1254 | - | MOBP | MPF_I | - | conjugative | DDBJ_LC508263.1,RefSeq_NZ_LC508263.1 | DDBJ,RefSeq | circular | AA002 |
| DDBJ_LC508722.1 | 0.983330 | 80 | 93 | 14 | False | 103 | 0 | 86197 | 0.507500 | 573.0 | ... | IncL/M,rc1254 | - | MOBP | MPF_I | - | conjugative | DDBJ_LC508722.1,RefSeq_NZ_LC508722.1 | DDBJ,RefSeq | circular | AA002 |
| DDBJ_AP025166.1 | 0.983330 | 179 | 192 | 14 | False | 419 | 2 | 388397 | 0.480689 | NaN | ... | IncU,rc1254 | A201A,ABK,ACR,AMK,AMP,AMX,APR,AST,ATM,AZD,AZM,... | MOBH | MPF_F | - | conjugative | DDBJ_AP025166.1 | DDBJ | circular | AC212 |
| DDBJ_LC744454.1 | 0.983330 | 143 | 156 | 14 | False | 227 | 0 | 198096 | 0.507431 | NaN | ... | IncC,rc1254 | A201A,ABK,ACR,AMK,AMP,AMX,ATM,AZD,AZM,BCM,BCT,... | MOBH | MPF_F | MOBH | conjugative | DDBJ_LC744454.1 | DDBJ | circular | AA860 |
| DDBJ_AP025165.1 | 0.983330 | 181 | 194 | 14 | False | 421 | 0 | 390753 | 0.480593 | 1463165.0 | ... | IncU,rc1254 | - | MOBH | MPF_F | - | conjugative | DDBJ_AP025165.1,RefSeq_NZ_AP025165.1 | DDBJ,RefSeq | circular | AC212 |
| DDBJ_LC505604.1 | 0.983330 | 81 | 94 | 14 | False | 104 | 0 | 86197 | 0.507547 | 573.0 | ... | IncL/M,rc1254 | - | MOBP | MPF_I | - | conjugative | DDBJ_LC505604.1,RefSeq_NZ_LC505604.1 | DDBJ,RefSeq | circular | AA002 |
| DDBJ_AP025164.1 | 0.983330 | 178 | 191 | 14 | False | 415 | 0 | 386364 | 0.480084 | 573.0 | ... | IncU,rc1254 | - | MOBH | MPF_F | - | conjugative | DDBJ_AP025164.1,RefSeq_NZ_AP025164.1 | DDBJ,RefSeq | circular | AC212 |
| GenBank_NPII01000030.1 | 0.983120 | 13 | 26 | 14 | False | 31 | 0 | 31892 | 0.482629 | NaN | ... | IncHI1B,rc1254 | - | - | - | - | non-mobilizable | GenBank_NPII01000030.1,RefSeq_NZ_NPII01000030.1 | GenBank,RefSeq | linear | AC237 |
| GenBank_NPJW01000035.1 | 0.983120 | 13 | 26 | 14 | False | 27 | 0 | 27570 | 0.488103 | NaN | ... | IncHI1B | - | - | - | - | non-mobilizable | GenBank_NPJW01000035.1,RefSeq_NZ_NPJW01000035.1 | GenBank,RefSeq | linear | AC237 |
| COMPASS_CP012902.1 | 0.982351 | 56 | 69 | 14 | False | 209 | 0 | 176048 | 0.513991 | 562.0 | ... | IncC,rc1254 | - | MOBH | MPF_F | MOBH | conjugative | COMPASS_CP012902.1,GenBank_CP012902.1,RefSeq_N... | COMPASS,GenBank,RefSeq | circular | AA860 |
15 rows Γ 23 columns
Analyze sequence using eggNOG modelο
Initialize PLAST object - load config, choose model and add loggerο
[14]:
plast = PLAST(data=pl_data, model="eggnog_model")
Load example plasmid sequence and GenBank annotation from .gb fileο
[15]:
plast = plast.load_gbff(Path("examples/NC_005000.1.gb"))
print("Plasmid of langth", plast.length, "has the following annotation:")
display(plast.parsed)
Plasmid of langth 24873 has the following annotation:
| start | end | strand | partial | type | coordinates | locus_tag | old_locus_tag | inference | note | ... | transl_table | product | protein_id | translation | EC_number | GO_function | GO_process | GO_component | pseudo | gene | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 1 | 291 | -1 | 0 | CDS | complement(1..291) | HKK39_RS00005 | pRUM_p01 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | hypothetical protein | WP_000026576.1 | MSINTFVYSHPINVYIIKNLGITVEQFCELYAYPQGTVASWITRQR... | NaN | NaN | NaN | NaN | NaN | NaN |
| 1 | 427 | 606 | -1 | 0 | CDS | complement(427..606) | HKK39_RS00010 | NaN | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | hypothetical protein | WP_001021554.1 | MNIIQQYELKYITFDQLSEEIWGYGQRLINEVGVERFSFYVEAAAG... | NaN | NaN | NaN | NaN | NaN | NaN |
| 2 | 603 | 953 | -1 | 0 | CDS | complement(603..953) | HKK39_RS00015 | pRUM_p02 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | hypothetical protein | WP_000568378.1 | MIDYNDRGRLKWAGFYLSDHTEEIDADNEQRTSQNLAKEQMTTEEI... | NaN | NaN | NaN | NaN | NaN | NaN |
| 3 | 946 | 2271 | -1 | 0 | CDS | complement(946..2271) | HKK39_RS00020 | pRUM_p03 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | Y-family DNA polymerase | WP_000969590.1 | MMDYSKEPVNDYFLIDMKSFYASVECIERNLDPLTTELVVMSRADN... | 2.7.7.7 | GO:0003684 - damaged DNA binding [EvidenceIEA]... | GO:0006281 - DNA repair [Evidence IEA];GO:0006... | NaN | NaN | NaN |
| 4 | 2721 | 3335 | 1 | 0 | CDS | 2721..3335 | HKK39_RS00025 | pRUM_p04 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | recombinase family protein | WP_001261742.1 | MRVAYIRVSSIDQNEQRQIEEMKKFGAERIFIEKQSGATITHRPVF... | NaN | GO:0003677 - DNA binding [Evidence IEA];GO:000... | GO:0015074 - DNA integration [Evidence IEA];GO... | NaN | NaN | NaN |
| 5 | 3500 | 4504 | -1 | 0 | CDS | complement(3500..4504) | HKK39_RS00030 | pRUM_p05 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | hypothetical protein | WP_000455809.1 | MEYKFNLNLKEVLPTQGTININGQDNDDDIVIKKIEFIDSDINVFF... | NaN | NaN | NaN | NaN | NaN | NaN |
| 6 | 4963 | 5220 | -1 | 0 | CDS | complement(4963..5220) | HKK39_RS00035 | pRUM_p06 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | Txe/YoeB family addiction module toxin | WP_000588503.1 | MIKAWSDDAWDDYLYWHEQGNKSNIKKINKLIKDIDRSPFAGLGKP... | NaN | NaN | GO:0008219 - cell death [Evidence IEA] | NaN | NaN | NaN |
| 7 | 5213 | 5482 | -1 | 0 | CDS | complement(5213..5482) | HKK39_RS00040 | pRUM_p07 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | type II toxin-antitoxin system Phd/YefM family... | WP_000388479.1 | MEAVAYSNFRQNLRSYMKQVNEDAETLIVTSKDVEDTVVVLSKRDY... | NaN | GO:0003677 - DNA binding [Evidence IEA];GO:009... | GO:0045927 - positive regulation of growth[Evi... | GO:0110001 - toxin-antitoxin complex[Evidence ... | NaN | NaN |
| 8 | 5613 | 5792 | -1 | 0 | CDS | complement(5613..5792) | HKK39_RS00045 | NaN | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | hypothetical protein | WP_001120991.1 | MPIAIGNKRLPVTLDEKRQKELQQLKQKYGKSESRIMCIALDLLIA... | NaN | NaN | NaN | NaN | NaN | NaN |
| 9 | 5890 | 6126 | 1 | 0 | CDS | 5890..6126 | HKK39_RS00185 | NaN | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | hypothetical protein | WP_306297428.1 | MKQNTSIAKNTTKFKCTAAAWRISISPTNRTNNRGMILFIWISFFL... | NaN | NaN | NaN | NaN | NaN | NaN |
| 10 | 6173 | 6868 | -1 | 0 | CDS | complement(6173..6868) | HKK39_RS00050 | pRUM_p10 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | hypothetical protein | WP_002326819.1 | MQQNPTEDVSHFLTNKEHLNEVIRRIQKDFSCMEEMKYFIQRVEEQ... | NaN | NaN | NaN | NaN | NaN | NaN |
| 14 | 8232 | 8774 | -1 | 0 | CDS | complement(8232..8774) | HKK39_RS00070 | pRUM_p14 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | streptothricin N-acetyltransferase Sat4 | WP_000627290.1 | MITEMKAGHLKDIDKPSEPFEVIGKIIPRYENENWTFTELLYEAPY... | NaN | NaN | NaN | NaN | NaN | sat4 |
| 15 | 8771 | 9679 | -1 | 0 | CDS | complement(8771..9679) | HKK39_RS00075 | pRUM_p16 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | aminoglycoside nucleotidyltransferase ANT(6)-Ia | WP_001255866.1 | MRSEKEMMDLVLSLAEQDERIRIVTLEGSRANINIPKDEFQDYDIT... | NaN | NaN | NaN | NaN | NaN | NaN |
| 16 | 9712 | 10446 | -1 | 0 | CDS | complement(9712..10446) | HKK39_RS00080 | pRUM_p17 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | class I SAM-dependent methyltransferase | WP_000662263.1 | MKENKYDDNIFFQKYSQMSRSQKGLAGAGEWETLKKMLPDFKGKRV... | 2.1.1.- | GO:0008168 - methyltransferase activity[Eviden... | GO:0032259 - methylation [Evidence IEA] | NaN | NaN | NaN |
| 17 | 10427 | 11296 | -1 | 0 | CDS | complement(10427..11296) | HKK39_RS00085 | pRUM_p18 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | nucleotidyltransferase domain-containingprotein | WP_000228166.1 | MVDNIIKSVAEKLSSLSYIEGIVLGGSRARGTHTEDSDIDIGIYYN... | NaN | GO:0016779 - nucleotidyltransferase activity[E... | NaN | NaN | NaN | NaN |
| 18 | 11399 | 11644 | -1 | 0 | CDS | complement(11399..11644) | HKK39_RS00090 | pRUM_p19 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | single-stranded DNA-binding protein | WP_000567888.1 | MIDVNELLEEAIRETENLNDGEVFLVKDLFKGYVGNRIPRKDRLLL... | NaN | NaN | NaN | NaN | NaN | NaN |
| 21 | 12938 | 13675 | -1 | 0 | CDS | complement(12938..13675) | HKK39_RS00105 | pRUM_p21 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | 23S rRNA (adenine(2058)-N(6))-methyltransferas... | WP_001038792.1 | MNKNIKYSQNFLTSEKVLNQIIKQLNLKETDTVYEIGTGKGHLTTK... | NaN | NaN | NaN | NaN | NaN | erm(B) |
| 22 | 13800 | 13883 | -1 | 0 | CDS | complement(13800..13883) | HKK39_RS00110 | NaN | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | 23S rRNA methyltransferase attenuation leaderp... | WP_001814874.1 | MLVFQMRNVDKTSTVLKQTKNSDYADK | NaN | NaN | GO:0046677 - response to antibiotic [EvidenceI... | NaN | NaN | NaN |
| 23 | 13904 | 14167 | -1 | 0 | CDS | complement(13904..14167) | HKK39_RS00115 | NaN | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | peptide-binding protein | WP_002311901.1 | MGNLGAQKEKRNDTPISAKKDIMGDKTVRVRADLHHIIKIETAKNG... | NaN | NaN | NaN | NaN | NaN | NaN |
| 25 | 14570 | 15250 | 1 | 0 | CDS | 14570..15250 | HKK39_RS00125 | pRUM_p22 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | IS6-like element IS1216 family transposase | WP_001015311.1 | MNHFKGKQFQQDVIIVAVGYYLRYNLSYREVQEILYDRGINVSHTT... | NaN | GO:0004803 - transposase activity [EvidenceIEA] | GO:0006313 - DNA transposition [EvidenceIEA] | NaN | NaN | NaN |
| 27 | 15987 | 17174 | 1 | 0 | CDS | 15987..17174 | HKK39_RS00135 | pRUM_p24 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | IS256-like element IS16 family transposase | WP_002296840.1 | MTQVHFTFESEEIQAIINESGANDTAKTLMTIMFNQLMEEQRNQYI... | NaN | GO:0004803 - transposase activity [EvidenceIEA] | GO:0006313 - DNA transposition [EvidenceIEA] | NaN | NaN | NaN |
| 28 | 17464 | 18111 | 1 | 0 | CDS | 17464..18111 | HKK39_RS00140 | pRUM_p25 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | type A-8 chloramphenicol O-acetyltransferase | WP_000143686.1 | MTFNIINLETWDRKEYFNHYFNQQTTYSVTKELDITLLKSMIKDKG... | 2.3.1.28 | NaN | NaN | NaN | NaN | NaN |
| 29 | 18426 | 18824 | 1 | 0 | CDS | 18426..18824 | HKK39_RS00145 | pRUM_p26 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | plasmid mobilization protein | WP_002340414.1 | MSEHDNNLASDLSVGGNRKPNRKEPKQISFRVNEGEYEKLRSSAET... | NaN | GO:0003677 - DNA binding [Evidence IEA] | NaN | NaN | NaN | NaN |
| 31 | 19246 | 19926 | 1 | 0 | CDS | 19246..19926 | HKK39_RS00155 | pRUM_p28 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | IS6-like element IS1216 family transposase | WP_002343844.1 | MNHFKGKQFQQDVIIVAVGYYLRYNLSYREVQEILYDRGINVSHTT... | NaN | GO:0004803 - transposase activity [EvidenceIEA] | GO:0006313 - DNA transposition [EvidenceIEA] | NaN | NaN | NaN |
| 32 | 20542 | 21582 | -1 | 0 | CDS | complement(20542..21582) | HKK39_RS00160 | pRUM_p29 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | replication initiator protein A | WP_000997689.1 | MNDFNYYKSKEIYREKYYQMPKVFFTNEKYMDLSNDAKIAYMLLKD... | NaN | NaN | NaN | NaN | NaN | NaN |
| 33 | 21931 | 22257 | -1 | 0 | CDS | complement(21931..22257) | HKK39_RS00165 | pRUM_p30 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | hypothetical protein | WP_000796719.1 | MAEDNRSQAAVSRLLGNKNKKNFKSKEVEEIELTKKNISKVIKDQG... | NaN | NaN | NaN | NaN | NaN | NaN |
| 34 | 22244 | 23047 | -1 | 0 | CDS | complement(22244..23047) | HKK39_RS00170 | pRUM_p31 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | ParA family protein | WP_002311905.1 | MGDILMARILSVANQKGGVSKTTTSVNLAACLKFVYGKNVLLVDID... | NaN | GO:0005524 - ATP binding [Evidence IEA];GO:001... | NaN | NaN | NaN | NaN |
| 35 | 23471 | 24658 | -1 | 0 | CDS | complement(23471..24658) | HKK39_RS00175 | pRUM_p32 | COORDINATES: similar to AAsequence:RefSeq:WP_0... | Derived by automated computational analysis us... | ... | 11 | IS256-like element IS16 family transposase | WP_002296840.1 | MTQVHFTFESEEIQAIINESGANDTAKTLMTIMFNQLMEEQRNQYI... | NaN | GO:0004803 - transposase activity [EvidenceIEA] | GO:0006313 - DNA transposition [EvidenceIEA] | NaN | NaN | NaN |
28 rows Γ 21 columns
Assign cluster identifiers to the plasmid proteinsο
[16]:
plast = plast.assign_eggnog_annot(processes=16)
print("Number of assigned clusters:", len(plast.vector))
print("Assigned clusters:")
print(plast.vector)
Number of assigned clusters: 28
Assigned clusters:
['348UX', '306TJ', '33CM8', 'COG0389', 'COG1961', '306WU', 'COG4115', '30A2H', '3072V', nan, '3072Z', 'COG1246', '2Z7S1', 'COG4976', '30URY', '33359', 'COG0030', '2ZU0Q', '32NBG', 'COG3316', 'COG3328', 'COG4845', '32ZHN', 'COG3316', '3304N', '30894', 'COG1192', 'COG3328']
Pass data through pLAST model and receive embeddingsο
[17]:
plast = plast.encode()
print("Plasmid embedding:")
print(plast.embedding)
Plasmid embedding:
[ 0.06329472 -0.04143739 0.06984315 0.21632679 -0.00855456 0.18253054
0.02088546 0.21080938 -0.00928008 0.01683181 0.02661998 0.02138225
-0.06070902 -0.18135379 0.19305757 0.11264715 0.00702482 -0.21246433
-0.12247914 0.00352493 0.154391 0.01665206 -0.00688221 -0.15605277
0.08608653 0.15692472 0.16208734 0.2544252 0.07329971 0.0497661
-0.00368475 -0.02327945 -0.04490764 0.12295408 0.19381781 -0.12716755
-0.00991008 -0.25971994 -0.09920156 0.14554374 -0.10447495 0.05955252
-0.0202443 -0.02432648 -0.01230781 -0.06949621 0.01995271 -0.07274803
0.05103639 0.01892512 -0.28953275 -0.13400112 -0.08602309 -0.10764287
0.29167795 -0.04042183 -0.01173846 0.15272175 0.00202008 0.09931558
-0.1024653 0.08236861 -0.22468589 0.17022073]
Find similar plasmids in the databaseο
[18]:
results = plast.get_most_similar(maxret=15)
[19]:
df = pd.DataFrame.from_dict(results, orient="index")
for c in ("pLAST_distance", "gc"):
if c in df.columns:
df[c] = pd.to_numeric(df[c], errors="coerce").round(6)
preferred = [
"pLAST_distance",
"length",
"gc",
"taxid",
"organism",
"definition",
"taxonomy",
"rep_type(s)",
"AMR",
"relaxase_type(s)",
"mpf_type",
"orit_type(s)",
"predicted_mobility",
]
cols = [c for c in preferred if c in df.columns] + [
c for c in df.columns if c not in preferred
]
display(df[cols])
| pLAST_distance | length | gc | taxid | organism | definition | taxonomy | rep_type(s) | AMR | relaxase_type(s) | mpf_type | orit_type(s) | predicted_mobility | accession | database | topology | primary_cluster_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| RefSeq_NZ_CP097025.1 | 0.992807 | 23514 | 0.341371 | 1352.0 | Enterococcus faecium | Enterococcus faecium strain AT45b plasmid pAT4... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc889 | - | MOBP | - | MOBP | mobilizable | GenBank_CP097025.1,PLSDB_NZ_CP097025.1,RefSeq_... | GenBank,PLDSB,RefSeq | circular | AD100 |
| RefSeq_NC_005000.1 | 0.988632 | 24873 | 0.340329 | 1352.0 | -,Enterococcus faecium | Enterococcus faecium plasmid pRUM, complete se... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc1118,rc889 | - | MOBP | - | MOBP | mobilizable | COMPASS_NC_005000.1,GenBank_AF507977.1,IMGPR_p... | COMPASS,GenBank,IMG-PR,RefSeq | circular | AD100 |
| RefSeq_NZ_KP842560.1 | 0.987638 | 23269 | 0.341957 | 1352.0 | Enterococcus faecium | Enterococcus faecium strain 17i48 ST17 plasmid... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc889 | - | MOBP | - | MOBP | mobilizable | COMPASS_KP842560.1,GenBank_KP842560.1,RefSeq_N... | COMPASS,GenBank,RefSeq | circular | AD100 |
| RefSeq_NZ_CP018131.1 | 0.986287 | 23736 | 0.348290 | 1352.0 | Enterococcus faecium | Enterococcus faecium strain A_020709_82 plasmi... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc1968,rc889 | - | - | - | - | non-mobilizable | COMPASS_NZ_CP018131.1,IMGPR_plasmid_2872254902... | COMPASS,IMG-PR,PLDSB,RefSeq | circular | AD100 |
| RefSeq_NZ_LN999989.1 | 0.976933 | 32402 | 0.345102 | 1352.0 | Enterococcus faecium | Enterococcus faecium isolate EFE11651 plasmid ... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc185,rc889 | - | MOBP | - | MOBP | mobilizable | EMBL_LN999989.1,IMGPR_plasmid_2875025650_00000... | ENA,IMG-PR,PLDSB,RefSeq | circular | AD100 |
| RefSeq_NZ_CP066675.1 | 0.976408 | 25974 | 0.347617 | 1352.0 | Enterococcus faecium | Enterococcus faecium strain Dallas 163_1 plasm... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc889 | - | - | - | - | non-mobilizable | GenBank_CP066675.1,PLSDB_NZ_CP066675.1,RefSeq_... | GenBank,PLDSB,RefSeq | circular | AD100 |
| RefSeq_NZ_LR135290.1 | 0.965348 | 26053 | 0.345066 | 1352.0 | Enterococcus faecium | Enterococcus faecium isolate E7199 plasmid 4 | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc889 | - | - | - | - | non-mobilizable | IMGPR_plasmid_2912394829_000004,PLSDB_NZ_LR135... | IMG-PR,PLDSB,RefSeq | linear | AD100 |
| RefSeq_NZ_OP378686.1 | 0.961236 | 32622 | 0.344062 | 1352.0 | Enterococcus faecium | Enterococcus faecium strain VRE33536 plasmid p... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc889 | AMK,AZM,CBM,CLI,CLR,CST,DAL,DBK,DIR,ERY,EVN,FF... | - | - | - | non-mobilizable | RefSeq_NZ_OP378686.1 | RefSeq | circular | AD100 |
| RefSeq_NZ_AP026603.1 | 0.957876 | 31114 | 0.347496 | 1352.0 | Enterococcus faecium | Enterococcus faecium strain JHP80 plasmid pJHP... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc185,rc889 | - | - | - | - | non-mobilizable | DDBJ_AP026603.1,PLSDB_NZ_AP026603.1,RefSeq_NZ_... | DDBJ,PLDSB,RefSeq | circular | AD100 |
| RefSeq_NC_021170.1 | 0.947730 | 31136 | 0.348953 | 1352.0 | Enterococcus faecium | Enterococcus faecium plasmid pF856, complete s... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc889 | - | - | - | - | non-mobilizable | COMPASS_JQ663598.1,GenBank_JQ663598.1,RefSeq_N... | COMPASS,GenBank,RefSeq | circular | AB173 |
| RefSeq_NZ_CP012431.1 | 0.944787 | 44226 | 0.354520 | 1352.0 | Enterococcus faecium | Enterococcus faecium strain ISMMS_VRE_1 plasmi... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc1763,rc2146,rc889 | - | MOBV | - | - | mobilizable | COMPASS_NZ_CP012431.1,GenBank_CP012431.1,IMGPR... | COMPASS,GenBank,IMG-PR,PLDSB,RefSeq | circular | AB173 |
| RefSeq_NZ_CP027516.1 | 0.944101 | 37152 | 0.355243 | 1352.0 | Enterococcus faecium | Enterococcus faecium strain AUSMDU00004028 pla... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc1763,rc889 | - | - | - | - | non-mobilizable | COMPASS_NZ_CP027516.1,PLSDB_NZ_CP027516.1,RefS... | COMPASS,PLDSB,RefSeq | circular | AB173 |
| RefSeq_NZ_CP027510.1 | 0.943327 | 33328 | 0.355797 | 1352.0 | Enterococcus faecium | Enterococcus faecium strain AUSMDU00004055 pla... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc889 | - | - | - | - | non-mobilizable | COMPASS_NZ_CP027510.1,PLSDB_NZ_CP027510.1,RefS... | COMPASS,PLDSB,RefSeq | circular | AB173 |
| RefSeq_NZ_KX574671.1 | 0.941715 | 37372 | 0.354758 | 1352.0 | Enterococcus faecium | Enterococcus faecium strain V24 plasmid pHvH-V... | Bacteria;Bacillota;Bacilli;Lactobacillales;Ent... | rc889 | - | - | - | - | non-mobilizable | COMPASS_KX574671.1,GenBank_KX574671.1,RefSeq_N... | COMPASS,GenBank,RefSeq | circular | AB173 |
| RefSeq_NZ_JACYGV010000007.1 | 0.940226 | 30475 | 0.359737 | NaN | Enterococcus faecium | Enterococcus faecium strain VREA4 plasmid pVRE... | NaN | rc889 | AMK,AZM,BUT,CBM,CLI,CLR,CST,DAL,DIR,ERY,EVN,FF... | - | - | - | non-mobilizable | RefSeq_NZ_JACYGV010000007.1 | RefSeq | circular | AB173 |
[ ]: