1、三種分析蛋白構造域(Domains) 的方法三種分析蛋白構造域(Domains兩方法1， SMART 入門，蛋白構造和功能分析SMART介紹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()， 可以說是蛋白構造預測和功能分析的工具集合。簡單點說，就是集合了一些工具，可以預測蛋白的一些二級構

4、造。如跨膜區 Transmembrane segments ,復合螺旋區coiled coil region ,信號肽Signal peptideS ,蛋白 構造域PFAM domains等。SMART 前該知道的SMART有兩種不同的模式：normal或genomic主要是用的數據庫不一樣。Normal SMART,用的數據庫Swiss-Prot,SP-TrEMBL 和 stable Ensembl proteomesGenomic SMART,用全基因組序列。詳細列表：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一些名詞解釋SMART進展時可以直接用各個數據庫蛋白的 ID。如Uniprot/Ensembl ID / Accession number (ACC或是直接蛋白序列。運行SMART也可選擇signal peptides PFAM domains等的預測，勾上就是。看以下圖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電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結果運行后的結果用圖表表示。其實運行后的結果都有明確的解釋。 詳細請看下 面。SGtiulK ef ml.。3晚Proc,他也笈Sai a 盹，5357-5604Ixlunic al 0曲抄 Fiiicaic 啟幸好，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不同構造的預測由不同的工具完成。 如果你想了解更多，可訪問去該工具的網站。跨膜區Transmembrane segments, TMHM

9、M2 program 。（用表示）復合螺旋區coiled coil regions , Coils2 program。（用表示） 信號肽Signal peptides , SignalPprogram。（ ）? 蛋白構造域PFAM, PFAM等等。不止這幾個的。其它不一一列舉。因為都是詳細的說明。點擊圖標鏈接， 就能看到該區域的序列，或是一些詳細的描述。如上圖的跨膜區，點擊進去就是 該跨膜區從開場到完畢的序列。Sctiutz 國 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電 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，不一定所有預測的區域都會用在圖示里看到。一般SMART的顯示順序是 SMART PFAM PROSPERO repeats Signal peptide Transmembrane Coiled coil Unstructured regions Low complexity 另外其它不用圖解顯示的區域，在底下的

12、表格也有詳細說明。Sanger)勺 Pfam 數據庫目前的版本：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)電口日QUICK LINKSAMALYZE YOUR PROTEIN SEQUENCE F個巴UEMCE 5力對VIEW A PFAM FAMILYPaste your pQt&i門 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數據庫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圖卜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+書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