RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6372
(88 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 = 137 bits (347), Expect = 2e-44
Identities = 54/69 (78%), Positives = 56/69 (81%)
Query: 8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
NPKPFLN LTGK VI KLKWG EYKG LVS D YMN QLA+TEE IDG TG LGEVLIR
Sbjct: 1 NPKPFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIR 60
Query: 68 CNNILYIRG 76
CNN+LYIR
Sbjct: 61 CNNVLYIRE 69
>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 = 85.3 bits (212), Expect = 6e-24
Identities = 34/68 (50%), Positives = 41/68 (60%)
Query: 8 NPKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIR 67
P FL + GK V+ KLK G EY+G+L DGYMN L TEE +DG K G+ IR
Sbjct: 1 TPSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIR 60
Query: 68 CNNILYIR 75
NN+LYI
Sbjct: 61 GNNVLYIS 68
>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 = 77.6 bits (192), Expect = 8e-21
Identities = 30/64 (46%), Positives = 34/64 (53%)
Query: 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNN 70
FL L GK V +LK G E +G L D +MN L EE I KLG VLIR NN
Sbjct: 1 KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNN 60
Query: 71 ILYI 74
I+ I
Sbjct: 61 IVLI 64
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 76.4 bits (189), Expect = 2e-20
Identities = 32/66 (48%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII-DGHCTGKLGEVLIRCN 69
FL L GK V+ +LK G EY+G L D +MN L EE + DG KLG V IR N
Sbjct: 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGN 60
Query: 70 NILYIR 75
NI+YI
Sbjct: 61 NIVYII 66
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 69.6 bits (171), Expect = 2e-17
Identities = 34/76 (44%), Positives = 40/76 (52%), Gaps = 4/76 (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 GKLGEVLIRCNNILYI 74
GEVLIR +NI+ I
Sbjct: 62 RLGGEVLIRGDNIVLI 77
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 65.0 bits (159), Expect = 7e-16
Identities = 24/56 (42%), Positives = 36/56 (64%)
Query: 19 KSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
V+ +LK G E++G L D +MN L + EEI DG KLG+V+IR +N++Y+
Sbjct: 15 SPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYV 70
>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 = 62.6 bits (153), Expect = 5e-15
Identities = 25/57 (43%), Positives = 38/57 (66%)
Query: 18 GKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
K+V+ KLK G E +G+L D ++N L + EEII+G KLG VL+R +N+++I
Sbjct: 11 NKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVRGDNVVFI 67
>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 = 3e-14
Identities = 26/63 (41%), Positives = 31/63 (49%)
Query: 13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNIL 72
L GK+V +LK G G LV+ D YMN L E LG VLIR +NI+
Sbjct: 1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIV 60
Query: 73 YIR 75
IR
Sbjct: 61 SIR 63
>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 = 40.6 bits (95), Expect = 3e-06
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 16 LTGKSVICKLKW-GHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYI 74
L G + ++K ++ +G LV+ D YMN L T E + LG V++R NNIL I
Sbjct: 8 LVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLRGNNILLI 67
>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 = 1e-05
Identities = 27/71 (38%), Positives = 36/71 (50%), Gaps = 4/71 (5%)
Query: 13 LNLLT---GKSVICKLKWGHEYKGILVSTDGYMNCQLAS-TEEIIDGHCTGKLGEVLIRC 68
L+LL G V+ +LK G Y G LV+ D +MN L + DG K+ E IR
Sbjct: 3 LSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIRG 62
Query: 69 NNILYIRGAEE 79
N I Y+R +E
Sbjct: 63 NTIKYLRLPDE 73
>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 = 35.6 bits (83), Expect = 3e-04
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLA-STEEIIDGHCTGKLGEVLIRCNN 70
L L G+ +L+ +GI+ + DG+MN L+ +T G E ++ N
Sbjct: 13 LLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQH-HFDEFFVQGRN 71
Query: 71 ILYI 74
I Y+
Sbjct: 72 IRYV 75
>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 = 32.1 bits (74), Expect = 0.005
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 21 VICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGK---LGEVLIRCNNILYI 74
V +LK G Y+G L+ + MNCQL +++ GK L +V IR + I +I
Sbjct: 13 VTVELKTGEVYRGKLIEAEDNMNCQL---KDVTVTARDGKVSKLEQVYIRGSQIRFI 66
>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 = 29.8 bits (68), Expect = 0.035
Identities = 19/66 (28%), Positives = 28/66 (42%)
Query: 9 PKPFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRC 68
P L K + KL + G+L D +MN L E + +G V+IR
Sbjct: 1 HPPELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGEKTPIGMVVIRG 60
Query: 69 NNILYI 74
N+I+ I
Sbjct: 61 NSIIMI 66
>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 = 0.091
Identities = 21/63 (33%), Positives = 30/63 (47%)
Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNI 71
FL L+ ++V +LK G G + D MN L + + + G L + IR NNI
Sbjct: 5 FLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLKGKNPVSLDTLSIRGNNI 64
Query: 72 LYI 74
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 = 0.19
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
>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 = 0.48
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
>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 = 0.66
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 12 FLNLLTGKSVICKLKWGHEYKGILVSTD 39
L L G+ V LK G Y+GI +
Sbjct: 6 LLTNLIGQRVEVTLKNGSVYEGIFHTAS 33
>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 = 26.8 bits (60), Expect = 0.82
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 21 VICKLKWGHEYKGILVSTDGYMNCQLASTEEII-----DGHCTGKLGEVLIRCNNILYIR 75
V KL+ E +G L + D ++N L EE I D ++ + R +L++R
Sbjct: 14 VYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTKRNIPMLFVR 73
Query: 76 G 76
G
Sbjct: 74 G 74
>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 = 1.5
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 33 GILVSTDGYMNCQLASTEEI-IDGHCTGKLGEVLIRCNNILYIR 75
G ++ D YMN L EE+ + + LG +L++ +NI I+
Sbjct: 35 GKIIGFDEYMNLVLDDAEEVHLKTNTRKPLGRILLKGDNITLIQ 78
>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 = 25.7 bits (57), Expect = 1.6
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
>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional.
Length = 89
Score = 25.8 bits (57), Expect = 1.8
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 32 KGILVSTDGYMNCQLASTEEIIDGHCTGK-LGEVLIRCNNILYIRGAE 78
+G ++ D YMN L EE+ T K LG +L++ +NI I A+
Sbjct: 42 EGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMAAK 89
>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 = 25.1 bits (55), Expect = 2.9
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 4/30 (13%)
Query: 24 KLKWGHEYKGILVSTDGYMNCQLASTEEII 53
KL+W + Y+G D N L T EI+
Sbjct: 39 KLEWVYGYRGR----DCRANLYLLPTGEIV 64
>gnl|CDD|222455 pfam13924, Lipocalin_5, Lipocalin-like domain. This family
includes domains distantly related to lipocalins.
However, they do contain the important GXW motif in the
first strand. The protein in this family include aln5,
which is involved in biosynthesis of alnumycin. The
family also includes the ZFK protein from Trypanosoma
brucei which is a protein kinase. This domain is at the
C-terminus of that protein. The domain is also found as
the C-terminal domain in StiJ a protein involved in
producing stigmatellin. This domain has been assumed to
catalyze a final cyclisation reaction.
Length = 140
Score = 25.4 bits (56), Expect = 3.5
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 27 WGHEYKGILV-STDGYMNCQLASTE 50
+G + G+L+ + DGYM+ QL T
Sbjct: 23 YGPDPSGLLIYTADGYMSAQLTRTG 47
>gnl|CDD|107286 cd06291, PBP1_Qymf_like, Ligand binding domain of the lacI-like
transcription regulator from a novel metal-reducing
bacterium Alkaliphilus Metalliredigens (strain Qymf) and
its close homologs. This group includes the ligand
binding domain of the lacI-like transcription regulator
from a novel metal-reducing bacterium Alkaliphilus
Metalliredigens (strain Qymf) and its close homologs.
Qymf is a strict anaerobe that could be grown in the
presence of borax and its cells are straight rods that
produce endospores. This group is a member of the
LacI-GalR family repressors that are composed of two
functional domains: an N-terminal HTH (helix-turn-helix)
domain, which is responsible for the DNA-binding
specificity, and a C-terminal ligand-binding domain,
which is homologous to the sugar-binding domain of
ABC-type transport systems that contain the type I
periplasmic binding protein-like fold. As also observed
in the periplasmic binding proteins, the C-terminal
domain of the bacterial transcription repressor
undergoes a conformational change upon ligand binding
which in turn changes the DNA binding affinity of the
repressor.
Length = 265
Score = 25.2 bits (56), Expect = 4.6
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 12/53 (22%)
Query: 35 LVSTDGYMNCQLASTEEIIDGHCTGKLGEVLIRCNNILYIRGAEEGDEEGEMR 87
+VS+D Y +LA EE+I+ G C +I +I G +R
Sbjct: 91 IVSSDNYEGGRLA-AEELIE---RG--------CKHIAHIGGPNNTVSPTNLR 131
>gnl|CDD|172047 PRK13424, PRK13424, F0F1 ATP synthase subunit gamma; Provisional.
Length = 291
Score = 25.1 bits (55), Expect = 6.2
Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 15/56 (26%)
Query: 45 QLAST--EEIIDGHCTGKLGEVLI-------------RCNNILYIRGAEEGDEEGE 85
QLA++ E+IDG+ TG+L EV++ IL I E +EE
Sbjct: 148 QLANSIGLEVIDGYLTGELDEVVLVYGEFVSMARQLPITLQILPIAPEEAEEEEAG 203
>gnl|CDD|218601 pfam05477, SURF2, Surfeit locus protein 2 (SURF2). Surfeit locus
protein 2 is part of a group of at least six sequence
unrelated genes (Surf-1 to Surf-6). The six Surfeit
genes have been classified as housekeeping genes, being
expressed in all tissue types tested and not containing
a TATA box in their promoter region. The exact function
of SURF2 is unknown.
Length = 244
Score = 24.9 bits (54), Expect = 7.2
Identities = 13/45 (28%), Positives = 16/45 (35%), Gaps = 12/45 (26%)
Query: 11 PFLNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEIIDG 55
PFL L+ V C L GHE C+L + G
Sbjct: 16 PFLELVENGKVRCVLT-GHELP-----------CRLPELQSYTRG 48
>gnl|CDD|212476 cd01729, LSm7, Like-Sm protein 7. 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 = 89
Score = 24.1 bits (53), Expect = 8.7
Identities = 13/41 (31%), Positives = 18/41 (43%)
Query: 13 LNLLTGKSVICKLKWGHEYKGILVSTDGYMNCQLASTEEII 53
L+ K + K + G E GIL D +N L T E +
Sbjct: 7 LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYL 47
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 0.140 0.437
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: 4,342,959
Number of extensions: 333241
Number of successful extensions: 201
Number of sequences better than 10.0: 1
Number of HSP's gapped: 198
Number of HSP's successfully gapped: 29
Length of query: 88
Length of database: 10,937,602
Length adjustment: 56
Effective length of query: 32
Effective length of database: 8,453,778
Effective search space: 270520896
Effective search space used: 270520896
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.0 bits)