RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1175
(155 letters)
>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 = 140 bits (354), Expect = 2e-44
Identities = 51/63 (80%), Positives = 61/63 (96%)
Query: 1 MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDE 60
+LVELKNGETYNGHLVNCD+WMNI+L+ VICTS+DGD+FW+MPECYIRG+ IKYLR+PDE
Sbjct: 14 VLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIRGNTIKYLRLPDE 73
Query: 61 IID 63
+ID
Sbjct: 74 VID 76
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 68.3 bits (168), Expect = 3e-16
Identities = 24/57 (42%), Positives = 36/57 (63%)
Query: 1 MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRI 57
+LVELKNG Y G L D +MN+ L +V T +DG+K ++ +IRG+ I Y+ +
Sbjct: 11 VLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67
>gnl|CDD|212468 cd01721, Sm_D3, Sm protein D3. The eukaryotic Sm proteins (B/B',
D1, D2, D3, E, F and G) assemble into a
hetero-heptameric ring around the Sm site of the
2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and
U5 snRNAs (Sm snRNAs) forming the core of the snRNP
particle. The snRNP particle, in turn, assembles with
other components onto the pre-mRNA to form the
spliceosome which is responsible for the excision of
introns and the ligation of exons. Members of this
family share a highly conserved Sm fold containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm subunit D3
heterodimerizes with subunit B and three such
heterodimers form a hexameric ring structure with
alternating B and D3 subunits. The D3 - B heterodimer
also assembles into a heptameric ring containing D1,
D2, E, F, and G subunits.
Length = 70
Score = 63.7 bits (156), Expect = 2e-14
Identities = 26/57 (45%), Positives = 38/57 (66%), Gaps = 1/57 (1%)
Query: 3 VELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPD 59
VELK GE Y G L+ + MN L++V T+RDG K ++ + YIRGS I+++ +PD
Sbjct: 15 VELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDG-KVSKLEQVYIRGSQIRFIILPD 70
>gnl|CDD|212462 cd00600, Sm_like, Sm and related proteins. The eukaryotic Sm and
Sm-like (LSm) proteins associate with RNA to form the
core domain of the ribonucleoprotein particles involved
in a variety of RNA processing events including
pre-mRNA splicing, telomere replication, and mRNA
degradation. Members of this family share a highly
conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet. Sm-like proteins exist in archaea as well
as prokaryotes that form heptameric and hexameric ring
structures similar to those found in eukaryotes.
Length = 63
Score = 54.9 bits (133), Expect = 4e-11
Identities = 24/56 (42%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 1 MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLR 56
+ VELK+G G LV D +MN+ L +V+ T RDG K + IRGS I +R
Sbjct: 9 VSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDG-KVRVLGLVLIRGSNIVSIR 63
>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 = 51.4 bits (124), Expect = 8e-10
Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 1 MLVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRI 57
+ VELKNG G L D +MN+ L +V T +DG ++ IRG+ I +
Sbjct: 11 VTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVN-KLGLVLIRGNNIVLISP 66
>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 = 50.3 bits (121), Expect = 5e-09
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 8/78 (10%)
Query: 3 VELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRM---PECYIRGSMIKYLRIPD 59
VELKN + G L + D ++NI L + D +K+ + C+IRGS+++Y+++P
Sbjct: 16 VELKNDLSITGTLHSVDQYLNIKLTNISVN--DPEKYPHLLSVKNCFIRGSVVRYVQLPA 73
Query: 60 EIIDMVKEDQVQRTRQRD 77
+ +D + +Q +R+
Sbjct: 74 DEVD---TELLQDATRRE 88
>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 = 48.7 bits (117), Expect = 1e-08
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 2 LVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIP 58
VEL+N + G + N D +MNI L + T R G + E +++G I+Y+ IP
Sbjct: 23 TVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQH-HFDEFFVQGRNIRYVHIP 78
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 48.5 bits (116), Expect = 2e-08
Identities = 24/57 (42%), Positives = 30/57 (52%), Gaps = 3/57 (5%)
Query: 2 LVELKNGETYNGHLVNCDHWMNINLREVICTSR-DGDKFWR--MPECYIRGSMIKYL 55
LV+LKNG Y G LV D +MN+ L +V DG+K R E IRG I +
Sbjct: 21 LVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLI 77
>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 = 38.0 bits (89), Expect = 2e-04
Identities = 22/75 (29%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 3 VELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRIPDEI- 61
+ELKNG +G + D MN +L+ V T + G + IRG+ I+Y+ +PD +
Sbjct: 16 IELKNGTVVHGTITGVDVSMNTHLKNVKLTLK-GKNPVSLDTLSIRGNNIRYIILPDSLN 74
Query: 62 IDMVKEDQVQRTRQR 76
+D + D + + +
Sbjct: 75 LDTLLVDDTPKAKAK 89
>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 = 36.7 bits (86), Expect = 4e-04
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 7/56 (12%)
Query: 2 LVELKNGETYNGHLVNCDHWMNINL---REVICTSRDGDKFWRMPECYIRGSMIKY 54
+V+LKNG Y G L D +MN+ L E + DG + + +IRG+ + Y
Sbjct: 15 VVKLKNGVEYRGVLACLDGYMNLVLEDTEEYV----DGQLVAKYGDAFIRGNNVLY 66
>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 = 31.1 bits (71), Expect = 0.036
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 6/57 (10%)
Query: 2 LVELKNGETYNGHLVNCDHW-MNINLREVICTSRDGDKFWRMPECYIRGSMIKYLRI 57
+V L NG+TY G LV D +NI L G+KF P+ I G+ I + +
Sbjct: 14 IVTLSNGKTYTGQLVGFDPSSLNIVLTNA--KDSSGNKF---PKVIINGNRISEILV 65
>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 = 31.4 bits (72), Expect = 0.036
Identities = 19/56 (33%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 2 LVELKNGETYNGHLVNCDHWMNINLREVICTSRDGDKFW-RMPECYIRGSMIKYLR 56
+V+LK G Y G LV+ D +MN+ L KF + E IR + + Y+R
Sbjct: 15 IVKLKWGMEYKGTLVSVDSYMNLQLAN--TEEYIDGKFTGNLGEVLIRCNNVLYIR 68
>gnl|CDD|233885 TIGR02479, FliA_WhiG, RNA polymerase sigma factor, FliA/WhiG
family. Most members of this family are the flagellar
operon sigma factor FliA, controlling transcription of
bacterial flagellar genes by RNA polymerase. An
exception is the sigma factor WhiG in the genus
Streptomyces, involved in the production of sporulating
aerial mycelium.
Length = 224
Score = 32.2 bits (74), Expect = 0.072
Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 6/57 (10%)
Query: 36 GDKFWRMPECYIRGSMIKYLR----IPDEIIDMVKEDQVQRTRQRDSNRGGRGGSNQ 88
G KF IRG+M+ LR +P + + +++R + R GR + +
Sbjct: 49 GAKFETYAVQRIRGAMLDELRRLDWVPRSLRQKAR--KLERAIRELEARLGREPTEE 103
>gnl|CDD|216171 pfam00883, Peptidase_M17, Cytosol aminopeptidase family, catalytic
domain. The two associated zinc ions and the active
site are entirely enclosed within the C-terminal
catalytic domain in leucine aminopeptidase.
Length = 311
Score = 31.1 bits (71), Expect = 0.16
Identities = 17/44 (38%), Positives = 22/44 (50%), Gaps = 7/44 (15%)
Query: 1 MLVELKNGETYNGHLVNCDHWMNINLREVICTSRD-GDKFWRMP 43
+V L G TY G N D N E+I + + G+K WRMP
Sbjct: 200 CVVAL--GTTYTGIFSNDDELAN----ELIKAAEESGEKVWRMP 237
>gnl|CDD|235529 PRK05601, PRK05601, DNA polymerase III subunit epsilon; Validated.
Length = 377
Score = 31.0 bits (70), Expect = 0.23
Identities = 10/36 (27%), Positives = 14/36 (38%)
Query: 72 RTRQRDSNRGGRGGSNQRGRGGHNMRGMRANNAPKP 107
+ + R R + RGG R R + PKP
Sbjct: 145 KRAMNAAARANRNRNRGNRRGGRGRRRQRVGHIPKP 180
>gnl|CDD|223338 COG0260, PepB, Leucyl aminopeptidase [Amino acid transport and
metabolism].
Length = 485
Score = 30.7 bits (70), Expect = 0.28
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 7/44 (15%)
Query: 1 MLVELKNGETYNGHLVNCDHWMNINLREVICTSRD-GDKFWRMP 43
+V L G Y G N D +++ S + G+ WR+P
Sbjct: 367 AVVAL--GNDYTGLFSNDDEL----ANQLLAASEETGEPLWRLP 404
>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 = 27.5 bits (62), Expect = 0.90
Identities = 15/50 (30%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 2 LVELKNGETYNGHLVNCDHWMNINLR--EVICTSRDGDKFWRMPECYIRG 49
LV+LK G+ G L D +N+ L E I +G+ ++ +RG
Sbjct: 15 LVKLKGGKEVRGVLKGFDQHLNLVLENAEEI---IEGESVRKLGTVLVRG 61
>gnl|CDD|222425 pfam13865, FoP_duplication, C-terminal duplication domain of Friend
of PRMT1. Fop, or Friend of Prmt1, proteins are
conserved from fungi and plants to vertebrates. There is
little that is actually conserved except for this
C-terminal LDXXLDAYM region where X is any amino acid).
The Fop proteins themselves are nuclear proteins
localised to regions with low levels of DAPI, with a
punctate/speckle-like distribution. Fop is a
chromatin-associated protein and it colocalises with
facultative heterochromatin. It is is critical for
oestrogen-dependent gene activation.
Length = 76
Score = 27.4 bits (61), Expect = 1.1
Identities = 11/40 (27%), Positives = 14/40 (35%), Gaps = 1/40 (2%)
Query: 76 RDSNRGGRGGSNQRGR-GGHNMRGMRANNAPKPTLNRNEL 114
R RG +RGR G R + A R +L
Sbjct: 8 RGGKFRPRGRGARRGRRRGRGGRKGKGGAAKPKPKTREDL 47
>gnl|CDD|114474 pfam05750, Rubella_Capsid, Rubella capsid protein. Rubella virus
is an enveloped positive-strand RNA virus of the family
Togaviridae. Virions are composed of three structural
proteins: a capsid and two membrane-spanning
glycoproteins, E2 and E1. During virus assembly, the
capsid interacts with genomic RNA to form nucleocapsids.
It has been discovered that capsid phosphorylation
serves to negatively regulate binding of viral genomic
RNA. This may delay the initiation of nucleocapsid
assembly until sufficient amounts of virus glycoproteins
accumulate at the budding site and/or prevent
non-specific binding to cellular RNA when levels of
genomic RNA are low. It follows that at a late stage in
replication, the capsid may undergo dephosphorylation
before nucleocapsid assembly occurs.
Length = 300
Score = 28.3 bits (62), Expect = 1.7
Identities = 18/46 (39%), Positives = 21/46 (45%), Gaps = 6/46 (13%)
Query: 74 RQRDS----NRGGRGGSNQRGRGGHNMRGMRAN--NAPKPTLNRNE 113
RQRDS + GR R R G+ RG R + AP P R E
Sbjct: 41 RQRDSSTSGDDSGRDSGGPRRRRGNRGRGQRKDWSRAPPPPEERQE 86
>gnl|CDD|164624 MTH00053, CYTB, cytochrome b; Provisional.
Length = 381
Score = 27.4 bits (61), Expect = 3.2
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 110 NRNELFYYCGIILLITCLFQMLK--SQVDLNMLRVMTMTTDINHGFCF 155
N L +C II +IT +F + + V+L V +T D+N+GF
Sbjct: 33 NFGSLLGFCLIIQIITGIFLAMHYCADVNLAFSSVAHITRDVNYGFIL 80
>gnl|CDD|216137 pfam00822, PMP22_Claudin, PMP-22/EMP/MP20/Claudin family.
Length = 161
Score = 26.9 bits (60), Expect = 3.4
Identities = 7/25 (28%), Positives = 13/25 (52%)
Query: 107 PTLNRNELFYYCGIILLITCLFQML 131
T+ + F GII L++ L ++
Sbjct: 92 FTMRKGGRFKLAGIIFLVSGLCVLV 116
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 27.6 bits (62), Expect = 3.6
Identities = 9/36 (25%), Positives = 13/36 (36%)
Query: 68 DQVQRTRQRDSNRGGRGGSNQRGRGGHNMRGMRANN 103
+ R RG R G ++RGR R +
Sbjct: 206 RDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGD 241
>gnl|CDD|235770 PRK06288, PRK06288, RNA polymerase sigma factor WhiG; Reviewed.
Length = 268
Score = 27.0 bits (60), Expect = 3.8
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 47 IRGSMIKYLRIPDEIIDMVKED--QVQRTRQRDSNRGGRGGSNQ 88
IRG++ LR D I V++ Q++R R GR S++
Sbjct: 95 IRGAIFDELRSIDWIPRSVRQKARQIERAIAMLEARLGRTPSDE 138
>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 = 25.5 bits (56), Expect = 4.0
Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 3 VELK-NGETYNGHLVNCDHWMNINLREVICTSRDGDKFWRMPECYIRGSMI 52
VE+K + G LV D +MN++L + + +K + +RG+ I
Sbjct: 15 VEMKGDENQLQGRLVAVDDYMNLHLTDTMECVG-EEKVRSLGTVVLRGNNI 64
>gnl|CDD|224806 COG1894, NuoF, NADH:ubiquinone oxidoreductase, NADH-binding (51
kD) subunit [Energy production and conversion].
Length = 424
Score = 26.8 bits (60), Expect = 4.8
Identities = 14/36 (38%), Positives = 15/36 (41%), Gaps = 18/36 (50%)
Query: 58 PDEIIDMVKEDQVQRTRQRDSNRGGRGGSNQRGRGG 93
PDEII+ VKE S RGRGG
Sbjct: 46 PDEIIEEVKE------------------SGLRGRGG 63
>gnl|CDD|192487 pfam10225, DUF2215, Uncharacterized conserved protein (DUF2215).
This entry is the central 200 residues of a family of
proteins conserved from worms to humans. The function is
unknown.
Length = 248
Score = 26.6 bits (59), Expect = 4.9
Identities = 9/31 (29%), Positives = 15/31 (48%), Gaps = 5/31 (16%)
Query: 107 PTLNRNELFYYC-----GIILLITCLFQMLK 132
P L+R+ LFYY G++ + + L
Sbjct: 28 PLLSRSVLFYYSSGIALGVLASLLLVVFQLM 58
>gnl|CDD|131014 TIGR01959, nuoF_fam, NADH-quinone oxidoreductase, F subunit.
This model describes the F chain of complexes that
resemble NADH-quinone oxidoreductases. The electron
acceptor is a quinone, ubiquinone, in mitochondria and
most bacteria, including Escherichia coli, where the
recommended gene symbol is nuoF. This family does not
have any members in chloroplast or cyanobacteria, where
the quinone may be plastoquinone and NADH may be
replaced by NADPH, nor in Methanosarcina, where NADH is
replaced by F420H2 [Energy metabolism, Electron
transport].
Length = 411
Score = 26.9 bits (60), Expect = 5.8
Identities = 12/36 (33%), Positives = 15/36 (41%), Gaps = 18/36 (50%)
Query: 58 PDEIIDMVKEDQVQRTRQRDSNRGGRGGSNQRGRGG 93
PD+II+ VK+ S RGRGG
Sbjct: 35 PDDIIEEVKD------------------SGLRGRGG 52
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 26.8 bits (60), Expect = 5.9
Identities = 7/33 (21%), Positives = 11/33 (33%)
Query: 66 KEDQVQRTRQRDSNRGGRGGSNQRGRGGHNMRG 98
++ Q Q QR +G +G Q
Sbjct: 609 RDLQEQFNAQRGEQQGQQGQGGQGQGQPGQQGQ 641
>gnl|CDD|226535 COG4049, COG4049, Uncharacterized protein containing
archaeal-type C2H2 Zn-finger [General function
prediction only].
Length = 65
Score = 25.0 bits (54), Expect = 6.3
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 26 LREVICTSRDGDKFWRMPEC 45
L+ + RDG++F R P C
Sbjct: 4 LKAIKVRDRDGEEFLRCPRC 23
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 26.7 bits (59), Expect = 6.3
Identities = 13/56 (23%), Positives = 20/56 (35%)
Query: 57 IPDEIIDMVKEDQVQRTRQRDSNRGGRGGSNQRGRGGHNMRGMRANNAPKPTLNRN 112
I E I ++ + R + RG + G +RG GG + P L
Sbjct: 382 IKAEPIQNGRQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDA 437
>gnl|CDD|235901 PRK06986, fliA, flagellar biosynthesis sigma factor; Validated.
Length = 236
Score = 26.3 bits (59), Expect = 7.0
Identities = 9/25 (36%), Positives = 11/25 (44%), Gaps = 8/25 (32%)
Query: 36 GDKFWRMPECY----IRGSMIKYLR 56
G F Y IRG+M+ LR
Sbjct: 61 GASFE----TYAGQRIRGAMLDELR 81
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional.
Length = 293
Score = 26.2 bits (58), Expect = 8.3
Identities = 11/20 (55%), Positives = 11/20 (55%)
Query: 74 RQRDSNRGGRGGSNQRGRGG 93
R GGRGG RGRGG
Sbjct: 22 RGGGGRGGGRGGGRGRGRGG 41
>gnl|CDD|233496 TIGR01622, SF-CC1, splicing factor, CC1-like family. This model
represents a subfamily of RNA splicing factors including
the Pad-1 protein (N. crassa), CAPER (M. musculus) and
CC1.3 (H.sapiens). These proteins are characterized by
an N-terminal arginine-rich, low complexity domain
followed by three (or in the case of 4 H. sapiens
paralogs, two) RNA recognition domains (rrm: pfam00706).
These splicing factors are closely related to the U2AF
splicing factor family (TIGR01642). A homologous gene
from Plasmodium falciparum was identified in the course
of the analysis of that genome at TIGR and was included
in the seed.
Length = 457
Score = 26.4 bits (58), Expect = 8.5
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 63 DMVKEDQVQRTRQRDSNRGGRGGSNQRGRGGHNMRGMRANNAPKP 107
D +E +R+R RD +R R RGR G R N +P
Sbjct: 18 DKGRERSRRRSRSRDRSRRRRDRDYYRGRRG-RSRSRSPNRYYRP 61
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
0.326 0.141 0.448
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: 7,793,438
Number of extensions: 683504
Number of successful extensions: 927
Number of sequences better than 10.0: 1
Number of HSP's gapped: 905
Number of HSP's successfully gapped: 40
Length of query: 155
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 66
Effective length of database: 6,990,096
Effective search space: 461346336
Effective search space used: 461346336
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (24.8 bits)