RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9934
(158 letters)
>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 = 138 bits (350), Expect = 9e-44
Identities = 54/69 (78%), Positives = 56/69 (81%)
Query: 78 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 137
NPKPFLN LTGK VI KLKWG EYKG LVS D YMN QLA+TEE IDG TG LGEVLIR
Sbjct: 1 NPKPFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIR 60
Query: 138 CNNILYIRG 146
CNN+LYIR
Sbjct: 61 CNNVLYIRE 69
Score = 115 bits (291), Expect = 8e-35
Identities = 47/60 (78%), Positives = 48/60 (80%)
Query: 8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
NPKPFLN LTGK VI KLKWG EYKG LVS D YMN QLA+TEE IDG TG LGEVLIR
Sbjct: 1 NPKPFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIR 60
>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 = 86.0 bits (214), Expect = 3e-23
Identities = 34/68 (50%), Positives = 41/68 (60%)
Query: 78 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 137
P FL + GK V+ KLK G EY+G+L DGYMN L TEE +DG K G+ IR
Sbjct: 1 TPSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIR 60
Query: 138 CNNILYIR 145
NN+LYI
Sbjct: 61 GNNVLYIS 68
Score = 73.3 bits (181), Expect = 4e-18
Identities = 29/60 (48%), Positives = 35/60 (58%)
Query: 8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
P FL + GK V+ KLK G EY+G+L DGYMN L TEE +DG K G+ IR
Sbjct: 1 TPSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIR 60
>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 = 78.0 bits (193), Expect = 5e-20
Identities = 30/64 (46%), Positives = 34/64 (53%)
Query: 81 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNN 140
FL L GK V +LK G E +G L D +MN L EE I KLG VLIR NN
Sbjct: 1 KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNN 60
Query: 141 ILYI 144
I+ I
Sbjct: 61 IVLI 64
Score = 66.0 bits (162), Expect = 2e-15
Identities = 26/57 (45%), Positives = 29/57 (50%)
Query: 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
FL L GK V +LK G E +G L D +MN L EE I KLG VLIR
Sbjct: 1 KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIR 57
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear ribonucleoprotein
particles (snRNPs) involved in pre-mRNA splicing.
Length = 67
Score = 77.2 bits (191), Expect = 1e-19
Identities = 32/66 (48%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 81 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCN 139
FL L GK V+ +LK G EY+G L D +MN L EE + DG KLG V IR N
Sbjct: 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGN 60
Query: 140 NILYIR 145
NI+YI
Sbjct: 61 NIVYII 66
Score = 64.8 bits (159), Expect = 6e-15
Identities = 27/58 (46%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIR 67
FL L GK V+ +LK G EY+G L D +MN L EE + DG KLG V IR
Sbjct: 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIR 58
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 70.0 bits (172), Expect = 8e-17
Identities = 34/76 (44%), Positives = 40/76 (52%), Gaps = 4/76 (5%)
Query: 73 TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG----HCT 128
+ L P FL L K V+ KLK G EY+G LV D YMN L EEII +
Sbjct: 2 SMLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVR 61
Query: 129 GKLGEVLIRCNNILYI 144
GEVLIR +NI+ I
Sbjct: 62 RLGGEVLIRGDNIVLI 77
Score = 58.9 bits (143), Expect = 2e-12
Identities = 31/69 (44%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 3 TPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG----HCT 58
+ L P FL L K V+ KLK G EY+G LV D YMN L EEII +
Sbjct: 2 SMLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVR 61
Query: 59 GKLGEVLIR 67
GEVLIR
Sbjct: 62 RLGGEVLIR 70
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 66.2 bits (162), Expect = 3e-15
Identities = 24/56 (42%), Positives = 36/56 (64%)
Query: 89 KSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
V+ +LK G E++G L D +MN L + EEI DG KLG+V+IR +N++Y+
Sbjct: 15 SPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYV 70
Score = 57.7 bits (140), Expect = 4e-12
Identities = 22/49 (44%), Positives = 30/49 (61%)
Query: 19 KSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
V+ +LK G E++G L D +MN L + EEI DG KLG+V+IR
Sbjct: 15 SPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIR 63
>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 = 63.0 bits (154), Expect = 3e-14
Identities = 25/57 (43%), Positives = 38/57 (66%)
Query: 88 GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
K+V+ KLK G E +G+L D ++N L + EEII+G KLG VL+R +N+++I
Sbjct: 11 NKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVRGDNVVFI 67
Score = 56.8 bits (138), Expect = 1e-11
Identities = 23/50 (46%), Positives = 32/50 (64%)
Query: 18 GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
K+V+ KLK G E +G+L D ++N L + EEII+G KLG VL+R
Sbjct: 11 NKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVR 60
>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 = 60.7 bits (148), Expect = 2e-13
Identities = 26/63 (41%), Positives = 31/63 (49%)
Query: 83 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNIL 142
L GK+V +LK G G LV+ D YMN L E LG VLIR +NI+
Sbjct: 1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIV 60
Query: 143 YIR 145
IR
Sbjct: 61 SIR 63
Score = 50.3 bits (121), Expect = 3e-09
Identities = 22/55 (40%), Positives = 25/55 (45%)
Query: 13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
L GK+V +LK G G LV+ D YMN L E LG VLIR
Sbjct: 1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIR 55
>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 = 41.3 bits (97), Expect = 7e-06
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 86 LTGKSVICKLKW-GHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 144
L G + ++K ++ +G LV+ D YMN L T E + LG V++R NNIL I
Sbjct: 8 LVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLRGNNILLI 67
Score = 32.5 bits (74), Expect = 0.014
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 16 LTGKSVICKLKW-GHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
L G + ++K ++ +G LV+ D YMN L T E + LG V++R
Sbjct: 8 LVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLR 60
>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 = 39.5 bits (93), Expect = 5e-05
Identities = 27/71 (38%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 83 LNLLT---GKSVICKLKWGHEYKGILVSTDGYMNCQLAS-TEEIIDGHCTGKLGEVLIRC 138
L+LL G V+ +LK G Y G LV+ D +MN L + DG K+ E IR
Sbjct: 3 LSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIRG 62
Query: 139 NNILYIRGAEE 149
N I Y+R +E
Sbjct: 63 NTIKYLRLPDE 73
Score = 30.6 bits (70), Expect = 0.068
Identities = 22/59 (37%), Positives = 29/59 (49%), Gaps = 4/59 (6%)
Query: 13 LNLLT---GKSVICKLKWGHEYKGILVSTDGYMNCQLAS-TEEIIDGHCTGKLGEVLIR 67
L+LL G V+ +LK G Y G LV+ D +MN L + DG K+ E IR
Sbjct: 3 LSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIR 61
>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 = 36.0 bits (84), Expect = 0.001
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLA-STEEIIDGHCTGKLGEVLIRCNN 140
L L G+ +L+ +GI+ + DG+MN L+ +T G E ++ N
Sbjct: 13 LLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQH-HFDEFFVQGRN 71
Query: 141 ILYI 144
I Y+
Sbjct: 72 IRYV 75
Score = 31.4 bits (72), Expect = 0.047
Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLA-STEEIIDGHCTGKLGEVLIRS 68
L L G+ +L+ +GI+ + DG+MN L+ +T G E ++
Sbjct: 13 LLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQH-HFDEFFVQG 69
>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 = 32.5 bits (75), Expect = 0.013
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 91 VICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK---LGEVLIRCNNILYI 144
V +LK G Y+G L+ + MNCQL +++ GK L +V IR + I +I
Sbjct: 13 VTVELKTGEVYRGKLIEAEDNMNCQL---KDVTVTARDGKVSKLEQVYIRGSQIRFI 66
Score = 27.5 bits (62), Expect = 0.81
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 21 VICKLKWGHEYKGILVSTDGYMNCQL 46
V +LK G Y+G L+ + MNCQL
Sbjct: 13 VTVELKTGEVYRGKLIEAEDNMNCQL 38
>gnl|CDD|212466 cd01719, Sm_G, Sm protein G. 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 G binds subunits E and F to form
a trimer which then assembles onto snRNA along with the
D1/D2 and D3/B heterodimers forming a seven-membered
ring structure.
Length = 70
Score = 30.2 bits (69), Expect = 0.082
Identities = 19/66 (28%), Positives = 28/66 (42%)
Query: 79 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRC 138
P L K + KL + G+L D +MN L E + +G V+IR
Sbjct: 1 HPPELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGEKTPIGMVVIRG 60
Query: 139 NNILYI 144
N+I+ I
Sbjct: 61 NSIIMI 66
Score = 25.6 bits (57), Expect = 4.8
Identities = 16/59 (27%), Positives = 23/59 (38%)
Query: 9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
P L K + KL + G+L D +MN L E + +G V+IR
Sbjct: 1 HPPELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGEKTPIGMVVIR 59
>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 = 29.1 bits (66), Expect = 0.39
Identities = 21/63 (33%), Positives = 30/63 (47%)
Query: 82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI 141
FL L+ ++V +LK G G + D MN L + + + G L + IR NNI
Sbjct: 5 FLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLKGKNPVSLDTLSIRGNNI 64
Query: 142 LYI 144
YI
Sbjct: 65 RYI 67
>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 = 28.0 bits (63), Expect = 0.56
Identities = 13/27 (48%), Positives = 13/27 (48%)
Query: 13 LNLLTGKSVICKLKWGHEYKGILVSTD 39
LN L K VI L G Y G LV D
Sbjct: 5 LNSLLDKEVIVTLSNGKTYTGQLVGFD 31
Score = 28.0 bits (63), Expect = 0.56
Identities = 13/27 (48%), Positives = 13/27 (48%)
Query: 83 LNLLTGKSVICKLKWGHEYKGILVSTD 109
LN L K VI L G Y G LV D
Sbjct: 5 LNSLLDKEVIVTLSNGKTYTGQLVGFD 31
>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 = 27.2 bits (61), Expect = 1.5
Identities = 14/39 (35%), Positives = 18/39 (46%)
Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTE 50
F L GK V +LK G L S D Y+N +L +
Sbjct: 5 FFKTLVGKEVTVELKNDLSITGTLHSVDQYLNIKLTNIS 43
Score = 27.2 bits (61), Expect = 1.5
Identities = 14/39 (35%), Positives = 18/39 (46%)
Query: 82 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTE 120
F L GK V +LK G L S D Y+N +L +
Sbjct: 5 FFKTLVGKEVTVELKNDLSITGTLHSVDQYLNIKLTNIS 43
>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 = 27.2 bits (61), Expect = 1.5
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 91 VICKLKWGHEYKGILVSTDGYMNCQLASTEEII-----DGHCTGKLGEVLIRCNNILYIR 145
V KL+ E +G L + D ++N L EE I D ++ + R +L++R
Sbjct: 14 VYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTKRNIPMLFVR 73
Query: 146 G 146
G
Sbjct: 74 G 74
>gnl|CDD|222754 pfam14438, SM-ATX, SM domain found in Ataxin-2. SM domain found
in Ataxin-2.
Length = 113
Score = 27.2 bits (61), Expect = 2.1
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTD 39
L L G+ V LK G Y+GI +
Sbjct: 6 LLTNLIGQRVEVTLKNGSVYEGIFHTAS 33
Score = 27.2 bits (61), Expect = 2.1
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 82 FLNLLTGKSVICKLKWGHEYKGILVSTD 109
L L G+ V LK G Y+GI +
Sbjct: 6 LLTNLIGQRVEVTLKNGSVYEGIFHTAS 33
>gnl|CDD|212465 cd01718, Sm_E, Sm protein E. 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 E binds subunits F and G to form
a trimer which then assembles onto snRNA along with the
D1/D2 and D3/B heterodimers forming a seven-membered
ring structure.
Length = 79
Score = 26.0 bits (58), Expect = 3.3
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 103 GILVSTDGYMNCQLASTEEI-IDGHCTGKLGEVLIRCNNILYIR 145
G ++ D YMN L EE+ + + LG +L++ +NI I+
Sbjct: 35 GKIIGFDEYMNLVLDDAEEVHLKTNTRKPLGRILLKGDNITLIQ 78
>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional.
Length = 89
Score = 25.8 bits (57), Expect = 4.3
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 102 KGILVSTDGYMNCQLASTEEIIDGHCTGK-LGEVLIRCNNILYIRGAE 148
+G ++ D YMN L EE+ T K LG +L++ +NI I A+
Sbjct: 42 EGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMAAK 89
>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 = 25.3 bits (56), Expect = 5.1
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 1/31 (3%)
Query: 9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTD 39
P + + + GK V G Y G + + D
Sbjct: 1 PLEWKSYV-GKEVKVTASDGKTYTGWVYTVD 30
Score = 25.3 bits (56), Expect = 5.1
Identities = 8/31 (25%), Positives = 13/31 (41%), Gaps = 1/31 (3%)
Query: 79 PKPFLNLLTGKSVICKLKWGHEYKGILVSTD 109
P + + + GK V G Y G + + D
Sbjct: 1 PLEWKSYV-GKEVKVTASDGKTYTGWVYTVD 30
>gnl|CDD|190637 pfam03451, HELP, HELP motif. The founding member of the EMAP
protein family is the 75 kDa Echinoderm
Microtubule-Associated Protein, so-named for its
abundance in sea urchin, sand dollar and starfish eggs.
The Hydrophobic EMAP-Like Protein (HELP) motif was
identified initially in the human EMAP-Like Protein 2
(EML2) and subsequently in the entire EMAP Protein
family. The HELP motif is approximately 60-70 amino
acids in length and is conserved amongst metazoans.
Although the HELP motif is hydrophobic, there is no
evidence that EMAP-Like Proteins are
membrane-associated. All members of the EMAP-Like
Protein family, identified to-date, are constructed with
an amino terminal HELP motif followed by a WD domain. In
C. elegans, EMAP-Like Protein-1 (ELP-1) is required for
touch sensation indicating that ELP-1 may play a role in
mechanosensation. The localization of ELP-1 to
microtubules and adhesion sites implies that ELP-1 may
transmit forces between the body surface and the touch
receptor neurons.
Length = 77
Score = 25.4 bits (56), Expect = 5.1
Identities = 13/56 (23%), Positives = 18/56 (32%), Gaps = 17/56 (30%)
Query: 68 SLTMSTPLPCNPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII 123
L P + KL+W + Y+G D N L T EI+
Sbjct: 26 DLEADKDPP-------------TKKLKLEWVYGYRGR----DCRANLYLLPTGEIV 64
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
0.318 0.139 0.438
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: 7,767,087
Number of extensions: 667337
Number of successful extensions: 378
Number of sequences better than 10.0: 1
Number of HSP's gapped: 374
Number of HSP's successfully gapped: 40
Length of query: 158
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 69
Effective length of database: 6,990,096
Effective search space: 482316624
Effective search space used: 482316624
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 (21.7 bits)
S2: 55 (24.8 bits)