RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 028623
(206 letters)
>gnl|CDD|240253 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
Length = 202
Score = 256 bits (655), Expect = 2e-87
Identities = 113/181 (62%), Positives = 139/181 (76%)
Query: 10 KRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNT 69
K +V+D + H+LGRLASV+AKELL GQK+VVVRCE++ ISG L R K+KY FLRKRMNT
Sbjct: 4 KVIVIDCKGHLLGRLASVVAKELLLGQKIVVVRCEDLNISGSLFRNKVKYEEFLRKRMNT 63
Query: 70 KPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDAL 129
P GP H RAP+ I WRT+RGM+PHKTKRGAAAL RLK +EGVPAPYDK KR+VIP AL
Sbjct: 64 NPRRGPFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVFEGVPAPYDKVKRVVIPSAL 123
Query: 130 KVLRLQKGHKYCLLGRLSSEVGWNYYDTIKELEKKRKERAQVAYERRKQLAKLRVKAEKA 189
+VLRL+ Y +LG LS+ VGW Y D + +LE+KRKERA Y+++ +L K +A K
Sbjct: 124 RVLRLKPERPYTVLGDLSAHVGWKYADVVAKLEEKRKERAAAYYKKKVKLRKAWKEARKK 183
Query: 190 A 190
A
Sbjct: 184 A 184
>gnl|CDD|162192 TIGR01077, L13_A_E, ribosomal protein L13, archaeal/eukaryotic.
This model represents ribosomal protein of L13 from the
Archaea and from the eukaryotic cytosol. Bacterial and
organellar forms are represented by model TIGR01066
[Protein synthesis, Ribosomal proteins: synthesis and
modification].
Length = 142
Score = 170 bits (432), Expect = 2e-54
Identities = 82/143 (57%), Positives = 99/143 (69%), Gaps = 1/143 (0%)
Query: 12 VVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKP 71
V+D H+LGRLASV+AK+LLNG+KVVVV E+I ISG R K+KY FLRKR T P
Sbjct: 1 TVIDGSGHILGRLASVVAKQLLNGEKVVVVNAEKIVISGNFYRNKLKYKEFLRKRTLTNP 60
Query: 72 SHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALKV 131
GP RAP++I RT+RGM+PHKT RG AAL RLK Y G+P DK KR+V+P+AL V
Sbjct: 61 RRGPFFPRAPSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDKKKRVVVPEAL-V 119
Query: 132 LRLQKGHKYCLLGRLSSEVGWNY 154
RL KY LG L+ +GW Y
Sbjct: 120 SRLSPTRKYVTLGELAKFLGWKY 142
>gnl|CDD|238230 cd00392, Ribosomal_L13, Ribosomal protein L13. Protein L13, a
large ribosomal subunit protein, is one of five proteins
required for an early folding intermediate of 23S rRNA
in the assembly of the large subunit. L13 is situated on
the bottom of the large subunit, near the polypeptide
exit site. It interacts with proteins L3 and L6, and
forms an extensive network of interactions with 23S
rRNA. L13 has been identified as a homolog of the human
breast basic conserved protein 1 (BBC1), a protein
identified through its increased expression in breast
cancer. L13 expression is also upregulated in a variety
of human gastrointestinal cancers, suggesting it may
play a role in the etiology of a variety of human
malignancies.
Length = 114
Score = 125 bits (317), Expect = 2e-37
Identities = 52/114 (45%), Positives = 64/114 (56%), Gaps = 13/114 (11%)
Query: 12 VVVDARHHMLGRLASVLAKELLN------------GQKVVVVRCEEICISGGLVRQKMKY 59
V+DA+ +LGRLAS +AK LL G VVVV E+I I+G RQK+ Y
Sbjct: 2 HVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVYY 61
Query: 60 MRFLRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGV 113
P+ GP+H RAP +IL R +RGM+P K K G AAL RLK YEG
Sbjct: 62 RHTGYPGGLKNPTAGPLHPRAPERILKRAVRGMLP-KNKLGRAALKRLKVYEGA 114
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 115 bits (291), Expect = 3e-33
Identities = 48/129 (37%), Positives = 63/129 (48%), Gaps = 15/129 (11%)
Query: 12 VVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKY 59
V+DA+ +LGRLAS +AK L G VVV+ E+I ++G R + KY
Sbjct: 2 HVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVINAEKIVLTG-KKRDQKKY 60
Query: 60 MR-FLRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYD 118
R P+ R P +IL R +RGM+P K K G AAL RLK Y G P P+
Sbjct: 61 YRHTGYPGGLKNPTAKGPLERKPERILERAVRGMLP-KNKLGRAALKRLKVYAGSPHPHA 119
Query: 119 KTKRMVIPD 127
K V+
Sbjct: 120 AQKPEVLEI 128
>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
Length = 146
Score = 108 bits (273), Expect = 2e-30
Identities = 59/144 (40%), Positives = 81/144 (56%), Gaps = 3/144 (2%)
Query: 12 VVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLRKRMNTKP 71
VV+DA +LGRLAS +AK LL G++VV+V E+ I+G R KY + + + P
Sbjct: 5 VVIDAEGQILGRLASYVAKRLLEGEEVVIVNAEKAVITGNRERVIEKYKQRRERGSHYNP 64
Query: 72 SHGPIHF-RAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALK 130
+ R P +I RTIRGM+P+K RG AL RLK Y GVP + + VI +A
Sbjct: 65 YRNGPKYPRRPDRIFKRTIRGMLPYKKPRGREALKRLKVYVGVPKELEGKEFEVIDEAD- 123
Query: 131 VLRLQKGHKYCLLGRLSSEVGWNY 154
+ RL KY LG +S E+G +
Sbjct: 124 LSRL-STIKYVTLGEVSKELGAKF 146
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 98.1 bits (245), Expect = 3e-26
Identities = 48/138 (34%), Positives = 68/138 (49%), Gaps = 18/138 (13%)
Query: 12 VVVDARHHMLGRLASVLAKELLN------------GQKVVVVRCEEICISGGLVRQKMKY 59
V+DA +LGRLAS +AK L G V+V+ E++ I+G + K Y
Sbjct: 16 YVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKYY 75
Query: 60 MRFLRKRMNTKPS-HGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYD 118
P+ GP+ R P +IL R +RGM+P K G AAL RLK Y G+P P+
Sbjct: 76 RHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLP-KNPLGRAALKRLKVYAGIPHPH- 133
Query: 119 KTKRMVIPDALKVLRLQK 136
P+AL++ L+
Sbjct: 134 ---EAQKPEALELKLLKG 148
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
Length = 144
Score = 43.5 bits (104), Expect = 8e-06
Identities = 30/123 (24%), Positives = 53/123 (43%), Gaps = 33/123 (26%)
Query: 12 VVVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKY 59
V+DA +LGRLAS +A L G V+V+ E++ ++G + K+ Y
Sbjct: 16 YVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIYY 75
Query: 60 --------MRF--LRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKA 109
++ + + K P +++ + ++GM+P K G A +LK
Sbjct: 76 RHSGYPGGLKEITFGELLAKK----------PERVIEKAVKGMLP-KNPLGRAMFKKLKV 124
Query: 110 YEG 112
Y G
Sbjct: 125 YAG 127
>gnl|CDD|162186 TIGR01066, rplM_bact, ribosomal protein L13, bacterial type. This
model distinguishes ribosomal protein L13 of bacteria
and organelles from its eukarytotic and archaeal
counterparts [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 140
Score = 43.4 bits (103), Expect = 1e-05
Identities = 33/122 (27%), Positives = 52/122 (42%), Gaps = 33/122 (27%)
Query: 13 VVDARHHMLGRLASVLAKELLNGQK------------VVVVRCEEICISGGLVRQKMKYM 60
VVDA LGRLAS +A+ L K V+V+ E++ ++G + QK+ Y
Sbjct: 15 VVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVYYR 74
Query: 61 ----------RFLRKRMNTKPSHGPIHFRAPAKILWRTIRGMIPHKTKRGAAALARLKAY 110
R + + R P ++L ++GM+P K + G +LK Y
Sbjct: 75 HSGYPGGLKSRTFEEMIA----------RKPERVLEHAVKGMLP-KNRLGRKLFKKLKVY 123
Query: 111 EG 112
G
Sbjct: 124 AG 125
>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
Length = 143
Score = 40.0 bits (94), Expect = 2e-04
Identities = 31/118 (26%), Positives = 52/118 (44%), Gaps = 25/118 (21%)
Query: 13 VVDARHHMLGRLASVLAKELL------------NGQKVVVVRCEEICISGGLVRQKMKYM 60
++DA+ LGRLA+ +A L G V+V+ E+I ++G
Sbjct: 18 IIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTG-----NKTSQ 72
Query: 61 RFLRKRMNTKPSHGPI------HFRAPAKILWRTIRGMIPHKTKRGAAALARLKAYEG 112
+F R + +P I R P +I+ + ++GM+P K G +LK Y+G
Sbjct: 73 KFYV-RHSGRPGGLKIETFEELQNRLPNRIIEKAVKGMLP-KGPLGRKLFTKLKVYKG 128
>gnl|CDD|235364 PRK05201, hslU, ATP-dependent protease ATP-binding subunit HslU;
Provisional.
Length = 443
Score = 30.4 bits (70), Expect = 0.57
Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 3/33 (9%)
Query: 171 VAYERRKQLAKLRVKAEKAAEERLGPQLEIIAP 203
V R ++ K+R KAE+AAEER+ L+ + P
Sbjct: 108 VKMVREEKREKVREKAEEAAEERI---LDALLP 137
>gnl|CDD|165330 PHA03033, PHA03033, hypothetical protein; Provisional.
Length = 142
Score = 29.2 bits (65), Expect = 0.90
Identities = 10/21 (47%), Positives = 18/21 (85%)
Query: 153 NYYDTIKELEKKRKERAQVAY 173
Y++IKEL+K++K++ +VAY
Sbjct: 43 KKYNSIKELKKQKKKKGEVAY 63
>gnl|CDD|233898 TIGR02500, type_III_yscD, type III secretion apparatus protein,
YscD/HrpQ family. This family represents a conserved
protein of bacterial type III secretion systems. Gene
symbols are variable from species to species. Members
are designated YscD in Yersinia, HrpQ in Pseudomonas
syringae, and EscD in enteropathogenic Escherichia coli.
In the Chlamydiae, this model describes the C-terminal
400 residues of a longer protein [Protein fate, Protein
and peptide secretion and trafficking, Cellular
processes, Pathogenesis].
Length = 410
Score = 29.7 bits (67), Expect = 1.1
Identities = 21/103 (20%), Positives = 36/103 (34%), Gaps = 15/103 (14%)
Query: 5 SGICAKRVVVDARHHMLGRLASVLAKELLNGQKVVVVRCEEICISGGLVRQKMKYMRFLR 64
+ R+V A + +LAS+L+ L G V EI +SG L +K ++ L
Sbjct: 267 VPLAGWRIVRVASDVI-AQLASLLSDAGLLGVVTVTESGREIALSGQLDSEKRSRLQELL 325
Query: 65 KRMNTK---------PSHGP---IHFRAPAKILWRTIRGMIPH 95
+ + P + +I G P+
Sbjct: 326 AAFKQRDGVIPDVVLQNIPAADGTSDELPFPV--VSISGSGPN 366
>gnl|CDD|214492 smart00055, FCH, Fes/CIP4 homology domain. Alignment extended from
original report. Highly alpha-helical. Also known as the
RAEYL motif or the S. pombe Cdc15 N-terminal domain.
Length = 87
Score = 28.1 bits (63), Expect = 1.2
Identities = 19/74 (25%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 134 LQKGHKYCLLGRLSSEVGWNYYDTIKELEKKRKERAQVAYERRKQLAKL--RVKAEKAAE 191
L G + LL RL + + ++L+K +ERA++ E K+L KL +++A + E
Sbjct: 7 LDDGFE-ALLSRLKNGLRLL-----EDLKKFMRERAKIEEEYAKKLQKLSKKLRAVRDTE 60
Query: 192 ERLGPQLEIIAPIK 205
G + +
Sbjct: 61 PEYGSLSKAWEVLL 74
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 29.2 bits (66), Expect = 1.5
Identities = 14/46 (30%), Positives = 26/46 (56%), Gaps = 4/46 (8%)
Query: 153 NYYDTIKELEKKRKERAQVAYERRKQLAKLRVK----AEKAAEERL 194
+ D I+ L +KR+ A++ ERR++LA+ R + + E R+
Sbjct: 603 DAEDEIERLREKREALAELNDERRERLAEKRERKRELEAEFDEARI 648
>gnl|CDD|153332 cd07648, F-BAR_FCHO, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of FCH domain Only proteins.
F-BAR domains are dimerization modules that bind and
bend membranes and are found in proteins involved in
membrane dynamics and actin reorganization. Proteins in
this group have been named FCH domain Only (FCHO)
proteins. Vertebrates have two members, FCHO1 and FCHO2.
These proteins contain an F-BAR domain and a C-terminal
domain of unknown function named SAFF which is also
present in endophilin interacting protein 1. F-BAR
domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 261
Score = 28.8 bits (65), Expect = 1.5
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 5/40 (12%)
Query: 153 NYYDTIKELEKKRKERAQVAYERRKQLAKLRVKAEKAAEE 192
Y+ ELE+ R+E A K++ K K +KA +E
Sbjct: 131 AYHARCLELERLRRENASP-----KEIEKAEAKLKKAQDE 165
>gnl|CDD|215180 PLN02316, PLN02316, synthase/transferase.
Length = 1036
Score = 28.7 bits (64), Expect = 2.5
Identities = 16/35 (45%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 159 KELEKKRKERAQVAYERRKQLA-KLRVKAEKAAEE 192
+ELEK KE A ER +Q + R + EKAA E
Sbjct: 256 RELEKLAKEEA----ERERQAEEQRRREEEKAAME 286
>gnl|CDD|227546 COG5221, DOP1, Dopey and related predicted leucine zipper
transcription factors [Transcription].
Length = 1618
Score = 28.7 bits (64), Expect = 2.9
Identities = 12/67 (17%), Positives = 27/67 (40%), Gaps = 7/67 (10%)
Query: 83 KILWRTIRGMIPHKTKRGAAALARLKAYEGVPAPYDKTKRMVIPDALKVLRLQKGHKYCL 142
+ W ++ G++ + + L L E + D ++R+++P A ++R L
Sbjct: 181 DVFWSSMWGILLNDERLRTGVLNSLMREENNDSHMDWSERLILPHAGLMVR-------AL 233
Query: 143 LGRLSSE 149
L
Sbjct: 234 CAGLGDN 240
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 28.2 bits (63), Expect = 3.2
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 6/35 (17%)
Query: 159 KELEKKRKERAQVAYERRKQLAKLRVKAEKAAEER 193
+ELEK +KERA+ ++ + KA + + R
Sbjct: 149 RELEKIKKERAE------EKEREEEEKAAEEEKAR 177
>gnl|CDD|226618 COG4134, COG4134, ABC-type uncharacterized transport system,
periplasmic component [General function prediction
only].
Length = 384
Score = 27.9 bits (62), Expect = 4.0
Identities = 15/51 (29%), Positives = 21/51 (41%), Gaps = 1/51 (1%)
Query: 153 NYYDTIKELEKKRKERAQVAYERRKQL-AKLRVKAEKAAEERLGPQLEIIA 202
N Y E K K +VA R A R+ AE AA G ++++
Sbjct: 48 NSYADWVSDEMKAKYGIKVAIVRLDAADAVKRLIAELAAGRDEGGSVDLLW 98
>gnl|CDD|240402 PTZ00399, PTZ00399, cysteinyl-tRNA-synthetase; Provisional.
Length = 651
Score = 28.1 bits (63), Expect = 4.0
Identities = 14/55 (25%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 152 WNYYDTIKELEKKRKERAQVAYERRKQLAKLRVKAEKAAEERLGPQLEIIAPIKY 206
W D +EL+++++E+ + + +K+L KL+ + EK +E + I P ++
Sbjct: 545 WKLDDK-EELQREKEEKEAL--KEQKRLRKLKKQEEKKKKELEKLEKAKIPPAEF 596
>gnl|CDD|236526 PRK09458, pspB, phage shock protein B; Provisional.
Length = 75
Score = 26.0 bits (58), Expect = 4.0
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 164 KRKERAQVAYERRKQLAKLRVKAEKAAE 191
KR+ ++ E +++LA+L KAE+ E
Sbjct: 29 KRQGSQGLSQEEQQRLAQLTEKAERMRE 56
>gnl|CDD|119400 cd06661, GGCT_like, GGCT-like domains, also called AIG2-like
family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes
the formation of pyroglutamic acid (5-oxoproline) from
dipeptides containing gamma-glutamyl, and is a dimeric
protein. In Homo sapiens, the protein is encoded by the
gene C7orf24, and the enzyme participates in the
gamma-glutamyl cycle. Hereditary defects in the
gamma-glutamyl cycle have been described for some of the
genes involved, but not for C7orf24. The synthesis and
metabolism of glutathione
(L-gamma-glutamyl-L-cysteinylglycine) ties the
gamma-glutamyl cycle to numerous cellular processes;
glutathione acts as a ubiquitous reducing agent in
reductive mechanisms involved in protein and DNA
synthesis, transport processes, enzyme activity, and
metabolism. AIG2 (avrRpt2-induced gene) is an
Arabidopsis protein that exhibits RPS2- and
avrRpt2-dependent induction early after infection with
Pseudomonas syringae pv maculicola strain ES4326
carrying avrRpt2. avrRpt2 is an avirulence gene that can
convert virulent strains of P. syringae to avirulence on
Arabidopsis thaliana, soybean, and bean. The family also
includes bacterial tellurite-resistance proteins (trgB);
tellurium (Te) compounds are used in industrial
processes and had been used as antimicrobial agents in
the past. Some members have been described proteins
involved in cation transport (chaC).
Length = 99
Score = 26.5 bits (59), Expect = 4.3
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 101 AAALARLKAYEGVPAPYDKTKRMVIPDALKVLR 133
LARL A+EGVP Y + + V + + +
Sbjct: 61 PEDLARLDAFEGVPGGYRREEVEVELEDGEGVE 93
>gnl|CDD|222242 pfam13584, BatD, Oxygen tolerance. This family of proteins carries
up to three membrane spanning regions and is involved in
tolerance to oxygen in in Bacteroides spp.
Length = 488
Score = 27.6 bits (62), Expect = 5.8
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 163 KKRKERAQVAYERRKQLAKLRVKAEKAAEERLG 195
K+R A VA R K+ KL K K A++ L
Sbjct: 451 KRRARNADVAGNRTKKANKLAKKRLKEAKKALA 483
>gnl|CDD|217206 pfam02731, SKIP_SNW, SKIP/SNW domain. This domain is found in
chromatin proteins.
Length = 158
Score = 26.5 bits (59), Expect = 6.9
Identities = 12/36 (33%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 159 KELEKKRKERAQVAY-ERRKQLAKLRVKAEKAAEER 193
+E+ ++ + + Q+A E++++ KLR A++A EER
Sbjct: 123 EEVRQRAELQRQLAEKEKQEKEEKLRELAQRAREER 158
>gnl|CDD|216949 pfam02254, TrkA_N, TrkA-N domain. This domain is found in a wide
variety of proteins. These protein include potassium
channels, phosphoesterases, and various other
transporters. This domain binds to NAD.
Length = 116
Score = 26.0 bits (58), Expect = 7.6
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 21 LGRLASVLAKELLNGQKVVVV 41
GR+ LA+EL G VVV
Sbjct: 6 YGRVGRSLAEELREGGPDVVV 26
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 26.8 bits (60), Expect = 8.0
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 171 VAYERRKQLAKLRVKAEKAAEERL 194
V R +++ K++ KAE+ AEER+
Sbjct: 108 VKLVREEKIEKVKDKAEELAEERI 131
>gnl|CDD|149160 pfam07926, TPR_MLP1_2, TPR/MLP1/MLP2-like protein. The sequences
featured in this family are similar to a region of human
TPR protein and to yeast myosin-like proteins 1 (MLP1)
and 2 (MLP2). These proteins share a number of features;
for example, they all have coiled-coil regions and all
three are associated with nuclear pores. TPR is thought
to be a component of nuclear pore complex- attached
intra-nuclear filaments, and is implicated in nuclear
protein import. Moreover, its N-terminal region is
involved in the activation of oncogenic kinases,
possibly by mediating the dimerisation of kinase domains
or by targeting these kinases to the nuclear pore
complex. MLP1 and MLP2 are involved in the process of
telomere length regulation, where they are thought to
interact with proteins such as Tel1p and modulate their
activity.
Length = 132
Score = 26.1 bits (58), Expect = 9.2
Identities = 12/37 (32%), Positives = 24/37 (64%), Gaps = 4/37 (10%)
Query: 156 DTIKELEKKRKERAQVAYERRKQLAKLRVKAEKAAEE 192
+ I+EL+ RK+ ++ +K++A+L+ +AE A E
Sbjct: 56 EDIEELQALRKQLNEL----KKEIAQLKAEAESAQAE 88
>gnl|CDD|153317 cd07633, BAR_OPHN1, The Bin/Amphiphysin/Rvs (BAR) domain of
Oligophrenin-1. BAR domains are dimerization, lipid
binding and curvature sensing modules found in many
different proteins with diverse functions.
Oligophrenin-1 (OPHN1) is a GTPase activating protein
(GAP) with activity towards RhoA, Rac, and Cdc42, that
is expressed in developing spinal cord and in adult
brain areas with high plasticity. It plays a role in
regulating the actin cystoskeleton as well as morphology
changes in axons and dendrites, and may also function in
modulating neuronal connectivity. Mutations in the OPHN1
gene causes X-linked mental retardation associated with
cerebellar hypoplasia, lateral ventricle enlargement and
epilepsy. OPHN1 contains an N-terminal BAR domain,
followed by a Pleckstrin homology (PH) domain, and a Rho
GAP domain. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 207
Score = 26.5 bits (58), Expect = 9.5
Identities = 11/24 (45%), Positives = 14/24 (58%)
Query: 158 IKELEKKRKERAQVAYERRKQLAK 181
IK LE RKE+ ER+K+ K
Sbjct: 95 IKPLENFRKEQIGFTKERKKKFEK 118
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.323 0.137 0.402
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,759,940
Number of extensions: 1032353
Number of successful extensions: 1783
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1731
Number of HSP's successfully gapped: 131
Length of query: 206
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 114
Effective length of database: 6,857,034
Effective search space: 781701876
Effective search space used: 781701876
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (25.8 bits)