RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7757
(143 letters)
>gnl|CDD|193593 cd09979, LOTUS_3_Limkain_b1, The third LOTUS domain on Limkain
b1(LKAP). The third LOTUS domain on Limkain b1(LKAP):
Limkain b1 is a novel human autoantigen, localized to a
subset of ABCD3 and PXF marked peroxisomes. Limkain b1
may be a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. The protein contains multiple copies of
LOTUS domains and a conserved RNA recognition motif.
The exact molecular function of LOTUS domain remains to
be identified. Its occurrence in proteins associated
with RNA metabolism suggests that it might be involved
in RNA binding function. The presence of several basic
residues and RNA fold recognition motifs support this
hypothesis. The RNA binding function might be the first
step of regulating mRNA translation or localization.
Length = 72
Score = 117 bits (295), Expect = 1e-35
Identities = 38/61 (62%), Positives = 53/61 (86%)
Query: 73 MSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQV 132
+ RE++DLLK+ P C + F++FIPAYHHHFG+QCRV+DYG+TKLI+LLEA+PHV+Q+
Sbjct: 1 LIQFSREVIDLLKSQPSCLLPFSRFIPAYHHHFGKQCRVSDYGYTKLIELLEAVPHVLQI 60
Query: 133 I 133
+
Sbjct: 61 L 61
>gnl|CDD|193595 cd09981, LOTUS_5_Limkain_b1, The fifth LOTUS domain on Limkain
b1(LKAP). The fifth LOTUS domain on Limkain b1(LKAP):
Limkain b1 is a novel human autoantigen, localized to a
subset of ABCD3 and PXF marked peroxisomes. Limkain b1
may be a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. The protein contains multiple copies of
LOTUS domains and a conserved RNA recognition motif.
The exact molecular function of LOTUS domain remains to
be identified. Its occurrence in proteins associated
with RNA metabolism suggests that it might be involved
in RNA binding function. The presence of several basic
residues and RNA fold recognition motifs support this
hypothesis. The RNA binding function might be the first
step of regulating mRNA translation or localization.
Length = 71
Score = 111 bits (280), Expect = 2e-33
Identities = 36/56 (64%), Positives = 48/56 (85%)
Query: 78 RELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVI 133
+E+V+LL+ PH +M F KFIP+YHHHFGRQC+++ YGFTKL++L EAIP VVQV+
Sbjct: 6 KEVVELLRHQPHFRMPFTKFIPSYHHHFGRQCKLSYYGFTKLLELFEAIPDVVQVL 61
>gnl|CDD|193585 cd08824, LOTUS, LOTUS is an uncharacterized small globular domain
found in Limkain b1, Oskar and Tudor-containing proteins
5 and 7. LOTUS is an uncharacterized small globular
domain found in Limkain b1, Oskar and Tudor-containing
proteins 5 and 7. The LOTUS containing proteins are
germline-specific and are found in the nuage/polar
granules of germ cells. Tudor-containing protein 5 and 7
belong to the evolutionary conserved Tudor
domain-containing protein (TDRD) family involved in germ
cell development. In mice, TDRD5 and TDRD7 are
components of the intermitochondrial cements (IMCs) and
the chromatoid bodies (CBs), which are cytoplasmic
ribonucleoprotein granules involved in RNA processing
for spermatogenesis. Oskar protein is a critical
component of the pole plasm in the Drosophila oocyte,
which is required for germ cell formation. Limkain b1 is
a novel human autoantigen, localized to a subset of
ABCD3 and PXF marked peroxisomes. Limkain b1 may be a
relatively common target of human autoantibodies
reactive to cytoplasmic vesicle-like structures. Limkain
b1 contains multiple copies of LOTUS domains and a
conserved RNA recognition motif. The exact molecular
function of LOTUS domain remains to be characterized.
Its occurrence in proteins associated with RNA
metabolism suggests that it might be involved in RNA
binding function. The presence of several basic residues
and RNA fold recognition motifs support this hypothesis.
The RNA binding function might be the first step of
regulating mRNA translation or localization.
Length = 70
Score = 68.8 bits (169), Expect = 1e-16
Identities = 22/55 (40%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 78 RELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQV 132
++L LL+++P + +K Y FG+ +++YGF+KL DLLEA+P VV V
Sbjct: 6 KQLRSLLQSYPGG-LPLSKLPQLYKKKFGKPLDLSEYGFSKLSDLLEALPGVVIV 59
>gnl|CDD|193594 cd09980, LOTUS_4_Limkain_b1, The fourth LOTUS domain on Limkain
b1(LKAP). The fourth LOTUS domain on Limkain b1(LKAP):
Limkain b1 is a novel human autoantigen, localized to a
subset of ABCD3 and PXF marked peroxisomes. Limkain b1
may be a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. The protein contains multiple copies of
LOTUS domains and a conserved RNA recognition motif.
The exact molecular function of LOTUS domain remains to
be identified. Its occurrence in proteins associated
with RNA metabolism suggests that it might be involved
in RNA binding function. The presence of several basic
residues and RNA fold recognition motifs support this
hypothesis. The RNA binding function might be the first
step of regulating mRNA translation or localization.
Length = 72
Score = 44.3 bits (105), Expect = 5e-07
Identities = 21/55 (38%), Positives = 27/55 (49%)
Query: 79 ELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVI 133
+L+ +LK+ Q++ F AY FGR DYG L DLL IP VI
Sbjct: 7 DLLRVLKSQASKQVIVKDFGQAYEWCFGRDWDPVDYGLCDLQDLLSEIPDNTIVI 61
>gnl|CDD|221822 pfam12872, OST-HTH, OST-HTH/LOTUS domain. A predicted RNA-binding
domain found in insect Oskar and vertebrate TDRD5/TDRD7
proteins that nucleate or organize structurally related
ribonucleoprotein (RNP) complexes, the polar granule and
nuage, is poorly understood. The domain adopts the
winged helix-turn- helix fold and bind RNA with a
potential specificity for dsRNA.In eukaryotes this
domain is often combined in the same polypeptide with
protein-protein- or lipid- interaction domains that
might play a role in anchoring these proteins to
specific cytoskeletal structures. Thus, proteins with
this domain might have a key role in the recognition and
localization of dsRNA, including miRNAs, rasiRNAs and
piRNAs hybridized to their targets. In other cases, this
domain is fused to ubiquitin-binding, E3 ligase and
ubiquitin-like domains indicating a previously
under-appreciated role for ubiquitination in regulating
the assembly and stability of nuage-like RNP complexes.
Both bacteria and eukaryotes encode a conserved family
of proteins that combines this predicted RNA-binding
domain with a previously uncharacterized RNAse domain
belonging to the superfamily that includes the 5'->3'
nucleases, PIN and NYN domains.
Length = 74
Score = 44.2 bits (105), Expect = 5e-07
Identities = 16/57 (28%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 78 RELVDLLKTFPH--CQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQV 132
+ L L++ ++ Y F +YG++KL DLLEAIP + +V
Sbjct: 8 KLLRKALESSSDEDGWASLSELGSEYRKLF-PDFDPRNYGYSKLSDLLEAIPDLFEV 63
>gnl|CDD|193598 cd09984, LOTUS_8_Limkain_b1, The eighth LOTUS domain on Limkain
b1(LKAP). The eighth LOTUS domain on Limkain b1(LKAP):
Limkain b1 is a novel human autoantigen, localized to a
subset of ABCD3 and PXF marked peroxisomes. Limkain b1
may be a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. The protein contains multiple copies of
LOTUS domains and a conserved RNA recognition motif.
The exact molecular function of LOTUS domain remains to
be identified. Its occurrence in proteins associated
with RNA metabolism suggests that it might be involved
in RNA binding function. The presence of several basic
residues and RNA fold recognition motifs support this
hypothesis. The RNA binding function might be the first
step of regulating mRNA translation or localization.
Length = 76
Score = 39.1 bits (91), Expect = 5e-05
Identities = 18/56 (32%), Positives = 30/56 (53%)
Query: 75 LLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVV 130
+ + LL T+ + Q+ ++F AY + G + +YG+ L +LL AIP VV
Sbjct: 3 QFAKNVRSLLHTYHYQQIFLHEFSSAYSKYVGETLQPKNYGYNSLEELLGAIPQVV 58
>gnl|CDD|193589 cd09975, LOTUS_2_TDRD5, The second LOTUS domain on Tudor-containing
protein 5 (TDRD5). The second LOTUS domain on
Tudor-containing protein 5 (TDRD5): TDRD5 contains three
N-terminal LOTUS domains and a C-terminal Tudor domain.
It belongs to the evolutionary conserved Tudor
domain-containing protein (TDRD) family involved in germ
cell development. In mice TDRD5 is a component of the
intermitochondrial cements (IMCs) and the chromatoid
bodies (CBs), which are cytoplasmic ribonucleoprotein
granules involved in RNA processing for spermatogenesis.
The exact molecular function of LOTUS domain on TDRD5
remains to be discovered. Its occurrence in proteins
associated with RNA metabolism suggests that it might be
involved in RNA binding function. The presence of
several basic residues and RNA fold recognition motifs
support this hypothesis. The RNA binding function might
be the first step of regulating mRNA translation or
localization.
Length = 70
Score = 34.9 bits (80), Expect = 0.002
Identities = 19/63 (30%), Positives = 25/63 (39%), Gaps = 3/63 (4%)
Query: 78 RELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVIMDFL 137
EL DLL P K AY FGR + YGF ++++L A + V
Sbjct: 6 SELKDLLSHSPVLLSELEK---AYVARFGRSFQYTQYGFFSMLEVLSAASDFIIVKQTRT 62
Query: 138 RSQ 140
S
Sbjct: 63 GSL 65
>gnl|CDD|193591 cd09977, LOTUS_1_Limkain_b1, The first LOTUS domain on Limkain
b1(LKAP). The first LOTUS domain on Limkain b1(LKAP):
Limkain b1 is a novel human autoantigen, localized to a
subset of ABCD3 and PXF marked peroxisomes. Limkain b1
may be a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. The protein contains multiple copies of
LOTUS domains and a conserved RNA recognition motif.
The exact molecular function of LOTUS domain remains to
be identified. Its occurrence in proteins associated
with RNA metabolism suggests that it might be involved
in RNA binding function. The presence of several basic
residues and RNA fold recognition motifs support this
hypothesis. The RNA binding function might be the first
step of regulating mRNA translation or localization.
Length = 62
Score = 32.2 bits (73), Expect = 0.013
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 73 MSLLCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVAD-YGFTKLIDLLE 124
+SLL E V +L+ P C + KF Y FG + V+D Y T + + E
Sbjct: 1 LSLLSSETVSILQDAPACCLPLFKFTEIYEKKFGHKLAVSDLYRLTDTVAIRE 53
>gnl|CDD|199214 cd10146, LabA_like_C, C-terminal domain of LabA_like proteins.
This C-terminal domain is found in a well conserved
group of mainly bacterial proteins with no defined
function, which contain an N-terminal LabA-like domain.
LabA from Synechococcus elongatus PCC 7942, (which does
not contain this C-terminal domain) has been shown to
play a role in cyanobacterial circadian timing.
LabA-like C-terminal domains described here may be
related to the LOTUS domain family (which also co-occurs
with LabA-like N-terminal domains).
Length = 69
Score = 27.9 bits (63), Expect = 0.57
Identities = 7/17 (41%), Positives = 13/17 (76%)
Query: 113 DYGFTKLIDLLEAIPHV 129
+YG++KL DL++A+
Sbjct: 39 NYGYSKLSDLIKALDLF 55
>gnl|CDD|193596 cd09982, LOTUS_6_Limkain_b1, The sixth LOTUS domain on Limkain
b1(LKAP). The sixth LOTUS domain on Limkain b1(LKAP):
Limkain b1 is a novel human autoantigen, localized to a
subset of ABCD3 and PXF marked peroxisomes. Limkain b1
may be a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. The protein contains multiple copies of
LOTUS domains and a conserved RNA recognition motif.
The exact molecular function of LOTUS domain remains to
be identified. Its occurrence in proteins associated
with RNA metabolism suggests that it might be involved
in RNA binding function. The presence of several basic
residues and RNA fold recognition motifs support this
hypothesis. The RNA binding function might be the first
step of regulating mRNA translation or localization.
Length = 71
Score = 27.9 bits (62), Expect = 0.58
Identities = 16/58 (27%), Positives = 30/58 (51%)
Query: 76 LCRELVDLLKTFPHCQMVFNKFIPAYHHHFGRQCRVADYGFTKLIDLLEAIPHVVQVI 133
L +LV LL++ ++ + Y FG R+ DY + + L++ + HVV+V+
Sbjct: 4 LAAQLVKLLRSQKDSCLMMCDLLTEYSKTFGYTLRLQDYDVSSVPALMQKLCHVVKVV 61
>gnl|CDD|193597 cd09983, LOTUS_7_Limkain_b1, The seventh LOTUS domain on Limkain
b1(LKAP). The seventh LOTUS domain on Limkain b1(LKAP):
Limkain b1 is a novel human autoantigen, localized to a
subset of ABCD3 and PXF marked peroxisomes. Limkain b1
may be a relatively common target of human
autoantibodies reactive to cytoplasmic vesicle-like
structures. The protein contains multiple copies of
LOTUS domains and a conserved RNA recognition motif.
The exact molecular function of LOTUS domain remains to
be identified. Its occurrence in proteins associated
with RNA metabolism suggests that it might be involved
in RNA binding function. The presence of several basic
residues and RNA fold recognition motifs support this
hypothesis. The RNA binding function might be the first
step of regulating mRNA translation or localization.
Length = 73
Score = 27.0 bits (60), Expect = 1.1
Identities = 9/20 (45%), Positives = 17/20 (85%)
Query: 113 DYGFTKLIDLLEAIPHVVQV 132
+YGF L +LL+++P++V+V
Sbjct: 42 EYGFMSLTELLKSLPYLVEV 61
>gnl|CDD|193590 cd09976, LOTUS_3_TDRD5, The third LOTUS domain on Tudor-containing
protein 5 (TDRD5). The third LOTUS domain on
Tudor-containing protein 5 (TDRD5): TDRD5 contains three
N-terminal LOTUS domains and a C-terminal Tudor domain.
It belongs to the evolutionary conserved Tudor
domain-containing protein (TDRD) family involved in germ
cell development. In mice TDRD5 is a component of the
intermitochondrial cements (IMCs) and the chromatoid
bodies (CBs), which are cytoplasmic ribonucleoprotein
granules involved in RNA processing for spermatogenesis.
The exact molecular function of LOTUS domain on TDRD5
remains to be identified. Its occurrence in proteins
associated with RNA metabolism suggests that it might be
involved in RNA binding function. The presence of
several basic residues and RNA fold recognition motifs
support this hypothesis. The RNA binding function might
be the first step of regulating mRNA translation or
localization.
Length = 74
Score = 27.4 bits (61), Expect = 1.1
Identities = 11/58 (18%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 76 LCRELVDLLKTFPHCQMVFNKFIPA-YHHHFGRQCRVADYGFTKLIDLLEAIPHVVQV 132
L E+ +++ P +F +P Y F + V GF + +L+ ++ ++ +
Sbjct: 4 LREEIRKVVENHP--NGLFIALLPTEYKVLFKEELPVKQLGFLSVTELVGSLSDILAI 59
>gnl|CDD|223058 PHA03366, PHA03366, FGAM-synthase; Provisional.
Length = 1304
Score = 28.5 bits (64), Expect = 1.3
Identities = 15/35 (42%), Positives = 19/35 (54%)
Query: 52 SSDEGGSSETSPSVSPSLQGQMSLLCRELVDLLKT 86
S +GGS S S P L + + RELV LL+T
Sbjct: 89 SRGKGGSRTLSFSYGPDLNRRPTTFSRELVALLQT 123
>gnl|CDD|206355 pfam14187, DUF4310, Domain of unknown function (DUF4310). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 214 and 231 amino
acids in length.
Length = 210
Score = 27.7 bits (62), Expect = 1.6
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 20 VKENMSTPVADIVMGAGDSMG 40
+ ++ ST ADI+MGAG++ G
Sbjct: 137 INQSNSTFGADIMMGAGNATG 157
>gnl|CDD|202341 pfam02671, PAH, Paired amphipathic helix repeat. This family
contains the paired amphipathic helix repeat. The
family contains the yeast SIN3 gene (also known as
SDI1) that is a negative regulator of the yeast HO
gene. This repeat may be distantly related to the
helix-loop-helix motif, which mediate protein-protein
interactions.
Length = 47
Score = 25.9 bits (58), Expect = 2.0
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 76 LCRELVDLLKTFPHCQMVFNKFIP 99
L + +LLK P + FN F+P
Sbjct: 24 LIARVAELLKGHPDLLLGFNVFLP 47
>gnl|CDD|220532 pfam10033, ATG13, Autophagy-related protein 13. Members of this
family of phosphoproteins are involved in cytoplasm to
vacuole transport (Cvt), and more specifically in Cvt
vesicle formation. They are probably involved in the
switching machinery regulating the conversion between
the Cvt pathway and autophagy. Finally, ATG13 is also
required for glycogen storage.
Length = 228
Score = 26.2 bits (58), Expect = 6.1
Identities = 9/40 (22%), Positives = 17/40 (42%)
Query: 49 IQHSSDEGGSSETSPSVSPSLQGQMSLLCRELVDLLKTFP 88
I+ + + S P++ + +L R L LL+ P
Sbjct: 111 IELDNSGTDTESDSGEELPTIYKRAIVLFRSLYTLLRLLP 150
>gnl|CDD|132618 TIGR03579, EF_0833, conserved hypothetical protein
EF_0833/AHA_3914. Members of this family of relatively
rare proteins are found in both Gram-positive (e.g.
Enterococcus faecalis) and Gram-negative (e.g. Aeromonas
hydrophila) bacteria, as part of a cluster of conserved
proteins. The function is unknown.
Length = 209
Score = 25.5 bits (56), Expect = 9.8
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 3/40 (7%)
Query: 1 MSARINAMVLVARHAATTIVKENMSTPVADIVMGAGDSMG 40
+ + ++++ R T+ + N ST AD++MGAG+S G
Sbjct: 118 LGLAVGYVIILIRK--FTVGQSN-STFGADVMMGAGNSSG 154
>gnl|CDD|193586 cd09972, LOTUS_TDRD_OSKAR, The first LOTUS domain in Oskar and
Tudor-containing proteins 5 and 7. The first LOTUS
domain in Oskar and Tudor-containing proteins 5 and 7:
The LOTUS containing proteins are germline-specific and
are found in the nuage/polar granules of germ cells.
Tudor-containing protein 5 and 7 belong to the
evolutionary conserved Tudor domain-containing protein
(TDRD) family involved in germ cell development. In
mice, TDRD5 and TDRD7 are components of the
intermitochondrial cements (IMCs) and the chromatoid
bodies (CBs), which are cytoplasmic ribonucleoprotein
granules involved in RNA processing for spermatogenesis.
Oskar protein is a critical component of the pole plasm
in the Drosophila oocyte, which is required for germ
cell formation.The exact molecular function of LOTUS
domain remains to be identified. Its occurrence in
proteins associated with RNA metabolism suggests that it
might be involved in RNA binding function. The presence
of several basic residues and RNA fold recognition
motifs support this hypothesis. The RNA binding function
might be the first step of regulating mRNA translation
or localization.
Length = 87
Score = 24.8 bits (55), Expect = 10.0
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 114 YGFTKLIDLLEAIPHVVQV 132
G++ L D L +IP VV V
Sbjct: 41 LGYSSLEDFLRSIPDVVTV 59
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 0.133 0.387
Gapped
Lambda K H
0.267 0.0689 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,046,583
Number of extensions: 602947
Number of successful extensions: 543
Number of sequences better than 10.0: 1
Number of HSP's gapped: 543
Number of HSP's successfully gapped: 21
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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: 54 (24.7 bits)