Detailed information    

experimental Experimentally validated

Overview

Name   amiF   Type   Regulator
Locus tag   STU_RS16110 Genome accession   NC_006448
Coordinates   1271744..1272673 (-) Length   309 a.a.
NCBI ID   WP_002951426.1    Uniprot ID   A0A7U7CIU5
Organism   Streptococcus thermophilus LMG 18311     
Function   internalize XIP   
Competence regulation

Function

XIP peptides are recognized by the oligopeptide-binding protein AmiA3 and internalized by the oligopeptide Ami transporter (AmiCDEF).


Related MGE

Note: This gene co-localizes with putative mobile genetic elements (MGEs) in the genome predicted by VRprofile2, as detailed below.

Gene-MGE association summary

MGE type MGE coordinates Gene coordinates Relative position Distance (bp)
ICE 1256209..1326298 1271744..1272673 within 0


Gene organization within MGE regions


Location: 1256209..1326298
Locus tag Gene name Coordinates (strand) Size (bp) Protein ID Product Description
  STU_RS16040 (stu1422) liaF 1256217..1256915 (-) 699 WP_011226289.1 cell wall-active antibiotics response protein LiaF -
  STU_RS20685 (stu1423) - 1257181..1257336 (-) 156 WP_011226290.1 ion channel -
  STU_RS16045 (stu1425) stkP/pknB 1257973..1259844 (-) 1872 WP_011226292.1 Stk1 family PASTA domain-containing Ser/Thr kinase Regulator
  STU_RS16050 (stu1426) - 1259844..1260581 (-) 738 WP_002946881.1 Stp1/IreP family PP2C-type Ser/Thr phosphatase -
  STU_RS16055 (stu1427) rsmB 1260625..1261947 (-) 1323 WP_014608533.1 16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB -
  STU_RS16060 (stu1428) fmt 1261937..1262872 (-) 936 WP_002951411.1 methionyl-tRNA formyltransferase -
  STU_RS16065 (stu1429) - 1262890..1265286 (-) 2397 WP_011226295.1 primosomal protein N' -
  STU_RS16070 (stu1430) rpoZ 1265428..1265742 (-) 315 WP_002951415.1 DNA-directed RNA polymerase subunit omega -
  STU_RS16075 (stu1431) gmk 1265764..1266393 (-) 630 WP_011226296.1 guanylate kinase -
  STU_RS16080 (stu1432) ftsY 1266626..1268017 (-) 1392 WP_011226297.1 signal recognition particle-docking protein FtsY -
  STU_RS16085 (stu1433) - 1268031..1268846 (-) 816 WP_011226298.1 Cof-type HAD-IIB family hydrolase -
  STU_RS16090 (stu1434) - 1268839..1269633 (-) 795 WP_011226299.1 HAD hydrolase family protein -
  STU_RS16095 (stu1435) - 1269817..1270194 (+) 378 WP_011226300.1 GntR family transcriptional regulator -
  STU_RS16100 (stu1436) - 1270199..1270897 (+) 699 WP_011226301.1 ABC transporter ATP-binding protein -
  STU_RS16105 (stu1437) - 1270909..1271694 (+) 786 WP_002951425.1 hypothetical protein -
  STU_RS16110 (stu1438) amiF 1271744..1272673 (-) 930 WP_002951426.1 ATP-binding cassette domain-containing protein Regulator
  STU_RS16115 (stu1439) amiE 1272666..1273751 (-) 1086 WP_011226304.1 ABC transporter ATP-binding protein Regulator
  STU_RS16120 (stu1440) amiD 1273761..1274687 (-) 927 WP_002946409.1 oligopeptide ABC transporter permease OppC Regulator
  STU_RS16125 (stu1441) amiC 1274687..1276180 (-) 1494 WP_002946410.1 ABC transporter permease Regulator
  STU_RS16130 (stu1442) amiA 1276242..1278209 (-) 1968 WP_011225333.1 peptide ABC transporter substrate-binding protein Regulator
  STU_RS16135 (stu1444) - 1278565..1279814 (+) 1250 Protein_1243 ISL3 family transposase -
  STU_RS16140 (stu1445) amiA3 1279859..1281832 (-) 1974 WP_011226306.1 peptide ABC transporter substrate-binding protein Regulator
  STU_RS19635 - 1282036..1282226 (-) 191 Protein_1245 IS3 family transposase -
  STU_RS16145 (stu1447) - 1282220..1282630 (-) 411 Protein_1246 ATP-binding cassette domain-containing protein -
  STU_RS20240 - 1282662..1282976 (-) 315 Protein_1247 TatD family hydrolase -
  STU_RS16155 (stu1450) - 1283326..1284531 (+) 1206 WP_011226310.1 L-lactate MFS transporter -
  STU_RS19640 - 1284577..1285928 (-) 1352 Protein_1249 IS3 family transposase -
  STU_RS16175 (stu1455) pta 1286014..1286997 (-) 984 WP_011226315.1 phosphate acetyltransferase -
  STU_RS16180 (stu1456) - 1287011..1287907 (-) 897 WP_011226316.1 RluA family pseudouridine synthase -
  STU_RS16185 (stu1457) - 1287904..1288740 (-) 837 WP_041827075.1 NAD kinase -
  STU_RS16190 (stu1459) - 1288712..1289386 (-) 675 WP_002951443.1 GTP pyrophosphokinase -
  STU_RS16195 (stu1458) - 1289482..1290057 (+) 576 WP_002951444.1 CYTH domain-containing protein -
  STU_RS16200 (stu1460) - 1290422..1291393 (+) 972 WP_002951446.1 ribose-phosphate diphosphokinase -
  STU_RS16205 (stu1461) - 1291397..1292509 (+) 1113 WP_002948029.1 cysteine desulfurase family protein -
  STU_RS16210 (stu1462) - 1292511..1292858 (+) 348 WP_011226321.1 DUF1831 domain-containing protein -
  STU_RS16215 (stu1463) - 1293003..1293662 (+) 660 WP_041828288.1 redox-sensing transcriptional repressor Rex -
  STU_RS16220 (stu1464) - 1293655..1294350 (+) 696 WP_011226323.1 gamma-glutamyl-gamma-aminobutyrate hydrolase family protein -
  STU_RS16225 (stu1465) radC 1294403..1295089 (-) 687 WP_011226324.1 RadC family protein -
  STU_RS16230 (stu1467) - 1295138..1296922 (-) 1785 WP_011226325.1 rhamnan synthesis F family protein -
  STU_RS16235 (stu1468) - 1296919..1297974 (-) 1056 WP_002948022.1 glycosyltransferase family 2 protein -
  STU_RS16240 (stu1469) - 1297994..1299199 (-) 1206 WP_011226326.1 ABC transporter ATP-binding protein -
  STU_RS16245 (stu1470) - 1299199..1300008 (-) 810 WP_002948020.1 ABC transporter permease -
  STU_RS16250 (stu1471) - 1299992..1300948 (-) 957 WP_011226328.1 glycosyltransferase family 2 protein -
  STU_RS16255 (stu1472) cps2T 1300945..1302093 (-) 1149 WP_041828290.1 beta 1-4 rhamnosyltransferase Cps2T -
  STU_RS16260 (stu1473) - 1302202..1303212 (-) 1011 WP_011226330.1 glycosyltransferase family 2 protein -
  STU_RS16265 (stu1480) - 1303212..1304486 (-) 1275 WP_011226331.1 lipopolysaccharide biosynthesis protein -
  STU_RS16270 (stu1481) - 1304479..1304811 (-) 333 WP_011226332.1 DUF2304 domain-containing protein -
  STU_RS16275 (stu1482) - 1304817..1305512 (-) 696 WP_173940715.1 glycosyltransferase family 2 protein -
  STU_RS16280 (stu1483) rfbD 1305589..1306440 (-) 852 WP_014621820.1 dTDP-4-dehydrorhamnose reductase -
  STU_RS16285 (stu1484) - 1306517..1307851 (-) 1335 WP_041828293.1 DUF3329 domain-containing protein -
  STU_RS16290 (stu1485) - 1307964..1308881 (-) 918 WP_002946425.1 glycosyltransferase family 2 protein -
  STU_RS16295 (stu1486) - 1308944..1310359 (-) 1416 WP_011226336.1 DUF2142 domain-containing protein -
  STU_RS16300 (stu1487) - 1310693..1311028 (-) 336 WP_002891474.1 metal-sulfur cluster assembly factor -
  STU_RS19995 (stu1488) rpoD 1311082..1312191 (-) 1110 WP_011226338.1 RNA polymerase sigma factor RpoD -
  STU_RS20000 (stu1489) dnaG 1312195..1314006 (-) 1812 WP_011226339.1 DNA primase -
  STU_RS16315 (stu1490) rpsU 1314377..1314553 (-) 177 WP_011226340.1 30S ribosomal protein S21 -
  STU_RS16320 (stu1492) - 1314748..1315542 (-) 795 WP_011226341.1 transporter substrate-binding domain-containing protein -
  STU_RS16325 (stu1493) - 1315635..1316744 (-) 1110 WP_041828295.1 aminotransferase -
  STU_RS16330 (stu1494) - 1317091..1317888 (-) 798 WP_011226343.1 transporter substrate-binding domain-containing protein -
  STU_RS16335 (stu1495) - 1317885..1318715 (-) 831 WP_041828297.1 transporter substrate-binding domain-containing protein -
  STU_RS16340 (stu1496) - 1318928..1319392 (-) 465 WP_011226345.1 8-oxo-dGTP diphosphatase -
  STU_RS16345 (stu1497) uvrB 1319437..1321428 (-) 1992 WP_002953358.1 excinuclease ABC subunit UvrB -
  STU_RS20995 - 1322115..1323051 (-) 937 Protein_1285 CPBP family intramembrane glutamic endopeptidase -
  STU_RS16365 (stu1501) - 1323250..1325460 (+) 2211 WP_011226350.1 ABC transporter substrate-binding protein/permease -
  STU_RS16370 (stu1502) - 1325460..1326200 (+) 741 WP_002945131.1 amino acid ABC transporter ATP-binding protein -

Regulatory network

Positive effect      
Negative effect
Regulator Target Regulation
  amiF comS positive effect
  comS comS positive effect
  comS comX positive effect
  amiC comS positive effect
  eeP comS positive effect
  amiD comS positive effect
  comR comS positive effect
  amiA3 comS positive effect
  amiE comS positive effect
  comX ssbA positive effect
  comX comGE positive effect
  comX comGB positive effect
  comX comGD positive effect
  comX comGF positive effect
  comX comGG positive effect
  comX radA positive effect
  comX comEC positive effect
  comX comFC positive effect
  comX recA positive effect
  comX comEA positive effect
  comX comGC positive effect
  comX cinA positive effect
  comX coiA positive effect
  comX comGA positive effect
  comX comFA positive effect
  comX dprA positive effect
  clpC comX negative effect
  comR comX positive effect
  clpP comX negative effect
  mecA comX negative effect

Sequence

Protein


Download         Length: 309 a.a.        Molecular weight: 35171.28 Da        Isoelectric Point: 6.5989

>NTDB_id=328 STU_RS16110 WP_002951426.1 1271744..1272673(-) (amiF) [Streptococcus thermophilus LMG 18311]
MPEKLVEVKDVEISFGEGRKKFVAVHNANFFINKGETFSLVGESGSGKTTIGRAIIGLNDTSNGEIIFDGKKINGYLSHS
EKNDLIRRIQMIFQDPAASLNERATVDYILSEGLYNFHLYKDEEERKAKIKEIIKEVGLLEEHLTRYPHEFSGGQRQRIG
IARSLVMQPDLVIADEPISALDVSVRAQVLNLLKKFQKELGLTYLFIAHDLSVVRFISDRIAVIYKGTIVEVAETEELYN
NPIHPYTKSLLSAVPIPDPILERKKVLKVYDPNQHDYSVDKPEMVEVRPGHFVWGNKTEIETYRKEQSK

Nucleotide


Download         Length: 930 bp        

>NTDB_id=328 STU_RS16110 WP_002951426.1 1271744..1272673(-) (amiF) [Streptococcus thermophilus LMG 18311]
ATGCCTGAGAAATTAGTTGAAGTAAAAGATGTGGAAATTTCCTTCGGCGAAGGAAGAAAGAAGTTCGTTGCTGTCCACAA
TGCTAATTTTTTCATCAACAAGGGTGAAACCTTCTCCCTCGTTGGTGAGTCTGGTAGTGGTAAAACGACTATTGGACGTG
CCATTATCGGTTTAAATGACACAAGTAATGGTGAGATTATTTTTGACGGTAAGAAGATCAATGGATACTTATCTCACTCT
GAGAAAAACGACCTTATCCGTCGTATTCAGATGATTTTCCAAGACCCTGCGGCTAGTTTGAATGAACGTGCGACAGTCGA
TTATATCTTGTCTGAGGGCTTGTACAATTTCCATCTTTATAAAGATGAGGAAGAACGTAAGGCTAAAATCAAGGAAATCA
TCAAAGAAGTAGGACTTCTTGAGGAGCACTTAACACGTTACCCTCACGAATTTTCTGGGGGACAACGTCAACGTATCGGG
ATTGCGCGTTCTTTGGTCATGCAGCCTGATTTGGTTATCGCTGATGAACCAATCTCAGCCCTTGACGTGTCAGTTCGTGC
CCAAGTTTTGAATTTGCTTAAGAAATTCCAAAAAGAGTTGGGGTTAACCTATCTCTTTATCGCTCACGATTTGTCAGTGG
TCCGTTTCATTTCTGACCGTATCGCTGTTATCTATAAGGGGACAATCGTGGAAGTTGCTGAGACAGAAGAGCTCTACAAC
AATCCTATCCATCCTTATACCAAGTCACTCTTGTCTGCTGTTCCTATTCCAGATCCAATCTTGGAACGTAAGAAAGTCTT
GAAGGTTTATGATCCAAACCAACACGACTATTCGGTTGATAAACCAGAAATGGTGGAAGTACGCCCAGGTCACTTCGTTT
GGGGTAACAAGACAGAAATTGAGACTTATCGTAAAGAACAAAGTAAGTAA

Domains

Predicted by InterproScan.

ABC transporter (ABC_tran)

(26-178)

Oligopeptide/dipeptide transporter, C-terminal region (oligo_HPY)

(230-262)


Secondary structure

Protein secondary structures were predicted by S4PRED and visualized by seqviz.



3D structure

Source ID Structure
  AlphaFold DB A0A7U7CIU5

Transmembrane helices

Transmembrane helices of protein were predicted by TMHMM 2.0 and visualized by seqviz and ECharts.


Visualization of predicted probability:


Similar proteins

Only experimentally validated proteins are listed.

Protein Organism Identities (%) Coverage (%) Ha-value
  amiF Streptococcus thermophilus LMD-9

99.676

100

0.997
  amiF Streptococcus salivarius strain HSISS4

98.058

100

0.981

Multiple sequence alignment    



References

[1] Laetitia Fontaine et al. (2010) A novel pheromone quorum-sensing system controls the development of natural competence in Streptococcus thermophilus and Streptococcus salivarius. Journal of Bacteriology 192(5):1444-54. [PMID: 20023010]
[2] Rozenn Gardan et al. (2009) The oligopeptide transport system is essential for the development of natural competence in Streptococcus thermophilus strain LMD-9. Journal of Bacteriology 191(14):4647-55. [PMID: 19447907]