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pasteseq |
To insert the sequence 'tsw:flav_nossm' after position 67 in sequence 'tsw:amir_pseae' and write the results to the file 'amir_pseae.fasta':
% pasteseq tsw:amir_pseae tsw:flav_nossm -pos=67 Insert one sequence into another output sequence [amir_pseae.fasta]: |
Go to the input files for this example
Go to the output files for this example
Example 2
This does the same thing, but the output qualifier is explicitly used:
% pasteseq tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=67 Insert one sequence into another |
Go to the output files for this example
Example 3
To insert the sequence 'tsw:flav_nossm' before the start of sequence 'tsw:amir_pseae' use -pos=0:
% pasteseq tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=0 Insert one sequence into another |
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-asequence] sequence (Gapped) sequence filename and optional
format, or reference (input USA)
[-bsequence] sequence Sequence to insert
-pos integer [$(asequence.end)] The position in the main
input sequence to insert after.
To insert before the start use the position
0. (Integer 0 or more)
[-outseq] seqout [
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-asequence] (Parameter 1) |
(Gapped) sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| [-bsequence] (Parameter 2) |
Sequence to insert | Readable sequence | Required |
| -pos | The position in the main input sequence to insert after. To insert before the start use the position 0. | Integer 0 or more | $(asequence.end) |
| [-outseq] (Parameter 3) |
Sequence filename and optional format (output USA) | Writeable sequence | <*>.format |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
ID AMIR_PSEAE Reviewed; 196 AA.
AC P10932;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 08-DEC-2000, sequence version 2.
DT 20-MAR-2007, entry version 55.
DE Aliphatic amidase regulator.
GN Name=amiR; OrderedLocusNames=PA3363;
OS Pseudomonas aeruginosa.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=287;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=PAC433;
RX MEDLINE=89211409; PubMed=2495988; DOI=10.1016/0014-5793(89)80249-2;
RA Lowe N., Rice P.M., Drew R.E.;
RT "Nucleotide sequence of the aliphatic amidase regulator gene (amiR) of
RT Pseudomonas aeruginosa.";
RL FEBS Lett. 246:39-43(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228;
RX MEDLINE=20437337; PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T.,
RA Reizer J., Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an
RT opportunistic pathogen.";
RL Nature 406:959-964(2000).
RN [3]
RP CHARACTERIZATION.
RX MEDLINE=95286483; PubMed=7539417;
RA Wilson S.A., Drew R.E.;
RT "Transcriptional analysis of the amidase operon from Pseudomonas
RT aeruginosa.";
RL J. Bacteriol. 177:3052-3057(1995).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF COMPLEX WITH AMIC.
RC STRAIN=PAC1;
RX MEDLINE=99437995; PubMed=10508151; DOI=10.1093/emboj/18.19.5175;
RA O'Hara B.P., Norman R.A., Wan P.T., Roe S.M., Barrett T.E., Drew R.E.,
RA Pearl L.H.;
RT "Crystal structure and induction mechanism of AmiC-AmiR: a ligand-
RT regulated transcription antitermination complex.";
RL EMBO J. 18:5175-5186(1999).
CC -!- FUNCTION: Positive controlling element of amiE, the gene for
CC aliphatic amidase. Acts as a transcriptional antitermination
[Part of this file has been deleted for brevity]
CC -!- SIMILARITY: Contains 1 ANTAR domain.
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DR EMBL; X13776; CAA32023.1; -; Genomic_DNA.
DR EMBL; AE004091; AAG06751.1; -; Genomic_DNA.
DR PIR; B83226; B83226.
DR PIR; S03884; S03884.
DR PDB; 1QO0; X-ray; D/E=1-196.
DR IntAct; P10932; -.
DR GenomeReviews; AE004091_GR; PA3363.
DR KEGG; pae:PA3363; -.
DR BioCyc; PAER287:PA3363-MONOMER; -.
DR InterPro; IPR005561; AmiR_NasR_reg.
DR InterPro; IPR011006; CheY_like.
DR InterPro; IPR008327; Res_reg_antiterm.
DR Pfam; PF03861; ANTAR; 1.
DR PIRSF; PIRSF036382; RR_antiterm; 1.
DR PROSITE; PS50921; ANTAR; 1.
KW 3D-structure; Complete proteome; Transcription;
KW Transcription antitermination; Transcription regulation.
FT CHAIN 1 196 Aliphatic amidase regulator.
FT /FTId=PRO_0000064582.
FT DOMAIN 129 190 ANTAR.
FT CONFLICT 48 48 S -> A (in Ref. 1).
FT CONFLICT 64 64 R -> G (in Ref. 1).
FT CONFLICT 141 141 E -> D (in Ref. 1).
FT CONFLICT 154 154 A -> V (in Ref. 1).
FT CONFLICT 170 170 Y -> H (in Ref. 1).
FT HELIX 3 8
FT HELIX 9 12
FT STRAND 14 19
FT HELIX 23 35
FT STRAND 38 42
FT STRAND 54 59
FT HELIX 65 75
FT STRAND 81 86
FT HELIX 91 100
FT STRAND 103 109
FT HELIX 112 114
FT HELIX 115 160
FT HELIX 164 175
FT TURN 176 179
FT HELIX 182 189
SQ SEQUENCE 196 AA; 21903 MW; 306A4F30E8E4C6C0 CRC64;
MSANSLLGSL RELQVLVLNP PGEVSDALVL QLIRIGCSVR QCWPPPESFD VPVDVVFTSI
FQNRHHDEIA ALLAAGTPRT TLVALVEYES PAVLSQIIEL ECHGVITQPL DAHRVLPVLV
SARRISEEMA KLKQKTEQLQ ERIAGQARIN QAKALLMQRH GWDEREAHQY LSREAMKRRE
PILKIAQELL GNEPSA
//
|
ID FLAV_NOSSM Reviewed; 35 AA.
AC P35707;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1994, sequence version 1.
DT 31-OCT-2006, entry version 30.
DE Flavodoxin (Fragment).
OS Nostoc sp. (strain MAC).
OC Bacteria; Cyanobacteria; Nostocales; Nostocaceae; Nostoc.
OX NCBI_TaxID=35822;
RN [1]
RP PROTEIN SEQUENCE.
RA Takruri I.A.H., Boulter D., Fitzgerald M.P., Hutber G.N., Rogers L.J.;
RT "N-terminal amino acid sequences of flavodoxins from Chondrus crispus
RT and Nostoc strain MAC.";
RL Phytochemistry 25:2113-2115(1986).
CC -!- FUNCTION: Low-potential electron donor to a number of redox
CC enzymes.
CC -!- COFACTOR: FMN.
CC -!- SIMILARITY: Belongs to the flavodoxin family.
CC -!- SIMILARITY: Contains 1 flavodoxin-like domain.
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CC Distributed under the Creative Commons Attribution-NoDerivs License
CC -----------------------------------------------------------------------
DR HSSP; P11241; 1RCF.
DR InterPro; IPR001226; Flavodoxin.
DR InterPro; IPR008254; Flavodoxin_1.
DR Pfam; PF00258; Flavodoxin_1; 1.
DR PROSITE; PS00201; FLAVODOXIN; 1.
DR PROSITE; PS50902; FLAVODOXIN_LIKE; 1.
KW Direct protein sequencing; Electron transport; Flavoprotein; FMN;
KW Transport.
FT CHAIN 1 >35 Flavodoxin.
FT /FTId=PRO_0000171640.
FT DOMAIN 4 >35 Flavodoxin-like.
FT NON_TER 35 35
SQ SEQUENCE 35 AA; 3820 MW; B6EEB5CA7A45DDA6 CRC64;
SKKIGLFYGT ZTGKTESVAE IIDEFGDEVV TLDID
//
|
>AMIR_PSEAE Aliphatic amidase regulator. MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI FQNRHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAG QARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELLGNEPSA |
>AMIR_PSEAE Aliphatic amidase regulator. MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI FQNRHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAG QARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELLGNEPSA |
>AMIR_PSEAE Aliphatic amidase regulator. SKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDMSANSLLGSLRELQVLVLNPPGEVS DALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVAL VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAG QARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELLGNEPSA |
| Program name | Description |
|---|---|
| biosed | Replace or delete sequence sections |
| codcopy | Reads and writes a codon usage table |
| cutseq | Removes a specified section from a sequence |
| degapseq | Removes gap characters from sequences |
| descseq | Alter the name or description of a sequence |
| entret | Reads and writes (returns) flatfile entries |
| extractalign | Extract regions from a sequence alignment |
| extractfeat | Extract features from a sequence |
| extractseq | Extract regions from a sequence |
| listor | Write a list file of the logical OR of two sets of sequences |
| makenucseq | Creates random nucleotide sequences |
| makeprotseq | Creates random protein sequences |
| maskfeat | Mask off features of a sequence |
| maskseq | Mask off regions of a sequence |
| newseq | Type in a short new sequence |
| noreturn | Removes carriage return from ASCII files |
| notseq | Exclude a set of sequences and write out the remaining ones |
| nthseq | Writes one sequence from a multiple set of sequences |
| revseq | Reverse and complement a sequence |
| seqret | Reads and writes (returns) sequences |
| seqretsplit | Reads and writes (returns) sequences in individual files |
| skipseq | Reads and writes (returns) sequences, skipping first few |
| splitter | Split a sequence into (overlapping) smaller sequences |
| trimest | Trim poly-A tails off EST sequences |
| trimseq | Trim ambiguous bits off the ends of sequences |
| union | Reads sequence fragments and builds one sequence |
| vectorstrip | Strips out DNA between a pair of vector sequences |
| yank | Reads a sequence range, appends the full USA to a list file |