Notes:BG873727:
Found longer MEC sequence using Assembled EST BLASTn:
>MEC_28007_P95-Mar06
Length = 812
Score = 1170 bits (590), Expect = 0.0
Identities = 604/606 (99%), Gaps = 2/606 (0%)
Strand = Plus / Minus
BG840297:
Found longer MEC sequence through Assembled EST BLASTn:
>MEC_28007_P95-Mar06
Length = 812
Score = 1170 bits (590), Expect = 0.0
Identities = 604/606 (99%), Gaps = 2/606 (0%)
Strand = Plus / Minus
This is the same sequence for both accessions, so I will be using the MEC sequence from now on.
Repeatmasker:
>MEC_28007_P95-Mar06 MEC_P95-Mar06.contigs_w_singletons 812 bp (142 bp masked -- 17.49% masked)
gcggcctggatcgacctccagaccttctccgcgccggtgcctctatgtctatggctccgcctccgcgctcccgaagctgc
tgctgctgcttctagctgcatcatcatccgcgcaagcccagcaagcggcgaggatgaagaccgatccagtcgaagcggcg
gcggtgaacgctttgttcgccaagctccgccagacagcgtcgtcggaatggaacatcagcggcgacccctgcaccggcat
cgccacggacggcaccgtcatcgaagacaacggcaacttcaacccgggcatcaagtgcgagtgctccgaccagaacaaca
tcaccgtctgccacgtcaccaagctgaagatatacgcgctcaatgccgttggccccataccacaggaactgcagaatctt
acgcgcttgatcaatctggatttaagcaagaattacttaacaggttctttgccatctttcctcgggaatttgactgctat
gcagtacatgactttgggcaccaatgcattgtctggatctgttccaaaggagcttgggaaccttgtgaatcttgtatctc
taggctttggctcgaactacttaaatggcccccttccttgggagttgggaaacctggcaaaactggagcaattcNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNtatacttcttcttttcatcttttt
cttccccttctt
Repeatmasker of original sequence:
Repeats
>BG873727 MEST9-F05.T3 ISUM4-TN Zea mays cDNA clone MEST9-F05 3', mRNA sequence. (264 bp masked -- 38.32% masked) TNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNATTGCTCCAGTTTTGCCAGGTTTCCCAACTCCCAAGGAAGGGGGCCATTTAAGTA GTTCGAGCCAAAGCCTAGAGATACAAGATTCACAAGGTTCCCAAGCTCCTTTGGAACAGATCCAGACAATGCATTGGTGC CCAAAGTCATGTACTGCATAGCAGTCAAATTCCCGAGGAAAGATGGCAAAGAACCTGTTAAGTAATTCTTGCTTAAATCC AGATTGATCAAGCGCGTAAGATTCTGCAGTTCCTGTGGTATGGGGCCAACGGCATTGAGCGCGTATATCTTCAGCTTGGT GACGTGGCAGACGGTGATGTTGTTCTGGTCGGAGCACTCGCACTTGATGCCCGGGTTGAAGTTGCCGTTGTCTTCGATGA CGGTGCCGTCCGTGGCGATGCCGGTGCAGGGGTCGCCGCTGATGTTCCA
Repeats
>BG840297 MEST9-F05.T7-1 ISUM4-TN Zea mays cDNA clone MEST9-F05 5', mRNA sequence. (142 bp masked -- 22.94% masked)
ACAGCGTCGTCGGAATGGAACATCAGCGGCGACCCCTGCACCGGCATCGCCACGGACGGCACCGTCATCGAAGACAACGG
CAACTTCAACCCGGGCATCAAGTGCGAGTGCTCCGACCAGAACAACATCACCGTCTGCCACGTCACCAAGCTGAAGATAT
ACGCGCTCAATGCCGTTGGCCCCATACCACAGGAACTGCAGAATCTTACGCGCTTGATCAATCTGGATTTAAGCAAGAAT
TACTTAACAGGTTCTTTGCCATCTTTCCTCGGGAATTTGACTGCTATGCAGTACATGACTTTGGGCACCAATGCATTGTC
TGGATCTGTTCCAAAGGAGCTTGGGAACCTTGTGAATCTTGTATCTCTAGGCTTTGGCTCGAACTACTTAAATGGCCCCC
TTCCTTGGGAGTTGGGAAACCTGGCAAAACTGGAGCAATTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNTATACTTCTTCTTTTCATCTTTTTCTTCCCCTTCTT
Repeat BLASTn:
ZRSiTERT0010074 (gi|18254408) Zea mays cultivar B73 putative pol... 224 1e-58
ZRSiTERTOOT0240 ji_af090447-2 ji_af090447-2 ji_af090447-2 af0904... 184 1e-46
ZRSiTERTOOT0235 ji_5BL-2 ji_5BL-2 5BL bases 48469. .57844 ||retr... 176 2e-44
ZRSiTERTOOT0211 ji_276N13-2 ji_276N13-2 276N13.fasta.screen.Cont... 157 2e-38
ZRSiTERTOOT0199 ji_013I05-1part ji_Z013I05-1part Z013I05 bases 4... 153 4e-37
ZRSiTERTOOT0208 ji_238E11-1 ji_238E11-1 RP1D_REGION bases 13407.... 147 2e-35
>ZRSiTERT0010074 (gi|18254408) Zea mays cultivar B73 putative
polyprotein
Length = 3051
Score = 224 bits (113), Expect = 1e-58
Identities = 217/252 (86%), Gaps = 6/252 (2%)
Strand = Plus / Plus
Query: 19 gtggtaagtccgatcactttattgctaaatgtccatatacaagtgacagtgacagggacg 78
|||||||||||| ||| ||||| ||||||||||||||||||||||| ||||| |||||||
Sbjct: 452 gtggtaagtccggtcattttatcgctaaatgtccatatacaagtgatagtgatagggacg 511
Query: 79 acgacaagaaggggaagaaaaagatggaaaagaagaagtattacaa------gaagggtg 132
| |||||||| |||||||| ||||| |||||| | |||||||| ||||||||
Sbjct: 512 atgacaagaaagggaagaaggagatgacaaagaaaagatattacaacaagaagaagggtg 571
Query: 133 gcgatacacatatagggcgagaatgggactccgacgaaagctccaccgactcctcctccg 192
|||| |||| || |||||| |||||||||||||| | ||||||||||||||||||| ||
Sbjct: 572 gcgaggcacacatggggcgaaaatgggactccgacaagagctccaccgactcctccttcg 631
Query: 193 acgaggacgctgccaacatcgccatcaacaaaggtcttattttccccaacgtcggccaca 252
|||||||||| |||||||||| |||||||||||| ||| | |||||||||||||||||||
Sbjct: 632 acgaggacgccgccaacatcgtcatcaacaaaggccttctcttccccaacgtcggccaca 691
Query: 253 agtgtctcatgg 264
| || |||||||
Sbjct: 692 aatgcctcatgg 703
BLASTx of longer MEC sequence:
gb|EAY95562.1| hypothetical protein OsI_016795 [Oryza sativa ... 230 6e-59
emb|CAJ86313.1| H0525G02.10 [Oryza sativa (indica cultivar-group 230 6e-59
ref|NP_001053877.1| Os04g0616300 [Oryza sativa (japonica cult... 227 6e-58  
emb|CAD41882.2| OSJNBa0093O08.1 [Oryza sativa (japonica cultivar 227 6e-58
emb|CAD41883.2| OSJNBa0093O08.2 [Oryza sativa (japonica cultivar 224 5e-57
gb|EAZ31985.1| hypothetical protein OsJ_015468 [Oryza sativa ... 220 6e-56
ref|NP_001053879.1| Os04g0616500 [Oryza sativa (japonica cult... 220 6e-56
emb|CAD41800.2| OSJNBa0008M17.16 [Oryza sativa (japonica cultiva 220 6e-56
emb|CAD41884.2| OSJNBa0093O08.3 [Oryza sativa (japonica cultivar 220 6e-56
gb|EAZ31982.1| hypothetical protein OsJ_015465 [Oryza sativa ... 219 1e-55
emb|CAJ86312.1| H0525G02.9 [Oryza sativa (indica cultivar-group) 219 1e-55
gb|EAY95563.1| hypothetical protein OsI_016796 [Oryza sativa ... 217 5e-55
emb|CAJ86314.1| H0525G02.11 [Oryza sativa (indica cultivar-group 217 5e-55
ref|NP_001053878.1| Os04g0616400 [Oryza sativa (japonica cult... 211 3e-53
ref|NP_001053881.1| Os04g0616700 [Oryza sativa (japonica cult... 204 3e-51
ref|NP_001061221.1| Os08g0203100 [Oryza sativa (japonica cult... 200 8e-50
ref|NP_001061225.1| Os08g0203700 [Oryza sativa (japonica cult... 199 1e-49
gb|AAY67902.1| SHR5-receptor-like kinase [Saccharum hybrid culti 196 2e-48
emb|CAD41886.2| OSJNBa0093O08.5 [Oryza sativa (japonica cultivar 194 6e-48
gb|EAY93453.1| hypothetical protein OsI_014686 [Oryza sativa ... 193 1e-47
Top Hit:
>gb|EAY95562.1| hypothetical protein OsI_016795 [Oryza sativa (indica cultivar-group)]
Length=917
Score = 230 bits (587), Expect = 6e-59
Identities = 113/167 (67%), Positives = 134/167 (80%), Gaps = 1/167 (0%)
Frame = +2
Query 137 KTDPVEAAAVNALFAKLRQTASSEWNISGDPCTGIATDGTVIEDNGNFNPGIKCECSDQN 316
+TDP EAAA+NA+FAKL Q A+S WN+SGDPCTG ATDGT I+DN NFNP IKC+C+ QN
Sbjct 30 RTDPTEAAALNAVFAKLGQQAASTWNLSGDPCTGAATDGTPIDDNPNFNPAIKCDCTFQN 89
Query 317 NITVCHVTKLKIYALNAVGPIPQELQNLTRLINLDLSKNYLTGSLPSFLGNLTAMQYMTL 496
N T+C +TKLKIYAL+ G IPQEL+NLTRL +L+L +N LTG LPSF+G LT MQ MT
Sbjct 90 N-TICRITKLKIYALDVPGTIPQELRNLTRLTHLNLGQNILTGPLPSFIGELTNMQNMTF 148
Query 497 GTNALSGSVPKELGNLVNLVSLGFGSNYLNGPLPWELGNLAKLEQFH 637
N+LSG +PKELGNL NLVSLG GSN NG LP ELGNL KL++ +
Sbjct 149 RINSLSGPIPKELGNLTNLVSLGLGSNRFNGSLPSELGNLDKLQELY 195
Score = 47.4 bits (111), Expect = 0.001
Identities = 28/76 (36%), Positives = 40/76 (52%), Gaps = 5/76 (6%)
Frame = +2
Query 341 KLKIYALNAVGPIPQELQNLTRLINLDLSKNYLTGSLPSFLG--NLTAMQYMTLGTNALS 514
+L I + GP+P LTR+ L S N TG +P ++G NLT +++ N+
Sbjct 193 ELYIDSAGLSGPLPSSFSKLTRMQTLWASDNDFTGQIPDYIGNWNLTDLRFQ---GNSFQ 249
Query 515 GSVPKELGNLVNLVSL 562
G +P L NLV L SL
Sbjct 250 GPIPSALSNLVQLSSL 265
Top Informative Hit:
>ref|NP_001061225.1| Os08g0203700 [Oryza sativa (japonica cultivar-group)]
dbj|BAD02997.1| putative Receptor-like serine/threonine kinase(RFK1) [Oryza sativa
(japonica cultivar-group)]
dbj|BAF23139.1| Os08g0203700 [Oryza sativa (japonica cultivar-group)]
Length=1023
Score = 199 bits (506), Expect = 1e-49
Identities = 95/167 (56%), Positives = 123/167 (73%), Gaps = 1/167 (0%)
Frame = +2
Query 137 KTDPVEAAAVNALFAKLRQTASSEWNISGDPCTGIATDGTVIEDNGNFNPGIKCECSDQN 316
+TDP E AA+N + + AS WNISG+PC+G+A D T +++N N NP IKC+CS N
Sbjct 31 RTDPAEVAALNTILGRWGLRASPAWNISGEPCSGVAIDETGVDNNPNINPAIKCDCSF-N 89
Query 317 NITVCHVTKLKIYALNAVGPIPQELQNLTRLINLDLSKNYLTGSLPSFLGNLTAMQYMTL 496
TVCH+ +L++++LN VG IP+ELQNL+ L NLDL +NYLTG LPSF+GN +AMQY+ +
Sbjct 90 AGTVCHIIRLRVFSLNVVGQIPEELQNLSYLNNLDLRRNYLTGPLPSFIGNFSAMQYLAV 149
Query 497 GTNALSGSVPKELGNLVNLVSLGFGSNYLNGPLPWELGNLAKLEQFH 637
N LSG +PKE+GNL NL+SLG SN G LP ELGNL KLEQ +
Sbjct 150 SLNPLSGPLPKEIGNLRNLLSLGISSNNFTGELPAELGNLEKLEQMY 196
Score = 53.5 bits (127), Expect = 1e-05
Identities = 33/91 (36%), Positives = 48/91 (52%), Gaps = 3/91 (3%)
Frame = +2
Query 398 LTRLINLDLSKNYLTGSLPSFLGNLTAMQYMTLGTNALSGSVPKELGNLVNLVSLGFGSN 577
L L LDLS N +TG +P + NL + ++ LG N+LSGS+P + +N +L F N
Sbjct 310 LAGLTLLDLSFNNITGHVPQSILNLDKLSFLFLGNNSLSGSLPYDKSPSLN--NLDFSYN 367
Query 578 YLNGPL-PWELGNLAKLEQFHETLVADVGEN 667
+L+G PW GN +L + D N
Sbjct 368 HLSGSFPPWVTGNNLQLNLVANDFILDSTNN 398
Score = 47.8 bits (112), Expect = 7e-04
Identities = 27/73 (36%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Frame = +2
Query 371 GPIPQELQNLTRLINLDLSKNYLTGSLPSFLGNLTAMQYMTLGTNALSGSVPKELGNLVN 550
GP P L L L S N LTG +P + G+ +Q + N+ G +P L NL
Sbjct 204 GPFPSTFSKLKNLKILWASDNDLTGKIPDYFGSFPNLQDLRFQGNSFQGPIPASLSNLTR 263
Query 551 LVSLGFGSNYLNG 589
L SL G + LNG
Sbjct 264 LTSLRIG-DILNG 275
Score = 37.0 bits (84), Expect = 1.2
Identities = 27/81 (33%), Positives = 38/81 (46%), Gaps = 6/81 (7%)
Frame = +2
Query 296 CECSDQ----NNITVCHVTKLKIYALNAVGPIPQELQNLTRLINLDLSKNYLTGSLPSFL 463
C+ SD N + +T L + N G +PQ + NL +L L L N L+GSLP
Sbjct 296 CKISDNLGTVNFSKLAGLTLLDLSFNNITGHVPQSILNLDKLSFLFLGNNSLSGSLP--Y 353
Query 464 GNLTAMQYMTLGTNALSGSVP 526
++ + N LSGS P
Sbjct 354 DKSPSLNNLDFSYNHLSGSFP 374
Interproscan:
KEEP IN MIND THAT THE FOLLOWING INTERPRO ENTRY HAD A VERY HIGH E-VALUE:
InterPro: IPR001611 Leucine-rich repeat
Matches
|
|
| Accession
|
IPR001611 LRR Matches: 13646 proteins |
| Type
|
Repeat |
| Signatures
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|
| InterPro Relationships
|
| Children |
IPR003591 Leucine-rich repeat, typical subtype
|
| Found in |
IPR006228 Polycystin cation channel
IPR008095 MHC class II transactivator
IPR008112 Relaxin receptor
IPR015763 Leucine rich repeat protein Toll-like receptor 9
IPR015764 Leucine rich repeat protein Toll-like receptor 8
IPR015766 Leucine-rich repeat protein
|
| GO Term annotation
|
| Function |
GO:0005515 protein binding
|
| InterPro annotation |
| Abstract
|
Leucine-rich repeats (LRR) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape [1]. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions [2]. Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response.
Sequence analyses of LRR proteins suggested the existence of several different subfamilies of LRRs. The significance of this classification is that repeats from different subfamilies never occur simultaneously and have most probably evolved independently. It is, however, now clear that all major classes of LRR have curved horseshoe structures with a parallel beta sheet on the concave side and mostly helical elements on the convex side. At least six families of LRR proteins, characterized by different lengths and consensus sequences of the repeats, have been identified. Eleven-residue segments of the LRRs (LxxLxLxxN/CxL), corresponding to the ß-strand and adjacent loop regions, are conserved in LRR proteins, whereas the remaining parts of the repeats (herein termed variable) may be very different. Despite the differences, each of the variable parts contains two half-turns at both ends and a "linear" segment (as the chain follows a linear path overall), usually formed by a helix, in the middle. The concave face and the adjacent loops are the most common protein interaction surfaces on LRR proteins. 3D structure of some LRR proteins-ligand complexes show that the concave surface of LRR domain is ideal for interaction with alpha-helix, thus supporting earlier conclusions that the elongated and curved LRR structure provides an outstanding framework for achieving diverse protein-protein interactions [2]. Molecular modeling suggests that the conserved pattern LxxLxL, which is shorter than the previously proposed LxxLxLxxN/CxL is sufficient to impart the characteristic horseshoe curvature to proteins with 20- to 30-residue repeats [3].
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| Structural links
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| Database links
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Pfam Clan: CL0022.24
|
| Interactions
|
This domain has been experimentally proven to be involved in Protein:Protein interactions. Representative data is shown with the following example proteins:
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Literature:
-
SHR5: a novel plant receptor kinase involved in plant-N2-fixing endophytic bacteria association.
Vinagre F, Vargas C, Schwarcz K, Cavalcante J, Nogueira EM, Baldani JI, Ferreira PC, Hemerly AS.
Instituto de Bioquimica Medica, CCS, Universidade Federal do Rio de Janeiro, 21941-590 Rio de Janeiro, RJ, Brazil.
Endophytic nitrogen-fixing bacteria have been isolated from graminaceous plants such as maize, rice, and sugarcane. They are thought to promote plant growth, not only by fixing nitrogen, but also by the production of plant hormones. The molecular mechanisms involved in this interaction are not yet clear. In this work, the identification of a receptor-like kinase (RLK), named SHR5, which may participate in signal transduction involved in the establishment of plant-endophytic bacteria interaction is described for the first time. SHR5 seems to be part of a novel subclass of RLKs present in a wide range of plant species. The expression of this gene is down-regulated in sugarcane plants associated exclusively with beneficial endophytic bacteria and is not a general response caused by micro-organisms or abiotic stress. In addition, more successful sugarcane-endophytic bacteria associations have a more pronounced decrease in SHR5 expression, suggesting that SHR5 mRNA levels in plant cells are inversely related to the efficiency of the association.
Publication Types:
PMID: 16397001 [PubMed - indexed for MEDLINE]
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