Transportadores

Utilizando a TransportDB (http://www.membranetransport.org/transportDB2/index.html), identificamos 21 genes que codificam proteínas transportadoras e construímos uma tabela com a seguinte informação:

  • Locus Tag
  • Substrate
  • Subtype
  • Family
  • Family Name
  • Transporter Class
  • TC number
In [5]:
import pandas as pd

df = pd.read_csv("files/transporters.csv", sep=";")
df
Out[5]:
Locus_tag Substrate Subtype Family Family Name Transporter Class TC number
0 lpg0388 daunorubicin binding ABC The ATP-binding Cassette (ABC) Superfamily ATP-Dependent 3.A.1
1 lpg0387 multidrug membrane ABC The ATP-binding Cassette (ABC) Superfamily ATP-Dependent 3.A.1
2 lpg0441 Unclassified No Subtype IVSP The Type IV (Conjugal DNA-Protein Transfer or ... ATP-Dependent 3.A.7
3 lpg0445 Unclassified No Subtype IVSP The Type IV (Conjugal DNA-Protein Transfer or ... ATP-Dependent 3.A.7
4 lpg0446 Unclassified No Subtype IVSP The Type IV (Conjugal DNA-Protein Transfer or ... ATP-Dependent 3.A.7
5 lpg0448 Unclassified No Subtype IVSP The Type IV (Conjugal DNA-Protein Transfer or ... ATP-Dependent 3.A.7
6 lpg0449 Unclassified No Subtype IVSP The Type IV (Conjugal DNA-Protein Transfer or ... ATP-Dependent 3.A.7
7 lpg0451 Unclassified No Subtype IVSP The Type IV (Conjugal DNA-Protein Transfer or ... ATP-Dependent 3.A.7
8 lpg0452 Unclassified No Subtype IVSP The Type IV (Conjugal DNA-Protein Transfer or ... ATP-Dependent 3.A.7
9 lpg0453 Unclassified No Subtype IVSP The Type IV (Conjugal DNA-Protein Transfer or ... ATP-Dependent 3.A.7
10 lpg0454 Unclassified No Subtype IVSP The Type IV (Conjugal DNA-Protein Transfer or ... ATP-Dependent 3.A.7
11 lpg0281 amino acid No Subtype APC The Amino Acid-Polyamine-Organocation (APC) Fa... Secondary Transporter 2.A.3
12 lpg0404 glutamate:GABA antiporter No Subtype APC The Amino Acid-Polyamine-Organocation (APC) Fa... Secondary Transporter 2.A.3
13 lpg0256 fusaric acid efflux? No Subtype ArAE The Aromatic Acid Exporter (ArAE) Family Secondary Transporter 2.A.85
14 lpg0291 chromate ion No Subtype CHR The Chromate Ion Transporter (CHR) Family Secondary Transporter 2.A.51
15 lpg0263 multidrug efflux? No Subtype MFS The Major Facilitator Superfamily (MFS) Secondary Transporter 2.A.1
16 lpg0273 multidrug efflux No Subtype MFS The Major Facilitator Superfamily (MFS) Secondary Transporter 2.A.1
17 lpg0357 multidrug efflux No Subtype MFS The Major Facilitator Superfamily (MFS) Secondary Transporter 2.A.1
18 lpg0421 multidrug efflux No Subtype MFS The Major Facilitator Superfamily (MFS) Secondary Transporter 2.A.1
19 lpg0457 multidrug efflux No Subtype MFS The Major Facilitator Superfamily (MFS) Secondary Transporter 2.A.1
20 lpg0267 magnesium/cobalt ion No Subtype MIT The CorA Metal Ion Transporter (MIT) Family Ion Channels 1.A.35

Fatores de Transcrição

Usando a Transcription factor prediction database (http://www.transcriptionfactor.org/index.cgi?Home), identificamos apenas 6 fatores de transcrição na nossa zona do genoma e preenchemos uma tabela com os seguintes campos:

  • Locus Tag
  • Protein_id
  • Superfamily Domains
  • Pfam Domains
Superfamily (SF) Domains Pfam (PF) domains
Locus_tag Protein_id Family Name Family Regions e-value Domain Arquitecture Family Name Family Regions e-value Domain Arquitecture
lpg0232 YP_094286.1 "Winged helix" DNA-binding domain 46785 36-169 7.4e-27 1 No hits No hits No hits No hits No hits
lpg0274 YP_094328.1 "Winged helix" DNA-binding domain; Periplasmic binding protein-like II 46785; 53850 1-106; 87-287 6.3e-20; 1.3e-33 2 Bacterial regulatory helix-turn-helix protein lysR family; LysR substrate binding domain HTH1; LysR substrate 4-63; 87-287 1.0e-18; 1.4e-34 4
lpg0280 YP_094334.1 "Winged helix" DNA-binding domain; Periplasmic binding protein-like II 46785; 53850 1-104; 85-288 1.4e-19; 2.1e-35 3 Bacterial regulatory helix-turn-helix protein, lysR family;LysR substrate binding domain HTH1; LysR substrate 3-62; 85-290 1.7e-18; 3.4e-27 5
lpg0423 YP_094467.1 No Hits No Hits No Hits No Hits No Hits Helix-Turn-Helix HTH-3 7-62 9.0e-6 6
lpg0426 YP_094470.1 Nucleic acid-binding proteins 50249 1-67 3.6e-21 9 "Cold-shock" DNA-binding domain CSD 1-67 2.1e-34 7
lpg0433 YP_094477.1 "Winged helix" DNA-binding domain 46785 11-108 1.9e-12 10 HxIR-like helix-turn-helix DUF24 21-111 2.8e-26 8

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