三种分析蛋白结构域(Domains)的方法

1、三种分析蛋白构造域(Domains) 的方法三种分析蛋白构造域(Domains两方法1， SMART 入门，蛋白构造和功能分析SMART介绍SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 500 domain families found in signalling, extracellular

2、and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomi

3、c information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa. For all the details, please refer to the publications on SMART.SMART()， 可以说是蛋白构造预测和功能分析的工具集合。简单点说，就是集合了一些工具，可以预测蛋白的一些二级构

4、造。如跨膜区 Transmembrane segments ,复合螺旋区coiled coil region ,信号肽Signal peptideS ,蛋白 构造域PFAM domains等。SMART 前该知道的SMART有两种不同的模式：normal或genomic主要是用的数据库不一样。Normal SMART,用的数据库Swiss-Prot,SP-TrEMBL 和 stable Ensembl proteomesGenomic SMART,用全基因组序列。详细列表：Schultz at aL (1998) P/oa. M匿t. Acad. Sa. USA 95 5857-5S64Let

5、uniQrfM-4004) Nucleic Acids Res 32, D142-D1445AQ ABOUT GLOS一些名词解释SMART进展时可以直接用各个数据库蛋白的 ID。如Uniprot/Ensembl ID / Accession number (ACC或是直接蛋白序列。运行SMART也可选择signal peptides PFAM domains等的预测，勾上就是。看以下图Letunio et alL (2008) 死而 左5 1 doi: 10.1 DSJar/gknSOSHOME SETUP FAC ABOUT GLOSSARY WHATS NEW FEEDBACKSMARG

6、ESecYou may use elltier a UniprotfEnsembl sequence Identifier CID) i accession numtj&rgCC) or sequence itself to request the ShtART service.Sequence ID or ACC0N9N1Sequ电nc。HMMER searches of the SMART data base occur by default You may also findutlierhomologues and hcmologues ofknown tNFtur& PFAM doma

7、ins signal peptides internal repeats Wins it protein disorderSMART结果运行后的结果用图表表示。其实运行后的结果都有明确的解释。 详细请看下 面。SGtiulK ef ml.。3晚Proc,他也笈Sai a 盹，5357-5604Ixlunic al 0曲抄 Fiiicaic 启幸好，fry . doi; 10.10d3iAiar/Qlfn$08二-三*受至北HOME SETIJF FAQ A日口UT GLOSSARY WHAT8 NEW FEEDBACKMouse over domain / undefined reg ion

8、for more nifo; click 口n rt to go to detailed annotation; Transmembrane segmenis as predicted by the TMM2 program （I）. called coil regions del peptides determined by the Sa/P program （）. Intron positions are indickd with 7e rti c a I不同构造的预测由不同的工具完成。 如果你想了解更多，可访问去该工具的网站。跨膜区Transmembrane segments, TMHM

9、M2 program 。（用表示）复合螺旋区coiled coil regions , Coils2 program。（用表示） 信号肽Signal peptides , SignalPprogram。（ ）? 蛋白构造域PFAM, PFAM等等。不止这几个的。其它不一一列举。因为都是详细的说明。点击图标链接， 就能看到该区域的序列，或是一些详细的描述。如上图的跨膜区，点击进去就是 该跨膜区从开场到完毕的序列。Sctiutz 国 al. (19d8 ftoc.岫4LSoi.85, 5857-S864臼1|甫心 E al. 口006) M/cAete 再oH皆 fihj4 34E D267-D2

10、601HOME SETUP FAD ADClUT CLOSSAR/ Vln-lAThG NEW FEE&DACKDomains within Homo sapiens protein NDUAfi_HUMAN (P5IMouse owr domain undefined region for moe info; click on it to go t电 detailed annctivn;Transmembrane segments aspredicteJ bytlie WHW2program (I), coiled coil regions depeptides deterniined by

11、 the Sa/P program (). Hits ontylbund by BLAST are indicated 的 covered by domains are Indicated byU Disordered regions detected byDlsEMBL(H).另外，不一定所有预测的区域都会用在图示里看到。一般SMART的显示顺序是 SMART PFAM PROSPERO repeats Signal peptide Transmembrane Coiled coil Unstructured regions Low complexity 另外其它不用图解显示的区域，在底下的

12、表格也有详细说明。Sanger)勺 Pfam 数据库目前的版本：Pfam 23.0 (July 2021, 10340 families)The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).Pfam 23.0 (July 2008f 10340 families)The Pfam datahsse is a large collection of protein f

13、amilies, each represented alignments 己nd hidden Markov models (hmms)电口日QUICK LINKSAMALYZE YOUR PROTEIN SEQUENCE F个巴UEMCE 5力对VIEW A PFAM FAMILYPaste your pQt&i门 sequence here to finYIEW A GLANVIEW A SEQUENCEVIEW A STRUCTUREKEYWORD SEARCHJUMP TOu&us rc kv&c&fsafs DimHiJ： KSLOT-Tnnrrs kks 1 TTSECUJKIEU

14、IDIEEI rEIBFCrTEEIOEKl EDHTHPH slqits irami KEmimii utp-lq lEEvumnsiqt nnm mrnmrFqifredittc41rMlWffilais CERPELCEIS UWIMfimq CfLn VDELQ T4 EFDtunu r vmf i vwcm mr owmiir mvTvwt u，Trwi This rch will usa bctfi global and lccl mode I1O1 Toy can i it your own search pdr4n-ieterf di fhrt*5 results page.j

15、r search sequence (7 significant and 8 inrignifieant) . You did not choose to ：ice that you submitted, Pfam domains on a new sequence.NCBI 的 CDDConserved Domain Database数据库Proteins often contain several modules or domains, each with a distinct evolutionary origin and function. NCBI s Conserved Domai

16、n Database is a collectionof multiple sequence alignments for ancient domains and full-length proteins.Conserved domains on 1卜7口41口=67,.1支二。Uocdl query sequtQuery seGraphical summarysite A aA abinding fp-hoplrMD-Lvro：spocket- k h 口hidr-oph obi bdnd.n- poc phoEptictyrosirifl binding pocke1!PLCcSH2p-r

17、* 1 ich 1 iecSearch for similar damain arList of domain hitsDB9crifition图卜1口口13乙 PLCa iMal/tic domwin; PlcnR。口洞口Oijd0sp&cific： Rh口hrholiT tdOO275, C2 2, Protein kinase C conserved region 2,知bgrnup 2; C2 C嵬+书Indiiig motif -H cdOI 240, PH_PLCp Phospholipase C (plc pieckstrin homology (PH) domalr. There are+ CI024Q6, PLCC Phospholipase % catalytic domain; Phosphoinaeitide-spccific phosphalii： + cd001 73, SH2hSrc hiQmolog/2 domains; Signal transduction! involved in recognition of pt+cd00173, SH2,Src hoinolog2 domains;9ignal transducti