Regex 过滤UniProt dat.-文件中的氨基酸序列
下面是我的输入示例：Regex 过滤UniProt dat.-文件中的氨基酸序列,regex,python-3.x,Regex,Python 3.x,下面是我的输入示例： ID CAR16_HUMAN Reviewed; 197 AA. AC Q5EG05; Q96RJ9; DT 02-SEP-2008, integrated into UniProtKB/Swiss-Prot. DT 15-MAR-2005, sequence version 1. DT 26-FEB-2020, entry version 116. DE RecName: Full=Caspase recru
ID CAR16_HUMAN Reviewed; 197 AA.
AC Q5EG05; Q96RJ9;
DT 02-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2005, sequence version 1.
DT 26-FEB-2020, entry version 116.
DE RecName: Full=Caspase recruitment domain-containing protein 16;
DE AltName: Full=Caspase recruitment domain-only protein 1;
DE Short=CARD-only protein 1;
DE AltName: Full=Caspase-1 inhibitor COP;
DE AltName: Full=Pseudo interleukin-1 beta converting enzyme;
DE Short=Pseudo-ICE;
DE Short=Pseudo-IL1B-converting enzyme;
GN Name=CARD16; Synonyms=COP, COP1;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION, TISSUE SPECIFICITY, AND
RP INTERACTION WITH CASP1 AND RIPK2.
RX PubMed=11536016; DOI=10.1038/sj.cdd.4400881;
RA Druilhe A., Srinivasula S.M., Razmara M., Ahmad M., Alnemri E.S.;
RT "Regulation of IL-1beta generation by Pseudo-ICE and ICEBERG, two dominant
RT negative caspase recruitment domain proteins.";
RL Cell Death Differ. 8:649-657(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RA Wang P.Z., Wang F., Wang X., Wu J.;
RT "Novel splicing variants of some human genes.";
RL Submitted (JAN-2005) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Spleen;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [6]
RP FUNCTION, TISSUE SPECIFICITY, SUBUNIT, AND INTERACTION WITH CASP1 AND
RP RIPK2.
RX PubMed=11432859; DOI=10.1074/jbc.m101415200;
RA Lee S.H., Stehlik C., Reed J.C.;
RT "Cop, a caspase recruitment domain-containing protein and inhibitor of
RT caspase-1 activation processing.";
RL J. Biol. Chem. 276:34495-34500(2001).
RN [7]
RP INTERACTION WITH CARD8.
RX PubMed=11821383; DOI=10.1074/jbc.m107811200;
RA Razmara M., Srinivasula S.M., Wang L., Poyet J.-L., Geddes B.J.,
RA DiStefano P.S., Bertin J., Alnemri E.S.;
RT "CARD-8 protein, a new CARD family member that regulates caspase-1
RT activation and apoptosis.";
RL J. Biol. Chem. 277:13952-13958(2002).
RN [8]
RP INDUCTION.
RX PubMed=16354923; DOI=10.1523/jneurosci.4181-05.2005;
RA Wang X., Wang H., Figueroa B.E., Zhang W.-H., Huo C., Guan Y., Zhang Y.,
RA Bruey J.-M., Reed J.C., Friedlander R.M.;
RT "Dysregulation of receptor interacting protein-2 and caspase recruitment
RT domain only protein mediates aberrant caspase-1 activation in Huntington's
RT disease.";
RL J. Neurosci. 25:11645-11654(2005).
RN [9]
RP FUNCTION, AND INTERACTION WITH CASP4.
RX PubMed=16920334; DOI=10.1016/j.bbadis.2006.06.015;
RA Wang X., Narayanan M., Bruey J.-M., Rigamonti D., Cattaneo E., Reed J.C.,
RA Friedlander R.M.;
RT "Protective role of Cop in Rip2/caspase-1/caspase-4-mediated HeLa cell
RT death.";
RL Biochim. Biophys. Acta 1762:742-754(2006).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
CC -!- FUNCTION: Caspase inhibitor. Acts as a regulator of procaspase-1/CASP1
CC activation implicated in the regulation of the proteolytic maturation
CC of pro-interleukin-1 beta (IL1B) and its release during inflammation.
CC Inhibits the release of IL1B in response to LPS in monocytes. Also
CC induces NF-kappa-B activation during the pro-inflammatory cytokine
CC response. Also able to inhibit CASP1-mediated neuronal cell death, TNF-
CC alpha, hypoxia-, UV-, and staurosporine-mediated cell death but not ER
CC stress-mediated cell death. Acts by preventing activation of caspases
CC CASP1 and CASP4, possibly by preventing the interaction between CASP1
CC and RIPK2. {ECO:0000269|PubMed:11432859, ECO:0000269|PubMed:11536016,
CC ECO:0000269|PubMed:16920334}.
CC -!- SUBUNIT: Homooligomer. Interacts with CASP1, CASP4, CARD8 and RIPK2.
CC {ECO:0000269|PubMed:11432859, ECO:0000269|PubMed:11536016,
CC ECO:0000269|PubMed:11821383, ECO:0000269|PubMed:16920334}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q5EG05-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q5EG05-2; Sequence=VSP_035216;
CC -!- TISSUE SPECIFICITY: Widely expressed. Expressed at higher level in
CC placenta, spleen, lymph node and bone marrow. Weakly or not expressed
CC in thymus. {ECO:0000269|PubMed:11432859, ECO:0000269|PubMed:11536016}.
CC -!- INDUCTION: Down-regulated in patients suffering of Huntington disease.
CC {ECO:0000269|PubMed:16354923}.
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DR EMBL; AF367017; AAK71682.1; -; mRNA.
DR EMBL; AY885669; AAW78563.1; -; mRNA.
DR EMBL; AK311902; BAG34843.1; -; mRNA.
DR EMBL; CH471065; EAW67062.1; -; Genomic_DNA.
DR EMBL; BC117478; AAI17479.1; -; mRNA.
DR EMBL; BC117480; AAI17481.1; -; mRNA.
DR CCDS; CCDS31661.1; -. [Q5EG05-1]
DR CCDS; CCDS41705.1; -. [Q5EG05-2]
DR RefSeq; NP_001017534.1; NM_001017534.1. [Q5EG05-1]
DR RefSeq; NP_443121.1; NM_052889.2. [Q5EG05-2]
DR SMR; Q5EG05; -.
DR BioGrid; 125339; 3.
DR IntAct; Q5EG05; 1.
DR MINT; Q5EG05; -.
DR STRING; 9606.ENSP00000364858; -.
DR iPTMnet; Q5EG05; -.
DR PhosphoSitePlus; Q5EG05; -.
DR BioMuta; CARD16; -.
DR DMDM; 74722547; -.
DR jPOST; Q5EG05; -.
DR MassIVE; Q5EG05; -.
DR MaxQB; Q5EG05; -.
DR PaxDb; Q5EG05; -.
DR PeptideAtlas; Q5EG05; -.
DR PRIDE; Q5EG05; -.
DR ProteomicsDB; 62773; -. [Q5EG05-1]
DR ProteomicsDB; 62774; -. [Q5EG05-2]
DR Ensembl; ENST00000375706; ENSP00000364858; ENSG00000204397. [Q5EG05-1]
DR Ensembl; ENST00000375704; ENSP00000364856; ENSG00000204397. [Q5EG05-2]
DR GeneID; 114769; -.
DR KEGG; hsa:114769; -.
DR UCSC; uc001pio.2; human. [Q5EG05-1]
DR CTD; 114769; -.
DR DisGeNET; 114769; -.
DR GeneCards; CARD16; -.
DR HGNC; HGNC:33701; CARD16.
DR HPA; HPA053981; -.
DR HPA; HPA062805; -.
DR MIM; 615680; gene.
DR neXtProt; NX_Q5EG05; -.
DR OpenTargets; ENSG00000204397; -.
DR PharmGKB; PA164717628; -.
DR eggNOG; KOG3573; Eukaryota.
DR eggNOG; ENOG410ZQIE; LUCA.
DR GeneTree; ENSGT00940000159114; -.
DR HOGENOM; CLU_119795_0_0_1; -.
DR InParanoid; Q5EG05; -.
DR KO; K12806; -.
DR OMA; CITDICE; -.
DR OrthoDB; 1327703at2759; -.
DR PhylomeDB; Q5EG05; -.
DR TreeFam; TF330675; -.
DR GeneWiki; COP1; -.
DR GenomeRNAi; 114769; -.
DR Pharos; Q5EG05; Tbio.
DR PRO; PR:Q5EG05; -.
DR Proteomes; UP000005640; Chromosome 11.
DR RNAct; Q5EG05; protein.
DR Bgee; ENSG00000204397; Expressed in leukocyte and 170 other tissues.
DR Genevisible; Q5EG05; HS.
DR GO; GO:0097179; C:protease inhibitor complex; IDA:UniProtKB.
DR GO; GO:0032991; C:protein-containing complex; IDA:UniProtKB.
DR GO; GO:0050700; F:CARD domain binding; IPI:UniProtKB.
DR GO; GO:0089720; F:caspase binding; IPI:UniProtKB.
DR GO; GO:0004869; F:cysteine-type endopeptidase inhibitor activity; IDA:UniProtKB.
DR GO; GO:0042802; F:identical protein binding; IDA:UniProtKB.
DR GO; GO:0019900; F:kinase binding; IPI:UniProtKB.
DR GO; GO:0071456; P:cellular response to hypoxia; IDA:UniProtKB.
DR GO; GO:0071222; P:cellular response to lipopolysaccharide; IDA:UniProtKB.
DR GO; GO:0071494; P:cellular response to UV-C; IDA:UniProtKB.
DR GO; GO:0097340; P:inhibition of cysteine-type endopeptidase activity; IDA:UniProtKB.
DR GO; GO:0043154; P:negative regulation of cysteine-type endopeptidase activity involved in apoptotic process; IDA:UniProtKB.
DR GO; GO:0050713; P:negative regulation of interleukin-1 beta secretion; IDA:UniProtKB.
DR GO; GO:0031665; P:negative regulation of lipopolysaccharide-mediated signaling pathway; IDA:UniProtKB.
DR GO; GO:0032091; P:negative regulation of protein binding; IDA:UniProtKB.
DR GO; GO:0010804; P:negative regulation of tumor necrosis factor-mediated signaling pathway; IMP:UniProtKB.
DR GO; GO:0043123; P:positive regulation of I-kappaB kinase/NF-kappaB signaling; IDA:UniProtKB.
DR GO; GO:0051092; P:positive regulation of NF-kappaB transcription factor activity; IDA:UniProtKB.
DR InterPro; IPR001315; CARD.
DR InterPro; IPR011029; DEATH-like_dom_sf.
DR Pfam; PF00619; CARD; 1.
DR SMART; SM00114; CARD; 1.
DR SUPFAM; SSF47986; SSF47986; 1.
DR PROSITE; PS50209; CARD; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Polymorphism; Protease inhibitor; Reference proteome;
KW Thiol protease inhibitor.
FT CHAIN 1..197
FT /note="Caspase recruitment domain-containing protein 16"
FT /id="PRO_0000349180"
FT DOMAIN 1..91
FT /note="CARD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00046"
FT VAR_SEQ 92..197
FT /note="ALQAVQDNPAMPTCSSPEGRIKLCFLEDAQRIWKQKLQRCHVQNTIIKWSER
FT YTSGSFEMQWLFLRTNFIERFWRNILLLPLHKGSLYPRIPGLGKELQTGTHKLS -> G
FT PIPGN (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:11536016,
FT ECO:0000303|PubMed:14702039, ECO:0000303|PubMed:15489334"
FT /id="VSP_035216"
FT VARIANT 33
FT /note="R -> S (in dbSNP:rs35966314)"
FT /id="VAR_046279"
FT VARIANT 37
FT /note="Q -> K (in dbSNP:rs1042744)"
FT /id="VAR_046280"
FT VARIANT 56
FT /note="A -> D (in dbSNP:rs34534919)"
FT /id="VAR_046281"
FT VARIANT 167
FT /note="N -> I (in dbSNP:rs542571)"
FT /id="VAR_046282"
SQ SEQUENCE 197 AA; 22625 MW; 5DCAC6A9B2FAE82F CRC64;
MADKVLKEKR KLFIHSMGEG TINGLLDELL QTRVLNQEEM EKVKRENATV MDKTRALIDS
VIPKGAQACQ ICITYICEED SYLAETLGLS AALQAVQDNP AMPTCSSPEG RIKLCFLEDA
QRIWKQKLQR CHVQNTIIKW SERYTSGSFE MQWLFLRTNF IERFWRNILL LPLHKGSLYP
RIPGLGKELQ TGTHKLS
//
我的想法是在SQ之后使用正则表达式（？我们可以尝试使用
re.findall['MADKVLKEKR', 'KLFIHSMGEG', 'TINGLLDELL', 'QTRVLNQEEM', 'EKVKRENATV',
'MDKTRALIDS', 'VIPKGAQACQ', 'ICITYICEED', 'SYLAETLGLS', 'AALQAVQDNP',
'AMPTCSSPEG', 'RIKLCFLEDA', 'QRIWKQKLQR', 'CHVQNTIIKW', 'SERYTSGSFE',
'MQWLFLRTNF', 'IERFWRNILL', 'LPLHKGSLYP', 'RIPGLGKELQ', 'TGTHKLS']
这里的策略是首先分离文本的结尾部分，以
SQ序列开始re.findall MADKVLKEKR KLFIHSMGEG TINGLLDELL QTRVLNQEEM EKVKRENATV MDKTRALIDS
VIPKGAQACQ ICITYICEED SYLAETLGLS AALQAVQDNP AMPTCSSPEG RIKLCFLEDA
QRIWKQKLQR CHVQNTIIKW SERYTSGSFE MQWLFLRTNF IERFWRNILL LPLHKGSLYP
RIPGLGKELQ TGTHKLS
inp = "..."
sq = re.findall(r'SQ\s+SEQUENCE(.*?;.*?;.*?;.*?[A-Z]{5,}(?:\s+[A-Z]{5,})*)', inp, flags=re.DOTALL)[0]
matches = re.findall(r'\b[A-Z]{5,}\b', sq, flags=re.DOTALL)
print(matches)
['MADKVLKEKR', 'KLFIHSMGEG', 'TINGLLDELL', 'QTRVLNQEEM', 'EKVKRENATV',
'MDKTRALIDS', 'VIPKGAQACQ', 'ICITYICEED', 'SYLAETLGLS', 'AALQAVQDNP',
'AMPTCSSPEG', 'RIKLCFLEDA', 'QRIWKQKLQR', 'CHVQNTIIKW', 'SERYTSGSFE',
'MQWLFLRTNF', 'IERFWRNILL', 'LPLHKGSLYP', 'RIPGLGKELQ', 'TGTHKLS']