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PR00338

Identifier
NUSGTNSCPFCT  [View Relations]  [View Alignment]  
Accession
PR00338
No. of Motifs
3
Creation Date
04-OCT-1994  (UPDATE 22-JUN-1999)
Title
Transcription termination factor NUSG signature
Database References

PROSITE; PS01014 NUSG
BLOCKS; BL01014
INTERPRO; IPR001062
Literature References
1. LI, J., MASON, W. AND GREENBLATT, J.
Elongation factor nusG interacts with termination factor rho to regulate
termination and antitermination of transcription.
GENES DEV. 7 161-72 (1993).
 
2. DOWNING, W.L., SULLIVAN, S.L., GOTTESMAN, M.E. AND DENNIS, P.P.
Sequence and transcriptional pattern of the essential Escherichia coli
secE-nusG operon.
J.BACTERIOL. 172 1621-1627 (1990).
 
3. LI, J., HORWITZ, R., MCCRACKEN, S. AND GREENBLATT, J.
NusG, a new Escherichia coli elongation factor involved in transcriptional
antitermination by the N protein of phage lambda.
J.BIOL.CHEM. 267 6012-6019 (1992).
 
4. NEHRKE, K.W., ZALATAN, F. AND PLATT, T.
NusG alters rho-dependent termination of transcription in vitro independent
of kinetic coupling.
GENE EXPR. 3 119-133 (1993).

Documentation
The nusG protein is a bacterial transcriptional elongation factor involved
in transcription termination and anti-termination [1,2] - it is thus 
essential for bacterial viability [2]. The protein forms part of the
transcription complex, interacting with RNA polymerase and the termination
factor rho [3,4].
 
NUSGTNSCPFCT is a 3-element fingerprint that provides a signature for nusG 
transcription termination proteins. The fingerprint was derived from an
initial alignment of 5 sequences: the motifs were drawn from conserved
regions in the central and C-terminal portions of the alignment, motif 3
including the region encoded by PROSITE pattern NUSG (PS01014). Two
iterations on OWL24.0 were required to reach convergence, at which point a
true set comprising 11 sequences was identified. A single partial match was
also found, NUSG_CGDAB, a nusG protein fragment from the citrus greening
disease-associated bacterium-like organism.
 
An update on SPTR37_9f identified a true set of 18 sequences, and 3
partial matches.
Summary Information
  18 codes involving  3 elements
2 codes involving 2 elements
Composite Feature Index
3181818
2112
123
True Positives
NUSG_BACSU    NUSG_BORBU    NUSG_ECOLI    NUSG_HAEIN    
NUSG_HELPY NUSG_RICPR NUSG_STAAU NUSG_STACA
NUSG_STRCO NUSG_STRGR NUSG_STRVG NUSG_SYNY3
NUSG_THEMA NUSG_THETH NUSG_TREPA O67757
O84322 P96930
True Positive Partials
Codes involving 2 elements
NUSG_STRGB YGP9_YEAST
Sequence Titles
NUSG_BACSU  TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - BACILLUS SUBTILIS. 
NUSG_BORBU TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
NUSG_ECOLI TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - ESCHERICHIA COLI.
NUSG_HAEIN TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - HAEMOPHILUS INFLUENZAE.
NUSG_HELPY TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
NUSG_RICPR TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - RICKETTSIA PROWAZEKII.
NUSG_STAAU TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - STAPHYLOCOCCUS AUREUS.
NUSG_STACA TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - STAPHYLOCOCCUS CARNOSUS.
NUSG_STRCO TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - STREPTOMYCES COELICOLOR.
NUSG_STRGR TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - STREPTOMYCES GRISEUS.
NUSG_STRVG TRANSCRIPTION ANTITERMINATION PROTEIN NUSG (BUTANOLIDE RECEPTOR) - STREPTOMYCES VIRGINIAE.
NUSG_SYNY3 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
NUSG_THEMA TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - THERMOTOGA MARITIMA.
NUSG_THETH TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - THERMUS AQUATICUS (SUBSP. THERMOPHILUS).
NUSG_TREPA TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - TREPONEMA PALLIDUM.
O67757 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - AQUIFEX AEOLICUS.
O84322 TRANSCRIPTIONAL TERMINATION PROTEIN - CHLAMYDIA TRACHOMATIS.
P96930 TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - MYCOBACTERIUM TUBERCULOSIS.

NUSG_STRGB TRANSCRIPTION ANTITERMINATION PROTEIN NUSG - STREPTOMYCES GALBUS.
YGP9_YEAST HYPOTHETICAL 41.6 KD PROTEIN IN SUT1-RCK1 INTERGENIC REGION - SACCHAROMYCES CEREVISIAE (BAKER'S YEAST).
Scan History
OWL24_0    2  100  NSINGLE    
OWL28_0 1 100 NSINGLE
SPTR37_9f 1 300 NSINGLE
Initial Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
RQNKLPGYVLVRM NUSG_STRCO 165 165 -
RKKLFPGYLFIQM NUSG_THETH 58 58 -
ERKFFPGYVLVQM NUSG_ECOLI 61 61 -
KKKVFPGYVLVEI NUSG_BACSU 57 57 -
RRKLFPGYVFVEM NUSG_THEMA 228 228 -

Motif 2 width=16
Element Seqn Id St Int Rpt
GPFATLQATINEINAD NUSG_STRCO 258 80 -
GPFADFTGTVTEINPE NUSG_THETH 142 71 -
GPFADFNGVVEEVDYE NUSG_ECOLI 139 65 -
GPFANFTGSIEEIDYD NUSG_BACSU 135 65 -
GPFEDFAGVIKEIDPE NUSG_THEMA 310 69 -

Motif 3 width=17
Element Seqn Id St Int Rpt
KVKGLVEIFGRETPVEL NUSG_STRCO 276 2 -
KVKVMVTIFGRETPVEL NUSG_THETH 160 2 -
RLKVSVSIFGRATPVEL NUSG_ECOLI 157 2 -
KVKVFVNMFGRETPVEL NUSG_BACSU 153 2 -
ELKVNVTIFGRETPVVL NUSG_THEMA 328 2 -
Final Motifs
Motif 1  width=13
Element Seqn Id St Int Rpt
RQNKLPGYVLVRM NUSG_STRCO 165 165 -
RQNKLPGYVLVRM NUSG_STRGR 159 159 -
RQNKLPGYVLVRM NUSG_STRVG 164 164 -
RKKLFPGYLFIQM NUSG_THETH 58 58 -
ERKFFPGYVLVEM NUSG_HAEIN 64 64 -
ERKFFPGYVLVQM NUSG_ECOLI 61 61 -
KKKVFPGYVLVEI NUSG_BACSU 57 57 -
RRKLFPGYVFVEM NUSG_THEMA 228 228 -
EEKIFPGYVLIRM NUSG_SYNY3 76 76 -
NRKVLPGYILVRM P96930 101 101 -
TKKTFPGYVLVEL NUSG_STACA 62 62 -
VKKTFPGYVLVEL NUSG_STAAU 62 62 -
RRKFFPGYLLVEM NUSG_TREPA 58 58 -
EKKLMPSYILIKM NUSG_RICPR 72 72 -
DNKIFPGYILIKA O67757 131 131 -
ERSLYPGYVFIKV NUSG_HELPY 57 57 -
ERKIWPGYILIEL NUSG_BORBU 57 57 -
EKYIWPGYLLVKM O84322 56 56 -

Motif 2 width=16
Element Seqn Id St Int Rpt
GPFATLQATINEINAD NUSG_STRCO 258 80 -
GPFATLQATINEINAD NUSG_STRGR 252 80 -
GPFATLQATINEINPD NUSG_STRVG 257 80 -
GPFADFTGTVTEINPE NUSG_THETH 142 71 -
GPFADFNGTVEEVDYE NUSG_HAEIN 142 65 -
GPFADFNGVVEEVDYE NUSG_ECOLI 139 65 -
GPFANFTGSIEEIDYD NUSG_BACSU 135 65 -
GPFEDFAGVIKEIDPE NUSG_THEMA 310 69 -
GPFKDFEGDVIEVSPE NUSG_SYNY3 162 73 -
GPFATLPATISEVNAE P96930 196 82 -
GPFANQVGEVQEIEAD NUSG_STACA 140 65 -
GPFANQVGEVQEIETD NUSG_STAAU 140 65 -
GPFATFSGEVEEVMSE NUSG_TREPA 143 72 -
GPFETFMGTVEAIDKA NUSG_RICPR 149 64 -
GPFMNFTGTVEEVHPE O67757 206 62 -
GPFANFTATVEEYDVE NUSG_HELPY 133 63 -
GPFDSFEGLISSIDYE NUSG_BORBU 142 72 -
GVFVNFVGVVSEVFHD O84322 132 63 -

Motif 3 width=17
Element Seqn Id St Int Rpt
KVKGLVEIFGRETPVEL NUSG_STRCO 276 2 -
KVKGLVEIFGRETPVEL NUSG_STRGR 270 2 -
KVKGLVEIFGRETPVEL NUSG_STRVG 275 2 -
KVKVMVTIFGRETPVEL NUSG_THETH 160 2 -
RLKVSVSMFGRATPVEL NUSG_HAEIN 160 2 -
RLKVSVSIFGRATPVEL NUSG_ECOLI 157 2 -
KVKVFVNMFGRETPVEL NUSG_BACSU 153 2 -
ELKVNVTIFGRETPVVL NUSG_THEMA 328 2 -
KLKALLSIFGRETPVEL NUSG_SYNY3 180 2 -
KLKVLVSIFGRETPVEL P96930 214 2 -
KLTVLVDMFGRETPVEV NUSG_STACA 158 2 -
KLTVLVDMFGRETPVEV NUSG_STAAU 158 2 -
KVRVAVTIFGRATPVEL NUSG_TREPA 161 2 -
RLKVSVSIFGKATPIEL NUSG_RICPR 167 2 -
KLTVMISIFGRMTPVEL O67757 224 2 -
KLKLNVSIFGRNTPIEI NUSG_HELPY 151 2 -
KLKVAVQIFGRSTPVEV NUSG_BORBU 160 2 -
RLSVMVSIFGRETRVDD O84322 150 2 -