17:
88:
101:
120:, either in an identical or a highly similar form. The degree of similarity can be highly variable, with some repeats maintaining only a few conserved amino acid positions and a characteristic length. Highly degenerate repeats can be very difficult to detect from sequence alone. Structural similarity can help to identify repetitive patterns in sequence.
305:
with Pfam are repeat regions. Alternatively, methods requiring no prior knowledge for the detection of repeated substrings can be based on self-comparison, clustering or hidden Markov models. Some others rely on complexity measurements or take advantage of meta searches to combine outputs from different sources.
304:
Sequence-based strategies, based on homology search or domain assignment, mostly underestimate TRs due to the presence of highly degenerate repeat units. A recent study to understand and improve Pfam coverage of the human proteome showed that five of the ten largest sequence clusters not annotated
139:. Repeats that are at least 30 to 40 amino acids long are far more likely to be folded as part of a domain. Such long repeats are frequently indicative of the presence of a solenoid domain in the protein.
128:
Repetitiveness does not in itself indicate anything about the structure of the protein. As a "rule of thumb", short repetitive sequences (e.g. those below the length of 10 amino acids) may be
301:
Protein tandem repeats can be either detected from sequence or annotated from structure. Specialized methods were built for the identification of repeat proteins.
359:
Andrade MA, Ponting CP, Gibson TJ, Bork P (May 2000). "Homology-based method for identification of protein repeats using statistical significance estimates".
296:
1865:
1822:
1708:
1653:
1600:
1488:
1374:
1131:
1065:
1002:
939:
886:
279:
and occur in at least 14% of all proteins. For example, they are present in almost every third human protein and even in every second protein from
581:
Liu J, Xing Y, Hinds TR, Zheng J, Xu W (June 2006). "The third 20 amino acid repeat is the tightest binding site of APC for beta-catenin".
80:. These periodic sequences are generated by internal duplications in both coding and non-coding genomic sequences. Repetitive units of
231:
structures with typical size of repeats over 50 residues, which are already large enough to fold independently into stable domains.
49:
146:
conformation being naturally unfolded. Examples of disordered repetitive sequences include the 7-mer peptide repeats found in the
84:
tandem repeats are considerably diverse, ranging from the repetition of a single amino acid to domains of 100 or more residues.
1162:
308:
Structure-based methods instead take advantage of the modularity of available PDB structures to recognize repetitive elements.
1927:
1858:
174:
has a plethora of shapes and functions. Examples of short repeats exhibiting ordered structures include the three-residue
129:
199:
143:
1235:"XSTREAM: a practical algorithm for identification and architecture modeling of tandem repeats in protein sequences"
2064:
1851:
194:
Depending on the length of the repetitive units, their protein structures can be subdivided into five classes:
706:
Stirnimann CU, Petsalaki E, Russell RB, MĂĽller CW (October 2010). "WD40 proteins propel cellular networks".
659:"RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures"
167:
1666:
902:"Homology-based method for identification of protein repeats using statistical significance estimates"
287:. Tandem repeats with short repetitive units (especially homorepeats) are more frequent than others.
2069:
1962:
489:
284:
2043:
1903:
1081:
1018:"InterPro in 2019: improving coverage, classification and access to protein sequence annotations"
746:
Marcotte EM, Pellegrini M, Yeates TO, Eisenberg D (October 1999). "A census of protein repeats".
214:
1977:
1616:"ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures"
952:
223:
1816:
1702:
1647:
1594:
1482:
1368:
1125:
1059:
1015:
996:
933:
880:
280:
65:
1724:"ConSole: using modularity of contact maps to locate solenoid domains in protein structures"
394:
Tompa P (September 2003). "Intrinsically unstructured proteins evolve by repeat expansion".
1669:"RAPHAEL: recognition, periodicity and insertion assignment of solenoid protein structures"
542:"Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated structural model"
33:
1416:
657:
Paladin L, Hirsh L, Piovesan D, Andrade-Navarro MA, Kajava AV, Tosatto SC (January 2017).
8:
1957:
1952:
249:
179:
105:
29:
1775:"TAPO: A combined method for the identification of tandem repeats in protein structures"
1390:"De novo identification of highly diverged protein repeats by probabilistic consistency"
252:
proteins, which specifically bind some globular proteins by their concave surfaces; and
198:
crystalline aggregates formed by regions with 1 or 2 residue long repeats, archetypical
1942:
1804:
1750:
1723:
1631:
1577:
1552:
1533:
1465:
1440:
1351:
1326:
1261:
1234:
1174:
1108:
1083:
1082:
Mistry J, Coggill P, Eberhardt RY, Deiana A, Giansanti A, Finn RD; et al. (2013).
1042:
1017:
979:
954:
863:
836:
809:
782:
683:
658:
517:
465:
438:
419:
263:
Tandem repeat proteins frequently function as protein-protein interaction modules. The
175:
163:
61:
1286:"T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm"
619:
Kajava AV (September 2012). "Tandem repeats in proteins: from sequence to structure".
337:
1991:
1967:
1796:
1755:
1690:
1635:
1582:
1525:
1470:
1421:
1356:
1307:
1266:
1215:
1166:
1113:
1047:
984:
953:
El-Gebali S, Mistry J, Bateman A, Eddy SR, Luciani A, Potter SC; et al. (2019).
921:
868:
814:
763:
723:
688:
636:
598:
563:
522:
508:
470:
411:
376:
341:
171:
151:
37:
1808:
1685:
1668:
1568:
1537:
1406:
1389:
1302:
1285:
1210:
1193:
1178:
439:"Tandem and cryptic amino acid repeats accumulate in disordered regions of proteins"
423:
1922:
1786:
1745:
1735:
1680:
1627:
1572:
1564:
1515:
1460:
1452:
1411:
1401:
1346:
1338:
1297:
1256:
1246:
1205:
1158:
1103:
1095:
1037:
1029:
1016:
Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A; et al. (2019).
974:
966:
913:
858:
848:
804:
794:
755:
715:
678:
670:
628:
590:
553:
512:
504:
460:
450:
403:
368:
333:
117:
1791:
1774:
133:
76:
is defined as several (at least two) adjacent copies having the same or similar
1996:
1917:
1912:
1893:
1667:
Walsh I, Sirocco FG, Minervini G, Di
Domenico T, Ferrari C, Tosatto SC (2012).
853:
719:
136:
77:
45:
1099:
632:
594:
558:
541:
324:
Heringa J (June 1998). "Detection of internal repeats: how common are they?".
2058:
1932:
1740:
837:"Ab initio detection of fuzzy amino acid tandem repeats in protein sequences"
799:
455:
53:
1251:
170:(adenomatous polyposis coli). The other half of the regions with the stable
2027:
1800:
1759:
1694:
1639:
1615:
1586:
1529:
1474:
1425:
1360:
1311:
1270:
1219:
1170:
1146:
1117:
1051:
988:
925:
917:
901:
872:
818:
767:
759:
727:
692:
640:
602:
567:
526:
474:
415:
380:
372:
155:
41:
16:
1033:
674:
345:
207:
structures stabilized by inter-chain interactions with 3-7 residue repeats
116:, a "repeat" is any sequence block that returns more than one time in the
2011:
2001:
1986:
1947:
1888:
1843:
1456:
1342:
1147:"Rapid automatic detection and alignment of repeats in protein sequences"
970:
899:
264:
253:
245:
244:, which plays a key role in the arrangement of the extracellular matrix;
25:
21:
87:
2006:
1937:
1327:"HHrep: de novo protein repeat detection and the origin of TIM barrels"
783:"Tandem Repeats in Proteins: Prediction Algorithms and Biological Role"
407:
183:
1520:
1503:
1163:
10.1002/1097-0134(20001101)41:2<224::aid-prot70>3.0.co;2-z
1553:"Swelfe: a detector of internal repeats in sequences and structures"
1839:
RepeatsDB: a database of annotated tandem repeat protein structures
656:
276:
241:
1838:
1084:"The challenge of increasing Pfam coverage of the human proteome"
834:
745:
113:
81:
1504:"The evolution and function of protein tandem repeats in plants"
705:
490:"Protein tandem repeats - the more perfect, the less structured"
1613:
1550:
147:
1772:
1324:
1441:"REPPER--repeats and their periodicities in fibrous proteins"
240:
Some well-known examples of proteins with tandem repeats are
222:(not elongated) structures with repeats of 30-60 residues as
159:
57:
1438:
100:
257:
20:
Common examples of protein tandem repeat structures: the
358:
1191:
1501:
1194:"Tracking repeats using significance and transitivity"
213:
structures with repeats of 5–40 residues dominated by
487:
142:
Approximately half of the tandem repeat regions have
1232:
256:, which regulate the expression of genes by binding
1387:
540:Meyer PA, Ye P, Zhang M, Suh MH, Fu J (June 2006).
488:Jorda J, Xue B, Uversky VN, Kajava AV (June 2010).
91:
Schematic representation of tandem repeat sequence.
1283:
900:Andrade MA, Ponting CP, Gibson TJ, Bork P (2000).
95:
1721:
580:
297:List of protein tandem repeat annotation software
248:having structural and oligomerization functions;
2056:
1144:
1077:
1075:
830:
828:
539:
1859:
787:Frontiers in Bioengineering and Biotechnology
1821:: CS1 maint: multiple names: authors list (
1766:
1715:
1707:: CS1 maint: multiple names: authors list (
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1652:: CS1 maint: multiple names: authors list (
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1599:: CS1 maint: multiple names: authors list (
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1487:: CS1 maint: multiple names: authors list (
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1373:: CS1 maint: multiple names: authors list (
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1138:
1130:: CS1 maint: multiple names: authors list (
1072:
1064:: CS1 maint: multiple names: authors list (
1009:
1001:: CS1 maint: multiple names: authors list (
955:"The Pfam protein families database in 2019"
946:
938:: CS1 maint: multiple names: authors list (
893:
885:: CS1 maint: multiple names: authors list (
825:
436:
270:
574:
533:
1873:
1866:
1852:
835:Pellegrini M, Renda ME, Vecchio A (2012).
780:
1790:
1749:
1739:
1684:
1576:
1519:
1464:
1415:
1405:
1350:
1301:
1260:
1250:
1209:
1107:
1041:
978:
862:
852:
808:
798:
682:
557:
516:
464:
454:
104:Example multiple sequence alignment of a
1614:Sabarinathan R, Basu R, Sekar K (2010).
1551:Abraham AL, Rocha EP, Pothier J (2008).
99:
86:
15:
1773:Do Viet P, Roche DB, Kajava AV (2015).
1325:Söding J, Remmert M, Biegert A (2006).
323:
2057:
618:
1928:Transcription activator-like effector
1847:
1439:Gruber M, Söding J, Lupas AN (2005).
741:
739:
737:
393:
326:Current Opinion in Structural Biology
290:
267:is a prime example of this function.
652:
650:
614:
612:
108:leading to a tandem repeat structure
13:
1632:10.1016/j.compbiolchem.2010.03.006
734:
699:
14:
2081:
1832:
647:
609:
275:Tandem repeats are ubiquitous in
189:
68:regulatory subunit R1a (magenta).
1192:Szklarczyk R, Heringa J (2004).
509:10.1111/j.1742-4658.2010.07684.x
1502:Schaper E, Anisimova M (2015).
774:
1417:11858/00-001M-0000-0017-DADF-9
708:Trends in Biochemical Sciences
481:
430:
387:
352:
317:
1:
1792:10.1016/j.febslet.2015.08.025
1686:10.1093/bioinformatics/bts550
1569:10.1093/bioinformatics/btn234
1451:(Web Server issue): W239-43.
1407:10.1093/bioinformatics/btn039
1337:(Web Server issue): W137-42.
1303:10.1093/bioinformatics/btp482
1233:Newman AM, Cooper JB (2007).
1211:10.1093/bioinformatics/bth911
621:Journal of Structural Biology
338:10.1016/s0959-440x(98)80068-7
311:
1388:Biegert A, Söding J (2008).
748:Journal of Molecular Biology
437:Simon M, Hancock JM (2009).
361:Journal of Molecular Biology
123:
7:
1284:Jorda J, Kajava AV (2009).
235:
10:
2086:
1722:Hrabe T, Godzik A (2014).
854:10.1186/1471-2105-13-S3-S8
720:10.1016/j.tibs.2010.04.003
294:
246:alpha-helical coiled coils
30:leucine-rich repeat domain
2036:
2020:
1976:
1902:
1881:
633:10.1016/j.jsb.2011.08.009
595:10.1016/j.jmb.2006.04.064
559:10.1016/j.str.2006.04.003
271:Distribution in proteomes
1963:Tetratricopeptide repeat
1741:10.1186/1471-2105-15-119
1145:Heger A, Holm L (2000).
800:10.3389/fbioe.2015.00143
456:10.1186/gb-2009-10-6-r59
285:Dictyostelium discoideum
144:intrinsically disordered
130:intrinsically disordered
2044:Repeated sequence (DNA)
1252:10.1186/1471-2105-8-382
1100:10.1093/database/bat023
38:armadillo repeat domain
2065:Protein tandem repeats
1875:Protein tandem repeats
918:10.1006/jmbi.2000.3684
760:10.1006/jmbi.1999.3136
663:Nucleic Acids Research
373:10.1006/jmbi.2000.3684
200:low complexity regions
132:, and not part of any
109:
92:
74:protein tandem repeats
69:
781:Pellegrini M (2015).
281:Plasmodium falciparum
103:
96:"Repeats" in proteins
90:
46:ankyrin repeat domain
19:
254:zinc-finger proteins
178:or the five-residue
1958:Pentapeptide repeat
1953:Leucine-rich repeat
1785:(19 Pt A): 2611–9.
1204:(Suppl 1): i311-7.
1034:10.1093/nar/gky1100
675:10.1093/nar/gkw1136
250:leucine-rich repeat
180:pentapeptide repeat
106:pentapeptide repeat
54:kelch repeat domain
2021:Beads-on-a-string:
1943:Antifreeze protein
1728:BMC Bioinformatics
1457:10.1093/nar/gki405
1343:10.1093/nar/gkl130
1239:BMC Bioinformatics
971:10.1093/nar/gky995
841:BMC Bioinformatics
408:10.1002/bies.10324
291:Annotation methods
110:
93:
70:
62:HEAT repeat domain
22:WD40 repeat domain
2052:
2051:
1992:Beta trefoil fold
1968:Trefoil knot fold
1521:10.1111/nph.13184
1445:Nucleic Acids Res
1331:Nucleic Acids Res
1088:Database (Oxford)
1028:(D1): D351–D360.
1022:Nucleic Acids Res
965:(D1): D427–D432.
959:Nucleic Acids Res
669:(D1): D308–D312.
229:beads on a string
215:solenoid proteins
152:RNA polymerase II
2077:
1923:Armadillo repeat
1868:
1861:
1854:
1845:
1844:
1827:
1826:
1820:
1812:
1794:
1770:
1764:
1763:
1753:
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1719:
1713:
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1706:
1698:
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1657:
1651:
1643:
1620:Comput Biol Chem
1611:
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1409:
1385:
1379:
1378:
1372:
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1322:
1316:
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1305:
1281:
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1230:
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1213:
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1006:
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944:
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832:
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497:The FEBS Journal
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349:
321:
154:, or the tandem
2085:
2084:
2080:
2079:
2078:
2076:
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2074:
2070:Protein domains
2055:
2054:
2053:
2048:
2032:
2016:
1972:
1898:
1877:
1872:
1835:
1830:
1814:
1813:
1771:
1767:
1720:
1716:
1700:
1699:
1679:(24): 3257–64.
1665:
1661:
1645:
1644:
1612:
1608:
1592:
1591:
1549:
1545:
1500:
1496:
1480:
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1437:
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1386:
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1366:
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1323:
1319:
1282:
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1231:
1227:
1190:
1186:
1143:
1139:
1123:
1122:
1080:
1073:
1057:
1056:
1014:
1010:
994:
993:
951:
947:
931:
930:
898:
894:
878:
877:
847:(Suppl 3): S8.
833:
826:
779:
775:
744:
735:
704:
700:
655:
648:
617:
610:
579:
575:
538:
534:
503:(12): 2673–82.
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435:
431:
392:
388:
357:
353:
322:
318:
314:
299:
293:
273:
238:
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176:collagen repeat
137:protein domains
126:
98:
78:sequence motifs
12:
11:
5:
2083:
2073:
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1999:
1997:Beta-propeller
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1965:
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1920:
1918:Ankyrin repeat
1915:
1913:Alpha solenoid
1909:
1907:
1900:
1899:
1897:
1896:
1894:Collagen helix
1891:
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1833:External links
1831:
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1673:Bioinformatics
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1606:
1563:(13): 1536–7.
1557:Bioinformatics
1543:
1514:(1): 397–410.
1494:
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1394:Bioinformatics
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1296:(20): 2632–8.
1290:Bioinformatics
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1198:Bioinformatics
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443:Genome Biology
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295:Main article:
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224:toroid repeats
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190:Classification
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1207:
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1199:
1195:
1188:
1180:
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1157:(2): 224–37.
1156:
1152:
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960:
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949:
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912:(3): 521–37.
911:
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754:(1): 151–60.
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627:(3): 279–88.
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589:(1): 133–44.
588:
584:
577:
569:
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552:(6): 973–82.
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402:(9): 847–55.
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367:(3): 521–37.
366:
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343:
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332:(3): 338–45.
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206:
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182:that forms a
181:
177:
173:
169:
165:
164:linear motifs
161:
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107:
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89:
85:
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60:(yellow) and
59:
55:
51:
47:
43:
39:
35:
31:
27:
23:
18:
2028:Sushi domain
1874:
1817:cite journal
1782:
1778:
1768:
1731:
1727:
1717:
1703:cite journal
1676:
1672:
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1648:cite journal
1623:
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1609:
1595:cite journal
1560:
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1546:
1511:
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1483:cite journal
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1126:cite journal
1091:
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1060:cite journal
1025:
1021:
1011:
997:cite journal
962:
958:
948:
934:cite journal
909:
905:
895:
881:cite journal
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786:
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586:
583:J. Mol. Biol
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274:
262:
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219:
210:
204:
193:
172:3D structure
156:beta-catenin
148:RPB1 subunit
141:
127:
111:
73:
72:An array of
71:
42:beta-catenin
2012:WD40 repeat
2002:Kelch motif
1987:Beta barrel
1948:HEAT repeat
1889:Coiled coil
265:WD40 repeat
186:structure.
2059:Categories
2007:TIM barrel
1938:Beta helix
1508:New Phytol
1094:: bat023.
906:J Mol Biol
449:(6): R59.
312:References
184:beta helix
52:(orange),
2037:See also:
1904:Elongated
1779:FEBS Lett
546:Structure
396:BioEssays
277:proteomes
211:elongated
124:Structure
28:(green),
26:beta-TrCP
1882:Fibrous:
1809:28423787
1801:26320412
1760:24766872
1695:22962341
1640:20430700
1587:18487242
1538:20656455
1530:25420631
1475:15980460
1426:18245125
1361:16844977
1312:19671691
1271:17931424
1220:15262814
1179:21757391
1171:10966575
1151:Proteins
1118:23603847
1052:30398656
989:30357350
926:10772867
873:22536906
819:26442257
768:10512723
728:20451393
693:27899671
641:21884799
603:16753179
568:16765890
527:20553501
475:19486509
424:32684524
416:12938174
381:10772867
242:collagen
236:Function
162:binding
118:sequence
114:proteins
44:(blue),
1751:4021314
1734:: 119.
1578:2718673
1466:1160166
1352:1538828
1262:2233649
1245:: 382.
1109:3630804
1043:6323941
980:6324024
864:3402919
810:4585158
793:: 143.
684:5210593
518:2928880
466:2718493
346:9666330
205:fibrous
82:protein
36:(red),
1978:Closed
1807:
1799:
1758:
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681:
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344:
220:closed
134:folded
50:ANKRA2
1805:S2CID
1534:S2CID
1175:S2CID
493:(PDF)
420:S2CID
64:of a
58:Keap1
1823:link
1797:PMID
1756:PMID
1709:link
1691:PMID
1654:link
1636:PMID
1601:link
1583:PMID
1526:PMID
1489:link
1471:PMID
1422:PMID
1375:link
1357:PMID
1308:PMID
1267:PMID
1216:PMID
1167:PMID
1132:link
1114:PMID
1092:2013
1066:link
1048:PMID
1003:link
985:PMID
940:link
922:PMID
887:link
869:PMID
815:PMID
764:PMID
724:PMID
689:PMID
637:PMID
599:PMID
564:PMID
523:PMID
471:PMID
412:PMID
377:PMID
342:PMID
160:axin
66:PP2A
34:TLR2
1787:doi
1783:589
1746:PMC
1736:doi
1681:doi
1628:doi
1573:PMC
1565:doi
1516:doi
1512:206
1461:PMC
1453:doi
1412:hdl
1402:doi
1347:PMC
1339:doi
1298:doi
1257:PMC
1247:doi
1206:doi
1159:doi
1104:PMC
1096:doi
1038:PMC
1030:doi
975:PMC
967:doi
914:doi
910:298
859:PMC
849:doi
805:PMC
795:doi
756:doi
752:293
716:doi
679:PMC
671:doi
629:doi
625:179
591:doi
587:360
554:doi
513:PMC
505:doi
501:277
461:PMC
451:doi
404:doi
369:doi
365:298
334:doi
283:or
258:DNA
168:APC
166:in
158:or
150:of
112:In
56:of
48:of
40:of
32:of
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