RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6026
(98 letters)
>gnl|CDD|212472 cd01725, LSm2, Like-Sm protein 2. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. Members of
this family share a highly conserved Sm fold containing
an N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet.
Length = 89
Score = 184 bits (470), Expect = 9e-63
Identities = 76/89 (85%), Positives = 85/89 (95%)
Query: 5 LFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCF 64
LF+SFFK+LVGK+V VELKND+SI GTLHSVDQYLNIKLT+ISV DP+KYPH+LSVKNCF
Sbjct: 1 LFFSFFKTLVGKEVTVELKNDLSITGTLHSVDQYLNIKLTNISVNDPEKYPHLLSVKNCF 60
Query: 65 IRGSVVRYVQLPGDEVDTQLLQDATRKEA 93
IRGSVVRYVQLP DEVDT+LLQDATR+EA
Sbjct: 61 IRGSVVRYVQLPADEVDTELLQDATRREA 89
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 68.7 bits (169), Expect = 3e-17
Identities = 27/68 (39%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67
F K L+GK V+VELKN GTL DQ++N+ L D+ T D + FIRG
Sbjct: 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGE-KKRKLGLVFIRG 59
Query: 68 SVVRYVQL 75
+ + Y+ L
Sbjct: 60 NNIVYIIL 67
>gnl|CDD|212480 cd01733, LSm10, Like-Sm protein 10. The eukaryotic Sm and
Sm-like (LSm) proteins associate with RNA to form the
core domain of the ribonucleoprotein particles involved
in a variety of RNA processing events including
pre-mRNA splicing, telomere replication, and mRNA
degradation. Members of this family share a highly
conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet. LSm10 is an SmD1-like protein which is
thought to bind U7 snRNA along with LSm11 and five
other Sm subunits to form a 7-membered ring structure.
LSm10 and the U7 snRNP of which it is a part are
thought to play an important role in histone mRNA 3'
processing.
Length = 78
Score = 66.0 bits (162), Expect = 6e-16
Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
++L G+ VEL+N+ S+ G + +VD ++NI L+D + TD H F++G
Sbjct: 13 LLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQHHFD--EFFVQGR 70
Query: 69 VVRYVQLP 76
+RYV +P
Sbjct: 71 NIRYVHIP 78
>gnl|CDD|201787 pfam01423, LSM, LSM domain. The LSM domain contains Sm proteins
as well as other related LSM (Like Sm) proteins. The
U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein
particles (snRNPs) involved in pre-mRNA splicing
contain seven Sm proteins (B/B', D1, D2, D3, E, F and
G) in common, which assemble around the Sm site present
in four of the major spliceosomal small nuclear RNAs.
The U6 snRNP binds to the LSM (Like Sm) proteins. Sm
proteins are also found in archaebacteria, which do not
have any splicing apparatus suggesting a more general
role for Sm proteins. All Sm proteins contain a common
sequence motif in two segments, Sm1 and Sm2, separated
by a short variable linker. This family also includes
the bacterial Hfq (host factor Q) proteins. Hfq are
also RNA-binding proteins, that form hexameric rings.
Length = 66
Score = 63.7 bits (156), Expect = 3e-15
Identities = 24/68 (35%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 8 SFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRG 67
F + L+GK V VELKN + GTL DQ++N+ L D+ T D + L IRG
Sbjct: 1 KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLG--LVLIRG 58
Query: 68 SVVRYVQL 75
+ + +
Sbjct: 59 NNIVLISP 66
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 63.5 bits (155), Expect = 5e-15
Identities = 24/77 (31%), Positives = 32/77 (41%), Gaps = 2/77 (2%)
Query: 1 MERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPH--ML 58
M L SF K L+ K V+V+LKN GTL DQY+N+ L D+
Sbjct: 3 MLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRR 62
Query: 59 SVKNCFIRGSVVRYVQL 75
IRG + +
Sbjct: 63 LGGEVLIRGDNIVLISP 79
>gnl|CDD|212470 cd01723, LSm4, Like-Sm protein 4. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. Members of
this family share a highly conserved Sm fold containing
an N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet.
Length = 76
Score = 55.7 bits (135), Expect = 6e-12
Identities = 24/69 (34%), Positives = 41/69 (59%), Gaps = 5/69 (7%)
Query: 15 GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPD--KYPHMLSVKNCFIRGSVVRY 72
G V+VELKN + G L + D ++NI L ++ T D ++ M C+IRG+ ++Y
Sbjct: 11 GHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKM---PECYIRGNTIKY 67
Query: 73 VQLPGDEVD 81
++LP + +D
Sbjct: 68 LRLPDEVID 76
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins. The eukaryotic Sm and
Sm-like (LSm) proteins associate with RNA to form the
core domain of the ribonucleoprotein particles involved
in a variety of RNA processing events including
pre-mRNA splicing, telomere replication, and mRNA
degradation. Members of this family share a highly
conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet. Sm-like proteins exist in archaea as well
as prokaryotes that form heptameric and hexameric ring
structures similar to those found in eukaryotes.
Length = 63
Score = 54.9 bits (133), Expect = 9e-12
Identities = 21/64 (32%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 11 KSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVV 70
K +GK V VELK+ + GTL + D+Y+N+ L D V + + + + IRGS +
Sbjct: 2 KDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDD--VVETGRDGKVRVLGLVLIRGSNI 59
Query: 71 RYVQ 74
++
Sbjct: 60 VSIR 63
>gnl|CDD|212471 cd01724, Sm_D1, Sm protein D1. The eukaryotic Sm proteins (B/B',
D1, D2, D3, E, F and G) assemble into a
hetero-heptameric ring around the Sm site of the
2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and
U5 snRNAs (Sm snRNAs) forming the core of the snRNP
particle. The snRNP particle, in turn, assembles with
other components onto the pre-mRNA to form the
spliceosome which is responsible for the excision of
introns and the ligation of exons. Members of this
family share a highly conserved Sm fold containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm subunit D1
heterodimerizes with subunit D2 and three such
heterodimers form a hexameric ring structure with
alternating D1 and D2 subunits. The D1 - D2 heterodimer
also assembles into a heptameric ring containing DB,
D3, E, F, and G subunits.
Length = 92
Score = 47.2 bits (113), Expect = 1e-08
Identities = 32/85 (37%), Positives = 46/85 (54%), Gaps = 6/85 (7%)
Query: 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGS 68
F L + V +ELKN + GT+ VD +N L ++ +T K P +S+ IRG+
Sbjct: 5 FLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLKGKNP--VSLDTLSIRGN 62
Query: 69 VVRYVQLPGDEV--DTQLLQDATRK 91
+RY+ LP D + DT LL D T K
Sbjct: 63 NIRYIILP-DSLNLDT-LLVDDTPK 85
>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. LSm657 is
believed to be an assembly intermediate for both the
LSm1-7 and LSm2-8 rings. Members of this family share a
highly conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 68
Score = 44.0 bits (105), Expect = 1e-07
Identities = 24/69 (34%), Positives = 34/69 (49%), Gaps = 10/69 (14%)
Query: 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKN----CF 64
F K ++GK VVV+LKN V G L +D Y+N+ L D + + F
Sbjct: 5 FLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQ------LVAKYGDAF 58
Query: 65 IRGSVVRYV 73
IRG+ V Y+
Sbjct: 59 IRGNNVLYI 67
>gnl|CDD|212468 cd01721, Sm_D3, Sm protein D3. The eukaryotic Sm proteins (B/B',
D1, D2, D3, E, F and G) assemble into a
hetero-heptameric ring around the Sm site of the
2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and
U5 snRNAs (Sm snRNAs) forming the core of the snRNP
particle. The snRNP particle, in turn, assembles with
other components onto the pre-mRNA to form the
spliceosome which is responsible for the excision of
introns and the ligation of exons. Members of this
family share a highly conserved Sm fold containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm subunit D3
heterodimerizes with subunit B and three such
heterodimers form a hexameric ring structure with
alternating B and D3 subunits. The D3 - B heterodimer
also assembles into a heptameric ring containing D1,
D2, E, F, and G subunits.
Length = 70
Score = 41.4 bits (98), Expect = 2e-06
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 4/60 (6%)
Query: 18 VVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPD-KYPHMLSVKNCFIRGSVVRYVQLP 76
V VELK G L + +N +L D++VT D K + V +IRGS +R++ LP
Sbjct: 13 VTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGKVSKLEQV---YIRGSQIRFIILP 69
>gnl|CDD|212469 cd01722, Sm_F, Sm protein F. The eukaryotic Sm proteins (B/B',
D1, D2, D3, E, F and G) assemble into a
hetero-heptameric ring around the Sm site of the
2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and
U5 snRNAs (Sm snRNAs) forming the core of the snRNP
particle. The snRNP particle, in turn, assembles with
other components onto the pre-mRNA to form the
spliceosome which is responsible for the excision of
introns and the ligation of exons. Members of this
family share a highly conserved Sm fold containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm subunit F is
capable of forming both homo- and hetero-heptamer ring
structures. To form the hetero-heptamer, Sm subunit F
initially binds subunits E and G to form a trimer which
then assembles onto snRNA along with the D3/B and D1/D2
heterodimers.
Length = 69
Score = 39.1 bits (92), Expect = 1e-05
Identities = 17/37 (45%), Positives = 24/37 (64%)
Query: 9 FFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45
F L GK V+V+LK + GTL SVD Y+N++L +
Sbjct: 5 FLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLAN 41
>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1. The archaeal Sm1
proteins: The Sm proteins are conserved in all three
domains of life and are always associated with U-rich
RNA sequences. They function to mediate RNA-RNA
interactions and RNA biogenesis. All Sm proteins
contain a common sequence motif in two segments, Sm1
and Sm2, separated by a short variable linker.
Eukaryotic Sm proteins form part of specific small
nuclear ribonucleoproteins (snRNPs) that are involved
in the processing of pre-mRNAs to mature mRNAs, and are
a major component of the eukaryotic spliceosome. Most
snRNPs consist of seven Sm proteins (B/B', D1, D2, D3,
E, F and G) arranged in a ring on a uridine-rich
sequence (Sm site), plus a small nuclear RNA (snRNA)
(either U1, U2, U5 or U4/6). Since archaebacteria do
not have any splicing apparatus, their Sm proteins may
play a more general role. Archaeal LSm proteins are
likely to represent the ancestral Sm domain.
Length = 69
Score = 38.3 bits (90), Expect = 3e-05
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 2/60 (3%)
Query: 14 VGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHMLSVKNCFIRGSVVRYV 73
+ K+V+V+LK + G L DQ+LN+ L + + L +RG V ++
Sbjct: 10 LNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKL--GTVLVRGDNVVFI 67
>gnl|CDD|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein. The archaeal
Sm-like (LSm): The Sm proteins are conserved in all
three domains of life and are always associated with
U-rich RNA sequences. They function to mediate RNA-RNA
interactions and RNA biogenesis. All Sm proteins
contain a common sequence motif in two segments, Sm1
and Sm2, separated by a short variable linker.
Eukaryotic Sm proteins form part of specific small
nuclear ribonucleoproteins (snRNPs) that are involved
in the processing of pre-mRNAs to mature mRNAs, and are
a major component of the eukaryotic spliceosome. Most
snRNPs consist of seven Sm proteins (B/B', D1, D2, D3,
E, F and G) arranged in a ring on a uridine-rich
sequence (Sm site), plus a small nuclear RNA (snRNA)
(either U1, U2, U5 or U4/6). Since archaebacteria do
not have any splicing apparatus, their Sm proteins may
play a more general role. Archaeal LSm proteins are
likely to represent the ancestral Sm domain. Members of
this family share a highly conserved Sm fold containing
an N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm-like proteins
exist in archaea as well as prokaryotes that form
heptameric and hexameric ring structures similar to
those found in eukaryotes.
Length = 69
Score = 35.9 bits (83), Expect = 2e-04
Identities = 18/36 (50%), Positives = 25/36 (69%), Gaps = 1/36 (2%)
Query: 11 KSLVGKDVVVELKNDVS-ICGTLHSVDQYLNIKLTD 45
KSLVG + VE+K D + + G L +VD Y+N+ LTD
Sbjct: 6 KSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTD 41
>gnl|CDD|212490 cd11679, archaeal_Sm_like, archaeal Sm-related protein. Archaeal
Sm-related proteins: The Sm proteins are conserved in
all three domains of life and are always associated
with U-rich RNA sequences. They function to mediate
RNA-RNA interactions and RNA biogenesis. All Sm
proteins contain a common sequence motif in two
segments, Sm1 and Sm2, separated by a short variable
linker. Eukaryotic Sm proteins form part of specific
small nuclear ribonucleoproteins (snRNPs) that are
involved in the processing of pre-mRNAs to mature
mRNAs, and are a major component of the eukaryotic
spliceosome. Most snRNPs consist of seven Sm proteins
(B/B', D1, D2, D3, E, F and G) arranged in a ring on a
uridine-rich sequence (Sm site), plus a small nuclear
RNA (snRNA) (either U1, U2, U5 or U4/6). Since
archaebacteria do not have any splicing apparatus,
their Sm proteins may play a more general role.
Archaeal Lsm proteins are likely to represent the
ancestral Sm domain.
Length = 65
Score = 33.8 bits (78), Expect = 0.002
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 7/63 (11%)
Query: 12 SLVGKDVVVELKNDVSICGTLHSVDQY-LNIKLTDISVTDPDKYPHMLSVKNCFIRGSVV 70
SL+ K+V+V L N + G L D LNI LT+ + +K+P + I G+ +
Sbjct: 7 SLLDKEVIVTLSNGKTYTGQLVGFDPSSLNIVLTNAKDSSGNKFPKV------IINGNRI 60
Query: 71 RYV 73
+
Sbjct: 61 SEI 63
>gnl|CDD|222754 pfam14438, SM-ATX, SM domain found in Ataxin-2. SM domain found
in Ataxin-2.
Length = 113
Score = 32.6 bits (75), Expect = 0.008
Identities = 20/81 (24%), Positives = 35/81 (43%), Gaps = 11/81 (13%)
Query: 2 ERLLFYSFFKSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHML--S 59
+RL++ +L+G+ V V LKN G H+ D V K +L S
Sbjct: 1 DRLVY--LLTNLIGQRVEVTLKNGSVYEGIFHTAS-----PEDDFGVV--LKMARVLPKS 51
Query: 60 VKNCFIRGSVVRYVQLPGDEV 80
+ +RG +V + +P ++
Sbjct: 52 DASGPLRGKIVDTLIIPSKDI 72
>gnl|CDD|212477 cd01730, LSm3, Like-Sm protein 3. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. Members of
this family share a highly conserved Sm fold containing
an N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet.
Length = 82
Score = 31.0 bits (71), Expect = 0.020
Identities = 14/38 (36%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 18 VVVELKNDVSICGTLHSVDQYLNIKLTDI--SVTDPDK 53
V V+L+ D + G LH+ DQ+LN+ L D+ ++T +
Sbjct: 14 VYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEI 51
>gnl|CDD|212475 cd01728, LSm1, Like-Sm protein 1. The eukaryotic LSm proteins
(LSm1-7) assemble into a hetero-heptameric ring around
the 3'-terminus of the gamma-methyl triphosphate
(gamma-m-P3) capped U6 snRNA. Accumulation of
uridylated RNAs in an lsm1 mutant suggests an
involvement of the LSm1-7 complex in recognition of the
3' uridylation tag and recruitment of the decapping
machinery. LSm1-7, together with Pat1, are also called
the decapping activator. Members of this family share a
highly conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 74
Score = 28.6 bits (65), Expect = 0.14
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 14 VGKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45
+ K ++V L++ + G L S DQ+ N+ L D
Sbjct: 11 LDKKILVVLRDGRKLIGILRSFDQFANLVLED 42
>gnl|CDD|214348 CHL00048, rps3, ribosomal protein S3.
Length = 214
Score = 29.4 bits (67), Expect = 0.21
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 6 FYSFFKSLVGKDV--VVELKNDVSICGTLHSVDQYLNIKLTDISVTDPDKYPHML 58
+ F K L+ + + EL+ ++ L+SV++ LNI +T V P P++L
Sbjct: 73 YTGFPKLLIERKGRGIEELQINLQ--KELNSVNRKLNINIT--EVKKPYGEPNIL 123
>gnl|CDD|212479 cd01732, LSm5, Like-Sm protein 5. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. Members of
this family share a highly conserved Sm fold containing
an N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet.
Length = 76
Score = 27.2 bits (61), Expect = 0.58
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 14 VGKDVVVELKNDVSICGTLHSVDQYLNIKLTDI 46
+G + + +K+D GTL D Y+N+ L D+
Sbjct: 12 IGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDV 44
>gnl|CDD|212474 cd01727, LSm8, Like-Sm protein 8. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. LSm657 is
believed to be an assembly intermediate for both the
LSm1-7 and LSm2-8 rings. Members of this family share a
highly conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 91
Score = 25.6 bits (57), Expect = 2.4
Identities = 24/95 (25%), Positives = 40/95 (42%), Gaps = 12/95 (12%)
Query: 8 SFFKSLVGKDVVVELKND-VSICGTLHSVDQYLNIKLTD-----ISVTDP-DKYPHMLSV 60
S + + K VVV + D I GTL DQ N+ L++ S + ++ P L +
Sbjct: 2 SLLEDYLNKRVVV-ITTDGRVIVGTLKGFDQTTNLILSNCHERVYSSDEGVEEVPLGLYL 60
Query: 61 KNCFIRGSVVRYVQLPGDEVDTQLLQDATRKEAVN 95
+RG V + +E+D + R E +
Sbjct: 61 ----LRGDNVAVIGEVDEELDGSIDLSKIRAEPLK 91
>gnl|CDD|212486 cd06168, LSMD1, LSM domain containing 1. The eukaryotic Sm and
Sm-like (LSm) proteins associate with RNA to form the
core domain of the ribonucleoprotein particles involved
in a variety of RNA processing events including
pre-mRNA splicing, telomere replication, and mRNA
degradation. Members of this family share a highly
conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet. LSMD1 proteins have a single Sm-like domain
structure. Sm-like proteins exist in archaea as well as
prokaryotes, forming heptameric and hexameric ring
structures similar to those found in eukaryotes.
Length = 73
Score = 25.2 bits (56), Expect = 3.0
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 11 KSLVGKDVVVELKNDVSICGTLHSVDQYLNIKLTD 45
+ L+G+ + V L + + GT D+ NI L++
Sbjct: 5 RKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSN 39
>gnl|CDD|212487 cd11676, Gemin6, Gemin 6. Gemins 6, together with the survival
motor neuron (SMN) protein, other Gemins, and
Unr-interacting protein (UNRIP) form the SMN complex,
which plays an important role in the Sm core assembly
reaction, by binding directly to the Sm proteins, as
well as UsnRNAs. Gemin 6 forms a heterodimer with Gemin
7, which serve as a surrogate for the SmB-SmD3 dimer
during the formation of the heptameric Sm ring.
Length = 63
Score = 24.9 bits (55), Expect = 3.1
Identities = 10/28 (35%), Positives = 17/28 (60%)
Query: 9 FFKSLVGKDVVVELKNDVSICGTLHSVD 36
+KS VGK+V V + + G +++VD
Sbjct: 3 EWKSYVGKEVKVTASDGKTYTGWVYTVD 30
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 25.0 bits (55), Expect = 4.0
Identities = 9/32 (28%), Positives = 14/32 (43%)
Query: 16 KDVVVELKNDVSICGTLHSVDQYLNIKLTDIS 47
V+V LK G L D ++N+ L +
Sbjct: 15 SPVLVRLKGGREFRGELQGYDIHMNLVLDNAE 46
>gnl|CDD|218598 pfam05470, eIF-3c_N, Eukaryotic translation initiation factor 3
subunit 8 N-terminus. The largest of the mammalian
translation initiation factors, eIF3, consists of at
least eight subunits ranging in mass from 35 to 170 kDa.
eIF3 binds to the 40 S ribosome in an early step of
translation initiation and promotes the binding of
methionyl-tRNAi and mRNA.
Length = 593
Score = 25.1 bits (55), Expect = 8.0
Identities = 14/48 (29%), Positives = 18/48 (37%), Gaps = 5/48 (10%)
Query: 9 FFKSLV-----GKDVVVELKNDVSICGTLHSVDQYLNIKLTDISVTDP 51
FFKSL D V LK++ S + V YL +V
Sbjct: 342 FFKSLQNIDPHSNDYVERLKDEPSFYALIERVQDYLERTGDSKAVCRV 389
>gnl|CDD|220448 pfam09863, DUF2090, Uncharacterized protein conserved in bacteria
(DUF2090). This domain, found in various prokaryotic
carbohydrate kinases, has no known function.
Length = 310
Score = 24.9 bits (55), Expect = 8.0
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 76 PGDEVDTQLLQDATRKEAVNATR 98
P D+ + Q+A K A R
Sbjct: 149 PDDDAALRAEQEAKLKRLYEACR 171
>gnl|CDD|198373 cd07805, FGGY_XK_like_2, uncharacterized xylulose kinase-like
proteins; a subgroup of the FGGY family of carbohydrate
kinases. This subgroup is composed of uncharacterized
proteins with similarity to bacterial D-Xylulose kinases
(XK, also known as xylulokinase; EC 2.7.1.17), which
catalyze the rate-limiting step in the ATP-dependent
phosphorylation of D-xylulose to produce D-xylulose
5-phosphate (X5P) and ADP. The presence of Mg2+ or Mn2+
is required for catalytic activity. D-XK exists as a
dimer with an active site that lies at the interface
between the N- and C-terminal domains. This model
includes both the N-terminal domain, which adopts a
ribonuclease H-like fold, and the structurally related
C-terminal domain. Members of this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 514
Score = 24.9 bits (55), Expect = 9.6
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 38 YLNIKLTDISVTDPD 52
YLN++LT TDPD
Sbjct: 168 YLNLRLTGRFATDPD 182
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
0.321 0.137 0.391
Gapped
Lambda K H
0.267 0.0838 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,827,333
Number of extensions: 387269
Number of successful extensions: 346
Number of sequences better than 10.0: 1
Number of HSP's gapped: 335
Number of HSP's successfully gapped: 31
Length of query: 98
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 34
Effective length of database: 8,098,946
Effective search space: 275364164
Effective search space used: 275364164
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: 53 (24.0 bits)