Rap – a putative rna-binding domain – documents

epithelial cells by association between vinculin and the Shigella IpaA

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2Membrane Biology Lab, Institute of Molecular and Cell Biology

2 Johnson, R.P. Chicken gizzard nutrition and Craig, S.W. Chicken gizzard recipe chinese (1995) The carboxy-terminal tail

domain of vinculin contains a cryptic binding site for acidic

3 Gilmore, A.P. Best chicken gizzard recipe and Burridge, K. Chicken gizzard soup (1996) Regulation of vinculin binding

to talin and actin by phosphatidyl-inositol-4-5-bisphosphate. Chicken gizzard stew Nature

4 Weekes, J. Chicken liver and gizzard recipe et al. Gizzard of chicken (1996) Acidic phospholipids inhibit the intramolecular

association between the N- and C-terminal regions of vinculin,

exposing actin-binding and protein kinase C phosphorylation sites.

5 Zamir, E. Gizzard chicken recipe and Geiger, B. Chicken liver and gizzard (2001) Molecular complexity and dynamics of

16 Bourdet-Sicard, R. Boiled chicken gizzard recipe et al. Pickled chicken gizzard recipe (1999) Binding of the Shigella protein IpaA to

vinculin induces F-actin depolymerization. Chicken gizzard recipes tenderizing EMBO J. Chicken gizzard indian recipe 18, 5853a??5862

17 Critchley, D.R. Spicy chicken gizzard recipe (2000) Focal adhesion a?? the cytoskeletal connection.

18 DeMali, K.A. Recipe for chicken liver and gizzard and Burridge, K. Chicken gizzard salad (2003) Coupling membrane protrusion

19 Subauste, M.C. Chicken gizzard soup recipe et al. Gizzard of a chicken (2004) Vinculin modulation of paxillina??FAK

interactions regulates ERK to control survival and motility.


Chicken gizzard and liver recipe J. Easy chicken gizzard recipe Cell

0968-0004/$ – see front matter Q 2004 Elsevier Ltd. Gizzard in chicken All rights reserved.

as visualized by high-resolution electron microscopy. Chinese chicken gizzard recipe J. Chicken gizzard benefits Struct. Chicken gizzard fried Biol.

1 Winkler, J. What is a chicken gizzard et al. Quick chicken gizzard recipe (1996) The ultrastructure of chicken gizzard vinculin

vinculin activation by talin. Chicken gizzard curry J. Portuguese chicken gizzard recipe Biol. Chicken gizzard in chinese Chem. Chicken gizzard cooked 279, 27667a??27678

15 Tran Van Nhieu, G. Chicken liver gizzard recipe et al. Best fried chicken gizzard recipe (1997) Modulation of bacterial entry into

I thank Ernesto Fuentes, Mike Schaller and Keith Burridge for their

6 Burridge, K. Simple chicken gizzard recipe and Mangeat, P. Chicken gizzard gravy (1984) An interaction between vinculin

7 Weiss, E.E. Chicken gizzard protein et al. Chicken gizzard chinese recipe (1998) Vinculin is part of the cadherina??catenin

junctional complex: complex formation between a-catenin and vincu-

8 Izard, T. Chicken gizzard cholesterol et al. Chicken gizzard price (2004) Vinculin activation by talin through helical

9 Bakolitsa, C. Chicken gizzard plant et al. Chicken gizzard stuffing (2004) Structural basis for vinculin activation at

10 Borgon, R.A. Chicken gizzard fry indian recipe et al. Chicken gizzard anatomy (2004) Crystal structure of human vinculin.

11 Bakolitsa, C. Chicken gizzard marinade et al. Chicken gizzard stir fry (1999) Crystal structure of the vinculin tail

12 DeMali, K.A. Chicken gizzard fry et al. Chicken gizzard filipino recipe (2002) Recruitment of the Arp2/3 complex to

vinculin: coupling membrane protrusion to matrix adhesion. Healthy chicken gizzard recipe J. Chicken gizzard recipe korean Cell

13 Bass, M.D. Chicken express fried chicken gizzard et al. What part of the chicken is the gizzard (1999) Talin contains three similar vinculin-binding

sites predicted to form an amphipathic helix. Chicken gizzard stew recipe Biochem. Baked chicken gizzard recipe J. Chicken gizzard location 341, 257a??263

14 Izard, T. Chicken gizzard adobo recipe and Vonrhein, C. Korean chicken gizzard (2004) Structural basis for amplifying

KIAA1792 Hs gi14017801 741-801 LAVQFTNRNQY-(8)-GLHNMKRRQLARLGYRVVELSYWEWLPLRTRLEKLAFLHE

Tbrg4 Hs gi21739306 561-619 LAFLRWEFPNF-(8)-GRFVLARRHIVAAGFLIVDVPFYEWLELKSEWQKGAYLKD

At2g31890 At gi30685105 607-665 VALEIDGPTHF-(8)-GHTMLKRRYVAAAGWKVVSLSLQEWEEHEGSHEQLEYLRE

OSJNBa0032H19.2 Os gi30089729 575-632 LAFEIDGPSHF-(8)-GHTAFKRRYIAAAGWNLVSLSHQEWENLEGEFEQLEYLRR

MGC5297 Hs gi40068497 591-649 IALCIDGPKRF-(8)-GKEAIKQRHLQLLGYQVVQIPYHEIGMLKSRRELVEYLQR

FAST Hs gi5729822 477-535 VVLVLRERWHF-(8)-GSRALRERHLGLMGYQLLPLPFEELESQRGLPQLKSYLRQ

GH07286p Dm gi16197813 496-555 VALMVIDFHDI-(9)-GVTNLTFDLLEKSGYHVIPVPYNEFSTSDKLLKRVQYLES

RIK5330408N05 Hs gi16550732 734-794 IALEFLDSKAL-(8)-GKSAMKKRHLEILGYRVIQISQFEWNSMSTKDARMDYLRE

CG31643PA Dm gi24582106 832-893 VAILLLKLDSF-(9)-GPESLKMRHLEMMGYKVMQINEHDWNSKASSTAKANYLKC

RIK281042lI24 Hs gi7578791 634-691 VAVLCVSRSAY-(8)-GFLAMKMRHLNAMGFHVILVNNWEMDKLEME-DAVTFLKT

PF14_0509 Pf gi23509731 1658-1716 VLNEMQKADPQ-(9)-GTTIFKHWLLQKSGWSIINVTSFEWNKINKD-EKKKHIIK

PFE0800w Pf gi23613182 1116-1175 IFGKEYLMRTL-(10)GIVTLQMRILHAHGWKIIPINAGEWLQLNFD-QKKNLLSE

PF10_0064 Pf gi23507868 805-862 NDVLYNPYKTF-(8)-SNVLVKINFLLIKGYNIIAIPFYTWRNMSYE-EKEKHVEL

PFL0605c Pf gi23508818 644-704 IFLQFENQWKL-(10)NFEMNKMNHLKKEGFKPIFICHDTFLKCKEEQEKLEYIHS

PFE0905w Pf gi23613203 1308-1368 IVIEIDGPNHF-(8)-SNTLFKKRLLRALGYTVISVPISDYTFMFSALDTMHFTKR

PFL1280w Pf gi23508950 1281-1339 IVIEVDGISHF-(7)-TNSVIKDYILKKLGWNVIHIPYQEWNQCFTFKKKVLYAIE

PF14_0673 Pf gi23509895 433-491 IAIEVDGPSHF-(8)-TYTKLKHRILTKLGYNVIHISYIDWRKLRNKSEREEFILK

PF13_0292 Pf gi23619474 892-950 LIIEVNGEHHF-(7)-SLSKFKHKLLSDLGYVVINIPYFDWAILNTDFDKKAYIKK

PF11_0247 Pf gi23508438 635-692 YIIELNAHFQY-(8)-TLSKWRHKFLSQMGYKVIHISYRIWNNLHNDTQKMEYIYS

PFE1295c Pf gi23613281 736-791 LINKTSSNQHT-(7)–NTKYKKWLLSNYPFHIIYIPYYKWNML-THKQKK-YLME

MAL6P1.211 Pf gi23612295 1542-1600 HLIDLIYEDVL-(8)-SSE-LRQKHLALKGWTVHSINFRDIYNSIKDKNIISYIFN

Raa3 Cr gi20532239 1713-1772 LAVGAAAGGAV-(9)-GAGALRRRLLTHAGWLVVPVRERQWKDLRSAEQQRRVVRE

CG2124PA Dm gi18858071 563-623 VVIVIAGWNNV-(8)-GQMDMKLRQLRQLGHQPLVIYWHEWRELENSADRQDFLKR

Consensus/80% hh..h.s…b…..s…b+b+bL..bGapll.l.bbpW.ph….pp..albp

995368_1998761.053.1 Tg VALDLLSEGNY-(8)-GVARLKRRHMKILGWKYVDVRRKTWLKLRTREERCNALRD

995363.178.1 Tg VQF-LDDETKI-(10)TPHIIKARHLKQLGYHYLLVDCWQWRRLRSEAEQTVFLKQ

995283.053.1 Tg VW-QCNTADRF-(8)-TAVKLQERITQAMGLKVGNCEYWQWMKMKRKRTRLEYIRM

994720.098.1 Tg TVDMFHASQTV-(16)TALKRRHQLLLSMGFKLVLVPHQRWGSLQTEEKKLLFLLP

995364_0.074.1 Tg FRDPEGAEIEL—–TAWTLRHELLHAQGWCVVAIPHFEWTALPDRLTRLRYLQR

995368_3464634.010.1 Tg EEKLLSSTGGV-(14)PSDLLKHRHLRLAGYTLLVIRLSQWQALDTVTEKREYIVS

995366_2595624.041.1 Tg QCWFVDGPSDF-(7)-TANKLQHRILSELGWNIRRVRWNDWVQLGTDMDKVEYLS-

995373.113.1 Tg IAIEVDGPTHF-(7)-TATKLKHRLLTRMGYKVLHVPYFEWRRLRGQKEREEYMRR

995363.185.1 Tg LAVEIDGPSHF-(7)-VASRLKQRLLREMGWTVLPVSFFEWRQLVTPERKVAY—

995368_0.144.1 Tg LVVEVDGEAHF-(7)-TATRMKRELLAAMGWRVVVVPQELWRN-KRKGKIKEFVAR

995362_1355687.059.1 Tg GEISLDNAVPQ-(6)-DSTRLKHRILTGAGWHVLHIAWFDWPR–RPHNQQAALMQ

995362_0.025.1 Tg VLGEKDGLKTL-(10)GVNLLRLRALKKRGWQIVTVNVHEWSEAQTPDNRLSLLLD

995361_1370831.051.1 Tg ILLPE–KKTV-(16)TASRLQQRLLELQGYSVCVLPYYEWSELQNPRFLWTFGRR

995279_0.075.1 Tg TSQHH-RWRGLa??(5)-TSSLFKQRLLERHGFRVVRIAYSDWMRLRDRPWLLKRLSP

995367.221.1 Tg RIAREEATKNL-(5)-PETKARLTHLKELGWRVLVVHYRDWTAINSPLSKAKFVRS

Tap787h09.q1kb.349 Ta MCIDILSKGSV-(8)-GSVNMTERHMNILGYKYIKIRKEEW—————

Tap579b07.q1c.217c Ta LVSFVDDERKL-(10)SNLSLKLRNLNALGYKASVVRYWEWRRLKTEKNELKYAFR

Tap579b07.q1c.64 Ta IAIEVDGPSHF-(7)-TATKLKHRLLTRMGYKVLHVPFFEWRRLRGAREREEYMRA

TapCf4.q1c.31c Ta FFIEIDGPYHY-(8)-SSSKAKHYIIESYGTKLVHIPYFEWSKCVGDEEKIKYIES

Tap821d03.p1c.86c Ta VAIEVNGYTHF-(8)-ALTQLKYKILKDMGWNVVGINYYNWKN-RNKQSRLDYIVK

Tap404f10.p1c.195 Ta LVWLCNSYHRF-(8)-ANSKLLTKLIKAFGYKVSVINYYQWGRMKCKRTRFAFLRM

TapCf4.q1c.54 Ta NRKLCFEYNYL-(11)GLVSFRRRLFNKFGYNTAVIHRHQWENLTI-LEKEEQLLQ

Tap404f10.p1c.206c Ta LLDENCDGEGI-(11)GKTIYRNNILSKLGYKLVSIPWFVIHQYNND-NVYNYVKD

Secretory_protein Ta gi46195393 201-270 NCWFIDGPSCF-(7)-TKVKLQHRILNNLGWNIRRVQWYKWVDYMNDEDKINYIRK

Figure 1. Chicken gizzard recipes slow cooker Multiple alignment and species distribution of the RAP (for RNA-binding domain abundant in Apicomplexans) domain. Chicken gizzard recipe south indian (a) Multiple sequence alignment of RAP

domains generated by CLUSTAL W [5] and annotated with CHROMA [17]. Chicken gizzard aralia Domains were identified by PSI-BLAST [2] and the secondary structure predicted using PHD [6] is

shown after the alignment (E, b strand; H, a helix). Chicken gizzard calories Sequences are denoted by protein, gene, complementary DNA or contig identifiers followed by species abbreviation,

accession codes and residue limits. Chicken gizzard recipe indian Residues are colored according to the 80% concensus sequence: orange against yellow, hydrophobic (ACLIVMHYFW); black against

yellow, aliphatic (ILV); blue against yellow, aromatic (FYHW); white against green, large (EFHIKLMQRWY); charged, cyan (KRED); blue, polar (KRHEDNST); red, tiny or small

(AGS). How to cook chicken liver and gizzard Invariant residues are colored against a gray background. Grilled chicken gizzard recipe Numbers in parenthesis represent amino acids not shown between alignment blocks. Puerto rican chicken gizzard recipe Species

abbreviations: At, Arabidopsis thaliana; Cr, Chlamydomonas reinhardtii; Dm, Drosophila melanogaster; Hs, Homo sapiens; Mm, Mus musculus; Os, Oryza sativa; Pf,

Plasmodium falciparum 3D7; Pyy, Plasmodium yoelli yoelli; Ta, Theileria annulata; Tg, Toxoplasma gondii. Chicken gizzard recipe panlasang pinoy Alignment of six-frame translated T. Korean chicken gizzard recipe annulata expressed

sequence tags and T. Deep fried chicken gizzard recipe gondii peptide data detected by HMMsearch. Chicken gizzard nutrition facts (b) Distribution of RAP proteins detected in completely sequenced genomes. Is chicken gizzard healthy Proteome sizes are

Update TRENDS in Biochemical Sciences Vol.29 No.11 November 2004568

Update TRENDS in Biochemical Sciences Vol.29 No.11 November 2004 569

Figure 2. What is a gizzard on a chicken Domain architecture of RAP (for RNA-binding domain abundant in Apicomp

(dark blue square) proteins determined through a local RPS-BLAST (http://www.ncbi.nlm

downloaded from the NCBI conserved domain database resource [18] (version 1.66; ftp

PFAM [19] and SMART [20] domain databases. Chicken gizzard slow cooker recipe Searches were repeated on BLASTP-ident

MGC5297, an otherwise undetected RNA polymerase III complex component C34 (PFA

putative mouse ortholog (gi26328905; BLASTP E valueZ0.0). What is a gizzard in a chicken PT (PFAM03247) refers to

bodies involved in 3 0 cleavage and polyadenylation of RNA. Whats a chicken gizzard Cwc15 (PFAM04889) refer

(PFAM03867) refers to the LxxLL-motif-containing nuclear co-activator. Chicken gizzard korean POX G5 (PFA

topoisomerase-like sequence present in poxvirus proteins. Chicken gizzard salad recipe ActA (PFAM05058) refers to a

refers to a domain resembling that of the bacterial glucose-inhibited division protein, G

Rivier et al. Chicken gizzard sisig recipe [8]. Chicken gizzard recipe kerala style (a) The Fas-activated serine/threonine kinase (FAST) family of cell-cycle re

interactions with BCL-XL [13], giving confidence about its boundaries and making it unlik

expression profiles generated from high-throughput proteomic techniques [15,16]. What part of the chicken is a gizzard (b) Pu

infection proteins that are salient at tropozoite and gametocyte stages. What is the gizzard of a chicken (d) PFE1295c is pa

proteins that have not been categorized due to unavailability of DNA expression profile

lexans) domain-containing proteins. Chicken gizzard stew slow cooker Schematic representation of the RAP-domain

.nih.gov/Structure/cdd/wrpsb.cgi) search against position-specific scoring matrices

://ftp.ncbi.nih.gov/pub/mmdb/cdd/cdd.tar.gz) as well as online searches against the

ified orthologs of RAP proteins (E value!10a??12, data not shown). Is chicken gizzard healthy to eat For Homo sapiens

M05158) was assigned based on a significant hit in a corresponding region of its

a sequence in prothymosin a a?? a nuclear protein that is co-localized with cleavage

s to a component of a multi-protein complex involved in pre-mRNA splicing. What part of a chicken is the gizzard FTZ

M04599) is a sequence in poxviruses. Chicken gizzard gravy recipe DNATop (SMART00435) refers to a DNA

domain in Listeriamonocytogenes ActA involved in cell motility. Chicken gizzard recipes indian style GIDA (PFAM01134)

idA. Chicken gizzard health benefits PDX refers to a pyridoxamine 50 phosphate oxidase-like sequence assigned by

gulators. What’s a chicken gizzard Functional sites flanking the RAP domain were found to be essential for its

ely to be an extension of the FAST domain. Chicken gizzard adobo (ba??e) Plasmodium proteins grouped by

tativemaintenance proteins that are expressed at all developmental stages. What does a chicken gizzard do (c) Post-

rt of a cluster of proteins expressed primarily in the tropozoite stage. Gizzard chicken part (e) Plasmodium

14 Anderson, P. Aralia chicken gizzard and Kedersha, N. What is the chicken gizzard (2002) Stressful initiations. Function of gizzard in chicken J. Chicken gizzard function Cell Sci.

17 Goodstadt, L. Chicken liver and gizzard adobo and Ponting, C.P. Chicken gizzard definition (2001) CHROMA: consensus-based

Update TRENDS in Biochemical Sciences Vol.29 No.11 November 2004570

catalytic site of PDX and is not essential for trans-splicing

ultimately, viral replication. Chicken gizzard uk Stalled translation initiation

coloring of multiple alignments for publication. Where is the chicken gizzard located Bioinformatics 17,

18 Marchler-Bauer, A. Chicken gizzard curry recipe et al. Chicken liver and gizzard recipe indian (2003) CDD: a curated Entrez database of

conserved domain alignments. Where is the gizzard on a chicken Nucleic Acids Res. Where is a chicken gizzard located 31, 383a??387

19 Bateman, A. What part of chicken is gizzard et al. What is a gizzard chicken (2000) The PFAM protein families database.Nucleic

20 Schultz, J. Chicken gizzard nutritional value et al. Is chicken gizzard good for you (1998) SMART, a simple modular architecture

research tool: identification of signaling domains. Chicken gizzard masala Proc. What part of chicken is the gizzard Natl. What part is the chicken gizzard Acad.

0968-0004/$ – see front matter Q 2004 Elsevier Ltd. Chicken gizzard pate All rights reserved.

15 Le Roch, K.G. What is gizzard of chicken et al. Function of chicken gizzard (2003) Discovery of gene function by expression

profiling of the malaria parasite life cycle. Chicken gizzard cooking time Science 301, 1503a??1508

16 Florens, L. Chicken gizzard images et al. What is the function of a chicken gizzard (2002) A proteomic view of the Plasmodium

proliferation within host cells and the last in proliferation

We acknowledge equipment support from the Bioinformatics Institute in

the form of a powerful Linux workstation on which various bioinformatics

1 Yeats, C. Where is the gizzard located on a chicken and Bateman, A. How to clean a chicken gizzard (2003) The Bon domain: a putative

2 Altschul, S.F. Gizzard function in chicken et al. What part of the chicken does the gizzard come from (1997) Gapped BLAST and PSI-BLAST: a new

generation of protein database search programs. What is the purpose of a chicken gizzard Nucleic Acids Res.

3 Neuwald, A.F. What does a chicken gizzard look like et al. Adobo chicken liver and gizzard (1997) Extracting protein alignment models from

4 Eddy, S.R. What part is a chicken gizzard (1998) Profile hidden Markov models. Chicken gizzard in spanish Bioinformatics 14,

5 Thompson, J.D. Chicken gizzard nutritional info et al. Chicken gizzard aralia plant (1994) CLUSTALW: improving the sensitivity of

progressive multiple sequence alignment through sequence weight-

ing, position-specific gap penalties and weight matrix choice. What is a chicken gizzards function Nucleic

6 Rost, B. What does the gizzard do in a chicken (1996) PHD: predicting one-dimensional protein structure by

profile based neural networks. Chicken gizzard dog treats (1996).Methods Enzymol. Purpose of chicken gizzard 266, 525a??539

7 Rivier, C. Calories chicken gizzards et al. Calories in chicken gizzards (2001) Identification of an RNAa??protein complex in

chloroplast group II intron trans-splicing in Chlamydomonas rein-

8 Furuyama, S. Health benefits of eating chicken gizzard and Bruzik, J.P. Recipe for pickled chicken gizzards (2002) Multiple roles for SR proteins in

9 Min, H. Chicken gizzards rice and gravy et al. Chicken gizzards pressure cooker (1997) A new regulatory protein, KSRP, mediates

exon inclusion through an intronic splicing enhancer. Fried chicken gizzards nutrition Genes Dev. Baked chicken gizzards and hearts recipes 11,

10 Ismaili, N. Fried chicken gizzards calories et al. Calories fried chicken gizzards (1999) Characterization of a SR protein from

11 Ismaili, N. Chicken gizzard plant care et al. Recipe for deep fried chicken gizzards (2000) Characterization of a Trypanosoma brucei

SR-domain containing protein bearing homology to cis-spliceosomal

12 Tange, T.O. Baked chicken gizzards and Kjems, J. Nutritional value of chicken gizzards (2001) SF2/ASF binds to a splicing enhancer

in the third HIV-1 Tat exon and stimulates U2AF binding indepen-

13 Li, W. Chicken gizzards in pressure cooker et al. How many calories in fried chicken gizzards (2004) FAST is a BCL-XL-associated mitochondrial

The Jan. Calories in fried chicken gizzards 22 and Jan. Calories in boiled chicken gizzards 31 letters between American Traffic Solutions and the U.S. Chicken gizzards healthy Postal Service regarding unpaid traffic infractions by mail carriers in East Cleveland, Ohio.

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