RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 028649
(206 letters)
>gnl|CDD|240253 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
Length = 202
Score = 258 bits (662), Expect = 1e-88
Identities = 115/185 (62%), Positives = 142/185 (76%)
Query: 10 KRVVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNT 69
K +V+D + H+LGRLAS+VAKELL GQK+V VRCE++ +SG L R K+KY FLRKRMNT
Sbjct: 4 KVIVIDCKGHLLGRLASVVAKELLLGQKIVVVRCEDLNISGSLFRNKVKYEEFLRKRMNT 63
Query: 70 KPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDAL 129
P GP H RAP+ IFWRTVRGM+PHKTKRGAAAL RLK +EGVPAPYDKVKR+VIP AL
Sbjct: 64 NPRRGPFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVFEGVPAPYDKVKRVVIPSAL 123
Query: 130 KVLRLQKGHKYCLLGRLASEVGWNYYDTIRELEKKRKERSQVAYERKKQLNKLRAKAEKV 189
+VLRL+ Y +LG L++ VGW Y D + +LE+KRKER+ Y++K +L K +A K
Sbjct: 124 RVLRLKPERPYTVLGDLSAHVGWKYADVVAKLEEKRKERAAAYYKKKVKLRKAWKEARKK 183
Query: 190 AEEKL 194
A KL
Sbjct: 184 ALAKL 188
>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 = 169 bits (430), Expect = 3e-54
Identities = 83/143 (58%), Positives = 99/143 (69%), Gaps = 1/143 (0%)
Query: 12 VVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKP 71
V+D H+LGRLAS+VAK+LLNG+KVV V E+I +SG R K+KY FLRKR T P
Sbjct: 1 TVIDGSGHILGRLASVVAKQLLNGEKVVVVNAEKIVISGNFYRNKLKYKEFLRKRTLTNP 60
Query: 72 SHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKV 131
GP RAP++IF RTVRGM+PHKT RG AAL RLK Y G+P DK KR+V+P+AL V
Sbjct: 61 RRGPFFPRAPSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDKKKRVVVPEAL-V 119
Query: 132 LRLQKGHKYCLLGRLASEVGWNY 154
RL KY LG LA +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 = 124 bits (315), Expect = 3e-37
Identities = 51/114 (44%), Positives = 62/114 (54%), Gaps = 13/114 (11%)
Query: 12 VVVDARHHMLGRLASIVAKELLN------------GQKVVAVRCEEICMSGGLVRQKMKY 59
V+DA+ +LGRLAS VAK LL G VV V E+I ++G RQK+ Y
Sbjct: 2 HVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVYY 61
Query: 60 MRFLRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGV 113
P+ GP+H RAP +I R VRGM+P K K G AAL RLK YEG
Sbjct: 62 RHTGYPGGLKNPTAGPLHPRAPERILKRAVRGMLP-KNKLGRAALKRLKVYEGA 114
>gnl|CDD|201314 pfam00572, Ribosomal_L13, Ribosomal protein L13.
Length = 128
Score = 116 bits (292), Expect = 2e-33
Identities = 48/129 (37%), Positives = 61/129 (47%), Gaps = 15/129 (11%)
Query: 12 VVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKY 59
V+DA+ +LGRLAS VAK L G VV + E+I ++G R + KY
Sbjct: 2 HVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVINAEKIVLTG-KKRDQKKY 60
Query: 60 MR-FLRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYD 118
R P+ R P +I R VRGM+P K K G AAL RLK Y G P P+
Sbjct: 61 YRHTGYPGGLKNPTAKGPLERKPERILERAVRGMLP-KNKLGRAALKRLKVYAGSPHPHA 119
Query: 119 KVKRMVIPD 127
K V+
Sbjct: 120 AQKPEVLEI 128
>gnl|CDD|235793 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
Length = 146
Score = 108 bits (271), Expect = 4e-30
Identities = 58/144 (40%), Positives = 81/144 (56%), Gaps = 3/144 (2%)
Query: 12 VVVDARHHMLGRLASIVAKELLNGQKVVAVRCEEICMSGGLVRQKMKYMRFLRKRMNTKP 71
VV+DA +LGRLAS VAK LL G++VV V E+ ++G R KY + + + P
Sbjct: 5 VVIDAEGQILGRLASYVAKRLLEGEEVVIVNAEKAVITGNRERVIEKYKQRRERGSHYNP 64
Query: 72 SHGPIHF-RAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALK 130
+ R P +IF RT+RGM+P+K RG AL RLK Y GVP + + VI +A
Sbjct: 65 YRNGPKYPRRPDRIFKRTIRGMLPYKKPRGREALKRLKVYVGVPKELEGKEFEVIDEAD- 123
Query: 131 VLRLQKGHKYCLLGRLASEVGWNY 154
+ RL KY LG ++ E+G +
Sbjct: 124 LSRL-STIKYVTLGEVSKELGAKF 146
>gnl|CDD|223180 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
structure and biogenesis].
Length = 148
Score = 93.9 bits (234), Expect = 1e-24
Identities = 47/138 (34%), Positives = 66/138 (47%), Gaps = 18/138 (13%)
Query: 12 VVVDARHHMLGRLASIVAKELLN------------GQKVVAVRCEEICMSGGLVRQKMKY 59
V+DA +LGRLAS VAK L G V+ + E++ ++G + K Y
Sbjct: 16 YVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKVVITGKKLTDKKYY 75
Query: 60 MRFLRKRMNTKPS-HGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYD 118
P+ GP+ R P +I R VRGM+P K G AAL RLK Y G+P P+
Sbjct: 76 RHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLP-KNPLGRAALKRLKVYAGIPHPH- 133
Query: 119 KVKRMVIPDALKVLRLQK 136
P+AL++ L+
Sbjct: 134 ---EAQKPEALELKLLKG 148
>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
Length = 144
Score = 42.7 bits (102), Expect = 2e-05
Identities = 31/123 (25%), Positives = 51/123 (41%), Gaps = 33/123 (26%)
Query: 12 VVVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKY 59
V+DA +LGRLAS VA L G V+ + E++ ++G + K+ Y
Sbjct: 16 YVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKVKLTGKKLTDKIYY 75
Query: 60 --------MRF--LRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKA 109
++ + + K P ++ + V+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 = 38.4 bits (90), Expect = 5e-04
Identities = 33/122 (27%), Positives = 50/122 (40%), Gaps = 33/122 (27%)
Query: 13 VVDARHHMLGRLASIVAKELLNGQK------------VVAVRCEEICMSGGLVRQKMKYM 60
VVDA LGRLAS VA+ L K V+ + E++ ++G + QK+ Y
Sbjct: 15 VVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKVRLTGKKLEQKVYYR 74
Query: 61 ----------RFLRKRMNTKPSHGPIHFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAY 110
R + + R P ++ V+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 = 37.3 bits (87), Expect = 0.001
Identities = 31/118 (26%), Positives = 50/118 (42%), Gaps = 25/118 (21%)
Query: 13 VVDARHHMLGRLASIVAKELL------------NGQKVVAVRCEEICMSGGLVRQKMKYM 60
++DA+ LGRLA+ +A L G V+ + E+I ++G
Sbjct: 18 IIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINAEKIKVTG-----NKTSQ 72
Query: 61 RFLRKRMNTKPSHGPI------HFRAPAKIFWRTVRGMIPHKTKRGAAALARLKAYEG 112
+F R + +P I R P +I + V+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 = 32.4 bits (75), Expect = 0.15
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 3/35 (8%)
Query: 171 VAYERKKQLNKLRAKAEKVAEEKLGSQLDILAPVK 205
V R+++ K+R KAE+ AEE++ LD L P
Sbjct: 108 VKMVREEKREKVREKAEEAAEERI---LDALLPPA 139
>gnl|CDD|236526 PRK09458, pspB, phage shock protein B; Provisional.
Length = 75
Score = 28.3 bits (64), Expect = 0.69
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 2/42 (4%)
Query: 164 KRKERSQVAYERKKQLNKLRAKAEKVAE--EKLGSQLDILAP 203
KR+ ++ E +++L +L KAE++ E + L + LD P
Sbjct: 29 KRQGSQGLSQEEQQRLAQLTEKAERMRERIQALEAILDAEHP 70
>gnl|CDD|205988 pfam13815, Dzip-like_N, Iguana/Dzip1-like DAZ-interacting protein
N-terminal. The DAZ gene-product - Deleted in
Azoospermia - and a closely related sequence are
required early in germ-cell development in order to
maintain germ-cell populations. This family is the
N-terminal region that is the only part of the protein
in some fungi and lower metazoa.
Length = 118
Score = 28.0 bits (63), Expect = 1.7
Identities = 11/37 (29%), Positives = 22/37 (59%)
Query: 156 DTIRELEKKRKERSQVAYERKKQLNKLRAKAEKVAEE 192
+ ELE++ +E Q A ER+++L+K + + + E
Sbjct: 80 QSNSELEERLQEALQEAEEREQELSKQSEELKSLKRE 116
>gnl|CDD|153294 cd07610, FCH_F-BAR, The Extended FES-CIP4 Homology (FCH) or F-BAR
(FCH and Bin/Amphiphysin/Rvs) domain, a dimerization
module that binds and bends membranes. F-BAR domains
are dimerization modules that bind and bend membranes
and are found in proteins involved in membrane dynamics
and actin reorganization. F-BAR domain containing
proteins, also known as Pombe Cdc15 homology (PCH)
family proteins, include Fes and Fer tyrosine kinases,
PACSINs/Syndapins, FCHO, PSTPIP, CIP4-like proteins and
srGAPs. Many members also contain an SH3 domain and play
roles in endocytosis. 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.
These tubules have diameters larger than those observed
with N-BARs. The F-BAR domains of some members such as
NOSTRIN and Rgd1 are important for the subcellular
localization of the protein.
Length = 191
Score = 28.5 bits (64), Expect = 2.1
Identities = 15/46 (32%), Positives = 25/46 (54%)
Query: 158 IRELEKKRKERSQVAYERKKQLNKLRAKAEKVAEEKLGSQLDILAP 203
+ E+ RK+ + KK+L +L AK K A+E+ Q++ L P
Sbjct: 92 KEDKEQARKKELAEGEKLKKKLQELWAKLAKKADEEYREQVEKLNP 137
>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 = 27.3 bits (61), Expect = 2.3
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 101 AAALARLKAYEGVPAPYDKVKRMVIPDALKVLR 133
LARL A+EGVP Y + + V + + +
Sbjct: 61 PEDLARLDAFEGVPGGYRREEVEVELEDGEGVE 93
>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 444
Score = 28.4 bits (64), Expect = 2.8
Identities = 13/33 (39%), Positives = 23/33 (69%), Gaps = 3/33 (9%)
Query: 171 VAYERKKQLNKLRAKAEKVAEEKLGSQLDILAP 203
V R++++ K++ KAE++AEE++ LD L P
Sbjct: 108 VKLVREEKIEKVKDKAEELAEERI---LDALVP 137
>gnl|CDD|224188 COG1269, NtpI, Archaeal/vacuolar-type H+-ATPase subunit I [Energy
production and conversion].
Length = 660
Score = 28.5 bits (64), Expect = 3.0
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 3/37 (8%)
Query: 158 IRELEKKRKERSQVAYERKKQLNKLRAKAEKVAEEKL 194
I ELE+ E E + ++L A AEK+AEE L
Sbjct: 231 ISELEEVIAEIQD---ELESLRSELEALAEKIAEELL 264
>gnl|CDD|165330 PHA03033, PHA03033, hypothetical protein; Provisional.
Length = 142
Score = 27.6 bits (61), Expect = 3.2
Identities = 9/21 (42%), Positives = 18/21 (85%)
Query: 153 NYYDTIRELEKKRKERSQVAY 173
Y++I+EL+K++K++ +VAY
Sbjct: 43 KKYNSIKELKKQKKKKGEVAY 63
>gnl|CDD|218215 pfam04696, Pinin_SDK_memA, pinin/SDK/memA/ protein conserved
region. Members of this family have very varied
localisations within the eukaryotic cell. pinin is known
to localise at the desmosomes and is implicated in
anchoring intermediate filaments to the desmosomal
plaque. SDK2/3 is a dynamically localised nuclear
protein thought to be involved in modulation of
alternative pre-mRNA splicing. memA is a tumour marker
preferentially expressed in human melanoma cell lines. A
common feature of the members of this family is that
they may all participate in regulating protein-protein
interactions.
Length = 131
Score = 27.4 bits (61), Expect = 3.3
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 160 ELEKKRKERSQVAYERKKQLNKLRAKAEKVAEEKL 194
E E+ RKE+ ++ ER+++ +LR +K+ +EKL
Sbjct: 51 EREELRKEKRELFEERRRKQLELRKLEQKMEDEKL 85
>gnl|CDD|227546 COG5221, DOP1, Dopey and related predicted leucine zipper
transcription factors [Transcription].
Length = 1618
Score = 28.4 bits (63), Expect = 3.6
Identities = 13/67 (19%), Positives = 27/67 (40%), Gaps = 7/67 (10%)
Query: 83 KIFWRTVRGMIPHKTKRGAAALARLKAYEGVPAPYDKVKRMVIPDALKVLRLQKGHKYCL 142
+FW ++ G++ + + L L E + D +R+++P A ++R L
Sbjct: 181 DVFWSSMWGILLNDERLRTGVLNSLMREENNDSHMDWSERLILPHAGLMVR-------AL 233
Query: 143 LGRLASE 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 = 27.4 bits (61), Expect = 4.4
Identities = 14/36 (38%), Positives = 25/36 (69%), Gaps = 3/36 (8%)
Query: 159 RELEKKRKERSQVAYERKKQLNKLRAKAEKVAEEKL 194
RELEK +KER++ E++++ + A+ EK EE++
Sbjct: 149 RELEKIKKERAE---EKEREEEEKAAEEEKAREEEI 181
>gnl|CDD|179379 PRK02155, ppnK, NAD(+)/NADH kinase family protein; Provisional.
Length = 291
Score = 27.6 bits (62), Expect = 4.4
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 145 RLASEVGWNYYDTIRE 160
R VG++YY T+R+
Sbjct: 267 RFLHPVGYSYYATLRK 282
>gnl|CDD|215819 pfam00251, Glyco_hydro_32N, Glycosyl hydrolases family 32
N-terminal domain. This domain corresponds to the
N-terminal domain of glycosyl hydrolase family 32 which
forms a five bladed beta propeller structure.
Length = 305
Score = 27.6 bits (62), Expect = 4.6
Identities = 7/21 (33%), Positives = 9/21 (42%), Gaps = 1/21 (4%)
Query: 67 MNTKPSHGPIHFRAPAKIFWR 87
+ P HFR P K+ W
Sbjct: 117 IINPPPGYTKHFRDP-KVAWY 136
>gnl|CDD|148332 pfam06667, PspB, Phage shock protein B. This family consists of
several bacterial phage shock protein B (PspB)
sequences. The phage shock protein (psp) operon is
induced in response to heat, ethanol, osmotic shock and
infection by filamentous bacteriophages. Expression of
the operon requires the alternative sigma factor sigma54
and the transcriptional activator PspF. In addition,
PspA plays a negative regulatory role, and the
integral-membrane proteins PspB and PspC play a positive
one.
Length = 75
Score = 26.0 bits (58), Expect = 5.0
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 164 KRKERSQVAYERKKQLNKLRAKAEKVAE 191
K K ++ E ++ L +L AEK+ E
Sbjct: 29 KWKVSQGLSEEDEQLLEELLETAEKLQE 56
>gnl|CDD|233012 TIGR00535, SAM_DCase, S-adenosylmethionine decarboxylase proenzyme,
eukaryotic form. This enzyme is a key regulatory enzyme
of the polyamine synthetic pathway. This protein is a
pyruvoyl-dependent enzyme. The proenzyme is cleaved at a
Ser residue that becomes a pyruvoyl group active site
[Central intermediary metabolism, Polyamine
biosynthesis].
Length = 334
Score = 27.5 bits (61), Expect = 5.3
Identities = 10/39 (25%), Positives = 13/39 (33%), Gaps = 1/39 (2%)
Query: 136 KGHKYCLLGRLASEVGWNYYDTIRELEKKRKERSQVAYE 174
G Y + G A W+ Y E E + E E
Sbjct: 136 NGKAYVV-GDPAKPQKWHLYVAETERETPKIEDPDETLE 173
>gnl|CDD|240226 PTZ00007, PTZ00007, (NAP-L) nucleosome assembly protein -L;
Provisional.
Length = 337
Score = 27.5 bits (61), Expect = 5.6
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 157 TIRELEKKRKERSQVAYERKKQLNKLRAKAEK 188
T+++L+ +KE + E +L KLR+K E
Sbjct: 42 TLKKLQLLQKEFDDLEVEYNAELRKLRSKYED 73
>gnl|CDD|220369 pfam09731, Mitofilin, Mitochondrial inner membrane protein.
Mitofilin controls mitochondrial cristae morphology.
Mitofilin is enriched in the narrow space between the
inner boundary and the outer membranes, where it forms a
homotypic interaction and assembles into a large
multimeric protein complex. The first 78 amino acids
contain a typical amino-terminal-cleavable mitochondrial
presequence rich in positive-charged and hydroxylated
residues and a membrane anchor domain. In addition, it
has three centrally located coiled coil domains.
Length = 493
Score = 27.3 bits (61), Expect = 6.2
Identities = 11/48 (22%), Positives = 20/48 (41%), Gaps = 2/48 (4%)
Query: 153 NYYDTIRELEKKRKERSQVAYERK--KQLNKLRAKAEKVAEEKLGSQL 198
+ E R E + A E++ + + + + K EEKL +L
Sbjct: 200 ELLSKLEEELLARLESKEAALEKQLRLEFEREKEELRKKYEEKLRQEL 247
>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 = 26.9 bits (59), Expect = 7.7
Identities = 16/42 (38%), Positives = 19/42 (45%), Gaps = 8/42 (19%)
Query: 158 IRELEKKRKERSQVAYERKKQLNKLRAKAEKVAEEKLGSQLD 199
I+ LE RKE+ ERKK+ K EK S LD
Sbjct: 95 IKPLENFRKEQIGFTKERKKKFEK--------DSEKFYSLLD 128
>gnl|CDD|233067 TIGR00641, acid_CoA_mut_N, methylmalonyl-CoA mutase N-terminal
domain. Methylmalonyl-CoA mutase (EC 5.4.99.2)
catalyzes a reversible isomerization between
L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an
adenosylcobalamin cofactor. It may be a homodimer, as in
mitochondrion, or a heterodimer with partially
homologous beta chain that does not bind the
adenosylcobalamin cofactor, as in Propionibacterium
freudenreichii. The most similar archaeal sequences are
separate chains, such as AF2215 abd AF2219 of
Archaeoglobus fulgidus, that correspond roughly to the
first 500 and last 130 residues, respectively of known
methylmalonyl-CoA mutases. This model describes the
N-terminal domain subfamily. In a neighbor-joining tree,
AF2215 branches with a bacterial isobutyryl-CoA mutase,
which is also the same length. Scoring between the noise
and trusted cutoffs are the non-catalytic, partially
homologous beta chains from certain heterodimeric
examples of 5.4.99.2.
Length = 524
Score = 27.0 bits (60), Expect = 7.8
Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 158 IRELEKKRKERSQVAYERKKQLNKLRAKAEKVAEEKLGSQLD 199
I +L+K R ER Q E L+ L AEK E L +D
Sbjct: 457 IAKLKKLRAERDQEKVEAA--LDALTKAAEKEDENLLALAID 496
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 27.0 bits (60), Expect = 9.0
Identities = 15/37 (40%), Positives = 25/37 (67%), Gaps = 3/37 (8%)
Query: 159 RELEKKRKERSQVAYE---RKKQLNKLRAKAEKVAEE 192
RE+E++RK R ++ E K++L LRA+ E+V +E
Sbjct: 343 REIEEERKRRDKLTEEYAELKEELEDLRAELEEVDKE 379
>gnl|CDD|151665 pfam11223, DUF3020, Protein of unknown function (DUF3020). This
family of fungal proteins is conserved towards the
C-terminus of HMG domains. The function is not known.
Length = 49
Score = 24.5 bits (53), Expect = 9.4
Identities = 10/35 (28%), Positives = 23/35 (65%)
Query: 163 KKRKERSQVAYERKKQLNKLRAKAEKVAEEKLGSQ 197
++RK++ + A + + N LR++ +K A++K G +
Sbjct: 2 RERKKKWREANSERNKDNDLRSRVKKKAKKKFGKE 36
>gnl|CDD|239789 cd04256, AAK_P5CS_ProBA, AAK_P5CS_ProBA: Glutamate-5-kinase (G5K)
domain of the bifunctional delta
1-pyrroline-5-carboxylate synthetase (P5CS), composed
of an N-terminal G5K (ProB) and a C-terminal glutamyl
5- phosphate reductase (G5PR, ProA), the first and
second enzyme catalyzing proline (and, in mammals,
ornithine) biosynthesis. G5K transfers the terminal
phosphoryl group of ATP to the gamma-carboxyl group of
glutamate, and is subject to feedback allosteric
inhibition by proline or ornithine. In plants, proline
plays an important role as an osmoprotectant and, in
mammals, ornithine biosynthesis is crucial for proper
ammonia detoxification, since a G5K mutation has been
shown to cause human hyperammonaemia.
Length = 284
Score = 26.6 bits (59), Expect = 9.7
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 21/74 (28%)
Query: 9 AKRVVV----------DARHHMLGRLASIV--AKELLN-GQKVVAVRCEEICMSG--GLV 53
AKR+VV D LGRLASIV EL + G++V+ V SG
Sbjct: 8 AKRIVVKLGSAVVTREDECGLALGRLASIVEQVSELQSQGREVILV------TSGAVAFG 61
Query: 54 RQKMKYMRFLRKRM 67
+Q++++ L M
Sbjct: 62 KQRLRHEILLSSSM 75
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
0.322 0.136 0.399
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: 10,653,357
Number of extensions: 1017519
Number of successful extensions: 1759
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1722
Number of HSP's successfully gapped: 107
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 (21.9 bits)
S2: 57 (25.8 bits)