RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9158
(133 letters)
>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 = 89.5 bits (223), Expect = 1e-24
Identities = 33/78 (42%), Positives = 53/78 (67%), Gaps = 9/78 (11%)
Query: 9 KEQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS---------REL 59
+E++ S N+L CL ++L G +T V+LRNE+SV G +++VDGFMNI +S ++
Sbjct: 1 RERYRSENSLVCLLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQH 60
Query: 60 TFESLFIQSRNVMFIHIP 77
F+ F+Q RN+ ++HIP
Sbjct: 61 HFDEFFVQGRNIRYVHIP 78
>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 = 35.2 bits (82), Expect = 0.001
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 9/61 (14%)
Query: 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYM--SRELT-------FESLFIQSRNVMF 73
K ++G V L+N G L +DG+MN+ + + E + FI+ NV++
Sbjct: 7 KKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIRGNNVLY 66
Query: 74 I 74
I
Sbjct: 67 I 67
>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 = 32.6 bits (75), Expect = 0.015
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 17/81 (20%)
Query: 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNI--------------YMSRELTFESLFIQS 68
K+LVG V+L+N+ S++G L VD ++NI ++ L+ ++ FI+
Sbjct: 7 KTLVGKEVTVELKNDLSITGTLHSVDQYLNIKLTNISVNDPEKYPHL---LSVKNCFIRG 63
Query: 69 RNVMFIHIPRHVSIVNKVEDA 89
V ++ +P ++DA
Sbjct: 64 SVVRYVQLPADEVDTELLQDA 84
>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 = 30.6 bits (70), Expect = 0.043
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 9/54 (16%)
Query: 32 VDLRNESSVSGRLEHVDGFMNIYMS---------RELTFESLFIQSRNVMFIHI 76
V+L+N + G L+ D FMN+ + + + I+ N++ I
Sbjct: 13 VELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNNIVLISP 66
>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 = 29.9 bits (68), Expect = 0.070
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 23 KSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMSR 57
K +G V+L++ ++G L D +MN+ +
Sbjct: 2 KDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDD 36
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 29.8 bits (68), Expect = 0.081
Identities = 14/55 (25%), Positives = 26/55 (47%), Gaps = 10/55 (18%)
Query: 32 VDLRNESSVSGRLEHVDGFMNIYMS--RELTFES--------LFIQSRNVMFIHI 76
V+L+N G L+ D FMN+ + E + +FI+ N+++I +
Sbjct: 13 VELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 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 = 29.8 bits (67), Expect = 0.091
Identities = 14/34 (41%), Positives = 24/34 (70%), Gaps = 1/34 (2%)
Query: 23 KSLVGMITCVDLR-NESSVSGRLEHVDGFMNIYM 55
KSLVG V+++ +E+ + GRL VD +MN+++
Sbjct: 6 KSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHL 39
>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 = 29.4 bits (67), Expect = 0.13
Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 9/60 (15%)
Query: 27 GMITCVDLRNESSVSGRLEHVDGFMNIYMS---------RELTFESLFIQSRNVMFIHIP 77
G I V+L+ G+L + MN + + E ++I+ + FI +P
Sbjct: 10 GHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGKVSKLEQVYIRGSQIRFIILP 69
>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 = 29.1 bits (66), Expect = 0.21
Identities = 9/24 (37%), Positives = 17/24 (70%)
Query: 32 VDLRNESSVSGRLEHVDGFMNIYM 55
V+L+N + +G L + D +MNI++
Sbjct: 16 VELKNGETYNGHLVNCDNWMNIHL 39
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 28.8 bits (65), Expect = 0.30
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 10 EQFLSFNTLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNIYMS 56
L L+ L K L + V L+N G L D +MN+ +
Sbjct: 1 MSMLGPLPLSFLKKLLNKRVL-VKLKNGREYRGTLVGFDQYMNLVLD 46
>gnl|CDD|178335 PLN02734, PLN02734, glycyl-tRNA synthetase.
Length = 684
Score = 29.7 bits (67), Expect = 0.50
Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 2/46 (4%)
Query: 88 DALQSKPRQSSSAGRTLKQKRANLMQQEVLEKIQALKKQKMAQGVM 133
Q+ +A R LK +A+ + E+ I+ LK K+ + +
Sbjct: 10 AEKQAAVTAQGNAVRALKASKAD--KAEIDAAIEKLKALKLEKSAL 53
>gnl|CDD|240780 cd12334, RRM1_SF3B4, RNA recognition motif 1 in splicing factor
3B subunit 4 (SF3B4) and similar proteins. This
subfamily corresponds to the RRM1 of SF3B4, also termed
pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or
spliceosome-associated protein 49 (SAP 49). SF3B4 a
component of the multiprotein complex splicing factor
3b (SF3B), an integral part of the U2 small nuclear
ribonucleoprotein (snRNP) and the U11/U12 di-snRNP.
SF3B is essential for the accurate excision of introns
from pre-messenger RNA, and is involved in the
recognition of the pre-mRNA's branch site within the
major and minor spliceosomes. SF3B4 functions to tether
U2 snRNP with pre-mRNA at the branch site during
spliceosome assembly. It is an evolutionarily highly
conserved protein with orthologs across diverse
species. SF3B4 contains two closely adjacent N-terminal
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains).
It binds directly to pre-mRNA and also interacts
directly and highly specifically with another SF3B
subunit called SAP 145. .
Length = 74
Score = 27.2 bits (61), Expect = 0.87
Identities = 11/23 (47%), Positives = 17/23 (73%), Gaps = 1/23 (4%)
Query: 56 SRELTFESLFIQSRNVMFIHIPR 78
+ EL +E LFIQ+ V+ +HIP+
Sbjct: 11 TEELLWE-LFIQAGPVVNVHIPK 32
>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 = 26.8 bits (60), Expect = 1.1
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 17 TLACLAKSLVGMITCVDLRNESSVSGRLEHVDGFMNI 53
L L +SL + V L+ V G L+ D +N+
Sbjct: 2 PLDVLNESLNKNVL-VKLKGGKEVRGVLKGFDQHLNL 37
>gnl|CDD|148614 pfam07106, TBPIP, Tat binding protein 1(TBP-1)-interacting protein
(TBPIP). This family consists of several eukaryotic
TBP-1 interacting protein (TBPIP) sequences. TBP-1 has
been demonstrated to interact with the human
immunodeficiency virus type 1 (HIV-1) viral protein Tat,
then modulate the essential replication process of HIV.
In addition, TBP-1 has been shown to be a component of
the 26S proteasome, a basic multiprotein complex that
degrades ubiquitinated proteins in an ATP-dependent
fashion. Human TBPIP interacts with human TBP-1 then
modulates the inhibitory action of human TBP-1 on
HIV-Tat-mediated transactivation.
Length = 169
Score = 26.5 bits (59), Expect = 3.9
Identities = 12/44 (27%), Positives = 25/44 (56%)
Query: 83 VNKVEDALQSKPRQSSSAGRTLKQKRANLMQQEVLEKIQALKKQ 126
+ ++ + +Q + S+ LK ++L +E+ E+IQ LKK+
Sbjct: 81 IEELREEVQLLKQDCSTLEIELKSLTSDLTTEELQEEIQELKKE 124
>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 = 24.5 bits (54), Expect = 8.4
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 9/42 (21%)
Query: 42 GRLEHVDGFMNI-------YMSRELTFE--SLFIQSRNVMFI 74
G L VD +MN+ Y+ + T + I+ NV++I
Sbjct: 26 GTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIRCNNVLYI 67
>gnl|CDD|131404 TIGR02351, thiH, thiazole biosynthesis protein ThiH. Members this
protein family are the ThiH protein of thiamine
biosynthesis, a homolog of the BioB protein of biotin
biosynthesis. Genes for the this protein generally are
found in operons with other thiamin biosynthesis genes
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Thiamine].
Length = 366
Score = 25.8 bits (57), Expect = 8.6
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 105 KQKRANLMQQEVLEKIQALKKQK 127
K KR L ++E+ +I+A+KK
Sbjct: 97 KIKRKKLNEEEIEREIEAIKKSG 119
>gnl|CDD|225301 COG2461, COG2461, Uncharacterized conserved protein [Function
unknown].
Length = 409
Score = 25.8 bits (57), Expect = 9.1
Identities = 9/33 (27%), Positives = 14/33 (42%)
Query: 69 RNVMFIHIPRHVSIVNKVEDALQSKPRQSSSAG 101
R V H P+ V IV K+ +S + +
Sbjct: 331 RRVQLCHPPKSVHIVEKILKDFKSGEKDFAEFW 363
>gnl|CDD|217679 pfam03701, UPF0181, Uncharacterized protein family (UPF0181). This
family contains small proteins of about 50 amino acids
of unknown function. The family includes YoaH.
Length = 52
Score = 23.8 bits (52), Expect = 9.8
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 113 QQEVLEKIQALKKQKMAQG 131
QQE +E+IQ L Q M+ G
Sbjct: 13 QQEAVERIQELMAQGMSSG 31
>gnl|CDD|219471 pfam07574, SMC_Nse1, Nse1 non-SMC component of SMC5-6 complex. S.
cerevisiae Nse1 forms part of a complex with SMC5-SMC6
This non-structural maintenance of chromosomes (SMC)
complex plays an essential role in genomic stability,
being involved in DNA repair and DNA metabolism. It is
conserved in eukaryotes from yeast to human.
Length = 180
Score = 25.4 bits (56), Expect = 9.9
Identities = 11/45 (24%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 80 VSIVNKVEDALQSKPRQSSSAGRTLKQKRANLMQQEVLEKIQALK 124
++ VN+ +D S +++ A + LK+ A +E+L+K+
Sbjct: 120 IAAVNETDDIASSAMKKTLPATKELKKSEA----EELLQKLVQDG 160
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 0.130 0.352
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: 6,306,091
Number of extensions: 525368
Number of successful extensions: 578
Number of sequences better than 10.0: 1
Number of HSP's gapped: 576
Number of HSP's successfully gapped: 42
Length of query: 133
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 47
Effective length of database: 7,123,158
Effective search space: 334788426
Effective search space used: 334788426
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)