RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11512
(62 letters)
>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 = 100 bits (252), Expect = 2e-30
Identities = 38/56 (67%), Positives = 45/56 (80%)
Query: 5 HPPELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
HPPELKK+MDK+++LKLN NR V+G+LRGFDPFMNLVLD+ VE D IGMV
Sbjct: 1 HPPELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGEKTPIGMV 56
>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 = 64.9 bits (159), Expect = 5e-16
Identities = 23/44 (52%), Positives = 33/44 (75%)
Query: 8 ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD 51
+L K++DKK+ +K R VTGIL+G+D +NLVLD+ VEY +D
Sbjct: 6 DLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRD 49
>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 = 7e-16
Identities = 25/54 (46%), Positives = 36/54 (66%)
Query: 7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
L+K + K+VT++L R + G L+GFD FMNLVLD+ E KD V+ +G+V
Sbjct: 1 KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLV 54
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 57.1 bits (139), Expect = 3e-13
Identities = 23/55 (41%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD-NTVHNIGMV 60
LKK + K+V ++L R G L+GFD FMNLVL++ E KD +G+V
Sbjct: 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLV 55
>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 = 50.3 bits (121), Expect = 1e-10
Identities = 24/52 (46%), Positives = 34/52 (65%)
Query: 9 LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
LK F+ K V+++L R +TG L FD +MNLVLD+ VE +D V +G+V
Sbjct: 1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLV 52
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 49.6 bits (119), Expect = 4e-10
Identities = 21/48 (43%), Positives = 28/48 (58%)
Query: 9 LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHN 56
LKK ++K+V +KL R G L GFD +MNLVLD+ E + N
Sbjct: 12 LKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKN 59
>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 = 46.8 bits (112), Expect = 4e-09
Identities = 19/52 (36%), Positives = 31/52 (59%)
Query: 9 LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
L + ++K V +KL + V G+L+GFD +NLVL+ E + +V +G V
Sbjct: 6 LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTV 57
>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 = 47.1 bits (113), Expect = 5e-09
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVE--YRKDNTVHNI 57
L+ +++K+V + R + G L+GFD NL+L E Y D V +
Sbjct: 2 SLLEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHERVYSSDEGVEEV 54
>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 = 45.2 bits (108), Expect = 2e-08
Identities = 19/50 (38%), Positives = 25/50 (50%)
Query: 9 LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIG 58
LKK + K V +KL G+L D +MNLVL++ EY V G
Sbjct: 6 LKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYG 55
>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 = 41.0 bits (97), Expect = 1e-06
Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 5/58 (8%)
Query: 8 ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHN-----IGMV 60
+L+K + + + + L R + G D N++L EYRK + + +G+V
Sbjct: 3 KLRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLGAEEPRSLGLV 60
>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 = 38.3 bits (90), Expect = 1e-05
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 17 VTLKLNANRNVTGILRGFDPFMNLVLDEGVE-YRKDNTVHNIG 58
+ L + + G + GFD +MNLVLD+ E + K NT +G
Sbjct: 23 IWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNTRKPLG 65
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 38.1 bits (89), Expect = 1e-05
Identities = 18/52 (34%), Positives = 26/52 (50%)
Query: 9 LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
L ++ V ++L R G L+G+D MNLVLD E + V +G V
Sbjct: 9 LNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKV 60
>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 = 36.0 bits (84), Expect = 8e-05
Identities = 18/35 (51%), Positives = 23/35 (65%)
Query: 14 DKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEY 48
DKK+ + L R + GILR FD F NLVL++ VE
Sbjct: 12 DKKILVVLRDGRKLIGILRSFDQFANLVLEDTVER 46
>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional.
Length = 89
Score = 36.2 bits (84), Expect = 8e-05
Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 22 NANRNVTGILRGFDPFMNLVLDEGVE-YRKDNTVHNIG 58
+ N + G + GFD +MN+VLD+ E Y K NT ++G
Sbjct: 36 HPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLG 73
>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 = 34.1 bits (79), Expect = 5e-04
Identities = 11/36 (30%), Positives = 22/36 (61%)
Query: 13 MDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEY 48
+D++V +KL +R + G L +D +N++L + E
Sbjct: 10 LDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEET 45
>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 = 33.7 bits (78), Expect = 5e-04
Identities = 15/42 (35%), Positives = 17/42 (40%)
Query: 7 PELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEY 48
P L K V +KL G L D +MNL L EY
Sbjct: 4 PFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEY 45
>gnl|CDD|212464 cd01717, Sm_B, Sm protein B. 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.
Length = 80
Score = 34.1 bits (79), Expect = 6e-04
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 9 LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRK 50
+ ++++ ++ + L R G FD MNLVL + E+RK
Sbjct: 5 MLQYINYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRK 46
>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 = 32.6 bits (75), Expect = 0.002
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 24 NRNVTGILRGFDPFMNLVLDEGVEY 48
++ G L GFD ++N+VL++ EY
Sbjct: 23 DKEFVGTLLGFDDYVNMVLEDVTEY 47
>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 = 29.5 bits (67), Expect = 0.025
Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 8 ELKKFMDKKVTLKLNANRNVTGILRGFDPF-MNLVLDEGVEYRKDNTVHNI 57
EL +DK+V + L+ + TG L GFDP +N+VL + N +
Sbjct: 4 ELNSLLDKEVIVTLSNGKTYTGQLVGFDPSSLNIVL-TNAKDSSGNKFPKV 53
>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 = 27.1 bits (60), Expect = 0.22
Identities = 13/53 (24%), Positives = 28/53 (52%), Gaps = 1/53 (1%)
Query: 9 LKKFMDKKVTLKLNANRN-VTGILRGFDPFMNLVLDEGVEYRKDNTVHNIGMV 60
+K + ++ +++ + N + G L D +MNL L + +E + V ++G V
Sbjct: 5 VKSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTV 57
>gnl|CDD|143442 cd07124, ALDH_PutA-P5CDH-RocA, Delta(1)-pyrroline-5-carboxylate
dehydrogenase, RocA. Delta(1)-pyrroline-5-carboxylate
dehydrogenase (EC=1.5.1.12 ), RocA: a proline catabolic
enzyme of the aldehyde dehydrogenase (ALDH) protein
superfamily. The proline catabolic enzymes, proline
dehydrogenase and Delta(1)-pyrroline-5-carboxylate
dehydrogenase (P5CDH), catalyze the two-step oxidation
of proline to glutamate; P5CDH catalyzes the oxidation
of glutamate semialdehyde, utilizing NAD+ as the
electron acceptor. In some bacteria, the two enzymes are
fused into the bifunctional flavoenzyme, proline
utilization A (PutA). In this CD, monofunctional enzyme
sequences such as seen in the Bacillus subtilis RocA
P5CDH are also present. These enzymes play important
roles in cellular redox control, superoxide generation,
and apoptosis.
Length = 512
Score = 27.6 bits (62), Expect = 0.36
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 6 PPELKKFMDKKVTLKLNANRNVTGILRGFDPF 37
P L++ + L ANR +TG L G PF
Sbjct: 450 PEHLERARREFEVGNLYANRKITGALVGRQPF 481
>gnl|CDD|212485 cd01739, LSm11_M, Like-Sm protein 11, middle domain. 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. LSm11 is an
SmD2-like subunit which binds U7 snRNA along with LSm10
and five other Sm subunits to form a 7-membered ring
structure. LSm11 and the U7 snRNP of which it is a part
are thought to play an important role in histone mRNA
3' processing.
Length = 63
Score = 25.7 bits (57), Expect = 0.74
Identities = 8/25 (32%), Positives = 11/25 (44%), Gaps = 1/25 (4%)
Query: 27 VTGILRGFDPFMNLVLDEGVE-YRK 50
G L FD NL L + E + +
Sbjct: 25 CEGYLVAFDKHWNLALVDVDETWTR 49
>gnl|CDD|212463 cd01716, Hfq, bacterial Hfq-like. Hfq, an abundant, ubiquitous
RNA-binding protein, functions as a pleiotropic
regulator of RNA metabolism in prokaryotes, required
for transcription of some transcripts and degradation
of others. Hfq binds small RNA molecules called
riboregulators that modulate the stability or
translation efficiency of RNA transcripts. Hfq binds
preferentially to unstructured A/U-rich RNA sequences
and is similar to the eukaryotic Sm proteins in both
sequence and structure. Hfq forms a homo-hexameric ring
similar to the heptameric ring of the Sm proteins.
Length = 60
Score = 25.2 bits (56), Expect = 0.84
Identities = 12/32 (37%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 15 KKVTLKL-NANRNVTGILRGFDPFMNLVLDEG 45
K VT+ L N R + G ++ FD F L+ +G
Sbjct: 15 KPVTIYLVNGVR-LKGKIKSFDNFTVLLESDG 45
>gnl|CDD|212488 cd11677, Gemin7, Gemin 7. Gemins 7, 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 7 forms a heterodimer with Gemin
6, which serve as a surrogate for the SmB-SmD3 dimer
during the formation of the heptameric Sm ring.
Length = 77
Score = 24.9 bits (55), Expect = 1.7
Identities = 7/28 (25%), Positives = 10/28 (35%)
Query: 9 LKKFMDKKVTLKLNANRNVTGILRGFDP 36
L K V ++ N VT + D
Sbjct: 17 LLALAGKPVEFTMHENTTVTATFKACDI 44
>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 = 24.1 bits (53), Expect = 2.9
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 6 PPELKKFMDKKVTLKLNANRNVTGILRGFDP 36
P E K ++ K+V + + + TG + DP
Sbjct: 1 PLEWKSYVGKEVKVTASDGKTYTGWVYTVDP 31
>gnl|CDD|212481 cd01734, YlxS_C, Bacillus subtilis YxlS-like, C-terminal domain.
YxlS is a Bacillus subtilis gene of unknown function
with two domains that each have an alpha/beta fold. The
N-terminal domain is composed of two alpha-helices and
a three-stranded beta-sheet, while the C-terminal
domain is composed of one alpha-helix and a
five-stranded beta-sheet. This CD represents the
C-terminal domain which has a fold similar to the Sm
fold of proteins like Sm-D3.
Length = 72
Score = 23.9 bits (53), Expect = 3.3
Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 4/32 (12%)
Query: 8 ELKKFMDKKVTLKLNA----NRNVTGILRGFD 35
+ ++F+ K+V +KL + TG L G D
Sbjct: 11 DFERFIGKEVKVKLKEPIDGRKKFTGELLGVD 42
>gnl|CDD|223417 COG0340, BirA, Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme
metabolism].
Length = 238
Score = 24.6 bits (54), Expect = 3.8
Identities = 13/50 (26%), Positives = 18/50 (36%), Gaps = 5/50 (10%)
Query: 8 ELKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKDNTVHNI 57
+ K+V L L GI +G D L+L+ D V I
Sbjct: 184 ARSLSLGKEVRLTLGGGVIFGGIAKGIDEDGALLLETD-----DGEVQTI 228
>gnl|CDD|217943 pfam04180, LTV, Low temperature viability protein. The
low-temperature viability protein LTV1 is involved in
ribosome biogenesis 40S subunit production.
Length = 426
Score = 24.2 bits (52), Expect = 5.0
Identities = 13/43 (30%), Positives = 21/43 (48%)
Query: 9 LKKFMDKKVTLKLNANRNVTGILRGFDPFMNLVLDEGVEYRKD 51
L +F + L A ++V + GF P M+ L E +E +D
Sbjct: 126 LSEFELDRGLLTYQAQQSVPDAIAGFQPDMDPRLREVLEALED 168
>gnl|CDD|178092 PLN02474, PLN02474, UTP--glucose-1-phosphate uridylyltransferase.
Length = 469
Score = 24.5 bits (53), Expect = 5.0
Identities = 12/23 (52%), Positives = 13/23 (56%)
Query: 6 PPELKKFMDKKVTLKLNANRNVT 28
P E KK +DK V LKLN T
Sbjct: 70 PEETKKLLDKLVVLKLNGGLGTT 92
>gnl|CDD|223281 COG0203, RplQ, Ribosomal protein L17 [Translation, ribosomal
structure and biogenesis].
Length = 116
Score = 23.7 bits (52), Expect = 7.1
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 4/29 (13%)
Query: 8 ELKKFMDKKVTL----KLNANRNVTGILR 32
EL++ ++K +TL L R LR
Sbjct: 43 ELRRVVEKLITLAKKGDLANRRLAFARLR 71
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
0.317 0.136 0.388
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: 3,127,905
Number of extensions: 221407
Number of successful extensions: 212
Number of sequences better than 10.0: 1
Number of HSP's gapped: 212
Number of HSP's successfully gapped: 33
Length of query: 62
Length of database: 10,937,602
Length adjustment: 33
Effective length of query: 29
Effective length of database: 9,473,920
Effective search space: 274743680
Effective search space used: 274743680
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)