RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10835
(80 letters)
>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 = 120 bits (304), Expect = 5e-38
Identities = 48/66 (72%), Positives = 59/66 (89%)
Query: 8 SQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGN 67
S+F+++I G+PVVVKL +GV+YRGVL+CLDGYMN+ LE TEEY++GQL KYGD FIRGN
Sbjct: 3 SKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIRGN 62
Query: 68 NVLYIS 73
NVLYIS
Sbjct: 63 NVLYIS 68
>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 = 79.9 bits (198), Expect = 6e-22
Identities = 31/64 (48%), Positives = 43/64 (67%)
Query: 9 QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNN 68
F+ + G+PV+VKL G++Y+G L +D YMN+ L TEEYI+G+ G+ IR NN
Sbjct: 4 PFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIRCNN 63
Query: 69 VLYI 72
VLYI
Sbjct: 64 VLYI 67
>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 = 66.4 bits (163), Expect = 1e-16
Identities = 27/65 (41%), Positives = 40/65 (61%)
Query: 9 QFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNN 68
+F+Q++ G+ V V+L +G + RG L D +MN+ L+ EE I NK G IRGNN
Sbjct: 1 KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNN 60
Query: 69 VLYIS 73
++ IS
Sbjct: 61 IVLIS 65
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 66.0 bits (162), Expect = 2e-16
Identities = 29/65 (44%), Positives = 44/65 (67%), Gaps = 1/65 (1%)
Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYIN-GQLKNKYGDTFIRGNN 68
F++++ G+ V+V+L +G +YRG L D +MN+ LE EE + G+ K K G FIRGNN
Sbjct: 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNN 61
Query: 69 VLYIS 73
++YI
Sbjct: 62 IVYII 66
>gnl|CDD|212478 cd01731, archaeal_Sm1, archaeal Sm protein 1. The archaeal Sm1
proteins: The Sm proteins are conserved in all three
domains of life and are always associated with U-rich
RNA sequences. They function to mediate RNA-RNA
interactions and RNA biogenesis. All Sm proteins
contain a common sequence motif in two segments, Sm1
and Sm2, separated by a short variable linker.
Eukaryotic Sm proteins form part of specific small
nuclear ribonucleoproteins (snRNPs) that are involved
in the processing of pre-mRNAs to mature mRNAs, and are
a major component of the eukaryotic spliceosome. Most
snRNPs consist of seven Sm proteins (B/B', D1, D2, D3,
E, F and G) arranged in a ring on a uridine-rich
sequence (Sm site), plus a small nuclear RNA (snRNA)
(either U1, U2, U5 or U4/6). Since archaebacteria do
not have any splicing apparatus, their Sm proteins may
play a more general role. Archaeal LSm proteins are
likely to represent the ancestral Sm domain.
Length = 69
Score = 63.4 bits (155), Expect = 3e-15
Identities = 25/59 (42%), Positives = 36/59 (61%)
Query: 15 HGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS 73
+ V+VKL G + RGVL D ++N+ LE EE I G+ K G +RG+NV++IS
Sbjct: 10 LNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVRGDNVVFIS 68
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 60.8 bits (148), Expect = 3e-14
Identities = 24/57 (42%), Positives = 37/57 (64%)
Query: 17 RPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS 73
PV+V+L G ++RG L D +MN+ L+ EE +G++ K G IRG+NV+Y+S
Sbjct: 15 SPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVS 71
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 55.0 bits (133), Expect = 6e-12
Identities = 25/73 (34%), Positives = 40/73 (54%), Gaps = 4/73 (5%)
Query: 5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQ---LKNKYGD 61
F++++ + V+VKL +G +YRG L D YMN+ L+ EE I+ + G
Sbjct: 6 PLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGG 65
Query: 62 T-FIRGNNVLYIS 73
IRG+N++ IS
Sbjct: 66 EVLIRGDNIVLIS 78
>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 = 2e-10
Identities = 19/58 (32%), Positives = 26/58 (44%)
Query: 16 GRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS 73
G+ V V+L G G L D YMN+ L+ E G IRG+N++ I
Sbjct: 6 GKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIVSIR 63
>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 = 40.3 bits (95), Expect = 4e-06
Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 15 HGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQ-TEEYINGQLKNKYGDTFIRGNNVLYIS 73
G PV+V+L +G Y G L D +MNI L+ +G K + +IRGN + Y+
Sbjct: 10 QGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIRGNTIKYLR 69
Query: 74 TQKR 77
Sbjct: 70 LPDE 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 = 38.3 bits (90), Expect = 2e-05
Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 6 SLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQ-TEEYINGQLKNKYGDTFI 64
SL +Q + GR V+L + RG++ +DG+MNI L T G+ + + F+
Sbjct: 9 SLVCLLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQH-HFDEFFV 67
Query: 65 RGNNVLYI 72
+G N+ Y+
Sbjct: 68 QGRNIRYV 75
>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 = 37.9 bits (89), Expect = 3e-05
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 31 GVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYI 72
GVL D +MN+ L+ E + K G IRGN+++ I
Sbjct: 25 GVLRGFDPFMNLVLDDAVEEVGDGEKTPIGMVVIRGNSIIMI 66
>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 = 37.1 bits (86), Expect = 5e-05
Identities = 16/43 (37%), Positives = 22/43 (51%)
Query: 31 GVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYIS 73
G L +D YMN+ L T E + + G +RGNN+L I
Sbjct: 26 GRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLRGNNILLIQ 68
>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 = 33.7 bits (78), Expect = 0.002
Identities = 22/69 (31%), Positives = 35/69 (50%), Gaps = 10/69 (14%)
Query: 10 FIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALE-----QTEEYIN-GQLKNKYGDTF 63
F + + G+ V V+L + + G L +D Y+NI L E+Y + +KN F
Sbjct: 5 FFKTLVGKEVTVELKNDLSITGTLHSVDQYLNIKLTNISVNDPEKYPHLLSVKN----CF 60
Query: 64 IRGNNVLYI 72
IRG+ V Y+
Sbjct: 61 IRGSVVRYV 69
>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 = 33.3 bits (77), Expect = 0.002
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 8/71 (11%)
Query: 7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGD----- 61
+ +++ + ++V L G G+L D + N+ LE T E I + N+YGD
Sbjct: 4 TASLEEEL-DKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERII--VGNQYGDIPRGL 60
Query: 62 TFIRGNNVLYI 72
IRG NV+ +
Sbjct: 61 FIIRGENVVLL 71
>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 = 32.2 bits (74), Expect = 0.006
Identities = 22/81 (27%), Positives = 35/81 (43%), Gaps = 15/81 (18%)
Query: 4 KES---LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYI--------N 52
KES LS+++ + + VK G + G+L D +N+ L+ T EY+
Sbjct: 1 KESILDLSKYV----DKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKL 56
Query: 53 GQLKNKYGDTFIRGNNVLYIS 73
G RG +V+ IS
Sbjct: 57 TDETRSLGLVVCRGTSVVLIS 77
>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 = 31.7 bits (73), Expect = 0.006
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 19 VVVKLVSGVDYRGVLSCLDGYMNIALEQ-TEEYINGQLKNKYGDTFIRGNNVLYI 72
V V+L +G YRG L + MN L+ T +G+ +K +IRG+ + +I
Sbjct: 13 VTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGK-VSKLEQVYIRGSQIRFI 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 = 31.5 bits (72), Expect = 0.008
Identities = 17/58 (29%), Positives = 25/58 (43%), Gaps = 5/58 (8%)
Query: 16 GRPVVVKLVSGVDYRGVLSCLD-GYMNIALEQTEEYINGQLKNKYGDTFIRGNNVLYI 72
+ V+V L +G Y G L D +NI L ++ NK+ I GN + I
Sbjct: 10 DKEVIVTLSNGKTYTGQLVGFDPSSLNIVLTNAKDSSG----NKFPKVIINGNRISEI 63
>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional.
Length = 89
Score = 30.8 bits (70), Expect = 0.017
Identities = 14/47 (29%), Positives = 22/47 (46%), Gaps = 1/47 (2%)
Query: 31 GVLSCLDGYMNIALEQTEE-YINGQLKNKYGDTFIRGNNVLYISTQK 76
G + D YMN+ L+ EE Y + G ++G+N+ I K
Sbjct: 43 GKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNITLIMAAK 89
>gnl|CDD|117020 pfam08443, RimK, RimK-like ATP-grasp domain. This ATP-grasp
domain is found in the ribosomal S6 modification enzyme
RimK.
Length = 190
Score = 31.7 bits (72), Expect = 0.020
Identities = 16/33 (48%), Positives = 18/33 (54%)
Query: 5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLD 37
E +FI+QI G PVVVK V G GV D
Sbjct: 28 EDAEKFIEQIKGFPVVVKSVFGSQGIGVFLAED 60
>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 = 29.8 bits (68), Expect = 0.039
Identities = 15/44 (34%), Positives = 18/44 (40%), Gaps = 4/44 (9%)
Query: 7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEY 50
L + + GR + V L G G C D NI L EEY
Sbjct: 4 LRKLL----GRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEY 43
>gnl|CDD|239202 cd02808, GltS_FMN, Glutamate synthase (GltS) FMN-binding domain.
GltS is a complex iron-sulfur flavoprotein that
catalyzes the reductive synthesis of L-glutamate from
2-oxoglutarate and L-glutamine via intramolecular
channelling of ammonia, a reaction in the plant, yeast
and bacterial pathway for ammonia assimilation. It is a
multifunctional enzyme that functions through three
distinct active centers, carrying out L-glutamine
hydrolysis, conversion of 2-oxoglutarate into
L-glutamate, and electron uptake from an electron donor.
Length = 392
Score = 30.2 bits (69), Expect = 0.071
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 4/30 (13%)
Query: 5 ESLSQFIQQIH----GRPVVVKLVSGVDYR 30
E L+Q I+ + G+P+ VKLV+G
Sbjct: 199 EDLAQLIEDLREATGGKPIGVKLVAGHGEG 228
>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 = 28.7 bits (65), Expect = 0.091
Identities = 19/69 (27%), Positives = 27/69 (39%), Gaps = 13/69 (18%)
Query: 19 VVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYING-------------QLKNKYGDTFIR 65
V VKL + RG L D ++N+ L EE I K F+R
Sbjct: 14 VYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTKRNIPMLFVR 73
Query: 66 GNNVLYIST 74
G+ V+ +S
Sbjct: 74 GDGVILVSP 82
>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 = 28.3 bits (64), Expect = 0.17
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 8/70 (11%)
Query: 7 LSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYG---DTF 63
L +F+ ++ V ++L +G G ++ +D MN L+ + LK K DT
Sbjct: 2 LVRFLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKN----VKLTLKGKNPVSLDTL 57
Query: 64 -IRGNNVLYI 72
IRGNN+ YI
Sbjct: 58 SIRGNNIRYI 67
>gnl|CDD|223267 COG0189, RimK, Glutathione synthase/Ribosomal protein S6
modification enzyme (glutaminyl transferase) [Coenzyme
metabolism / Translation, ribosomal structure and
biogenesis].
Length = 318
Score = 28.5 bits (64), Expect = 0.24
Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 1/62 (1%)
Query: 3 RKESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDT 62
+ ++F+ + G PVV+K + G RGV D + L E K
Sbjct: 142 DPDEAAEFVAEHLGFPVVLKPLDGSGGRGVFLVEDADPEL-LSLLETLTQEGRKLIIVQE 200
Query: 63 FI 64
+I
Sbjct: 201 YI 202
>gnl|CDD|235127 PRK03467, PRK03467, hypothetical protein; Provisional.
Length = 144
Score = 28.4 bits (64), Expect = 0.25
Identities = 9/25 (36%), Positives = 17/25 (68%)
Query: 14 IHGRPVVVKLVSGVDYRGVLSCLDG 38
++G+P V L+ GV ++G + L+G
Sbjct: 70 VNGQPKTVALIRGVQFKGEIRRLEG 94
>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 = 0.51
Identities = 7/22 (31%), Positives = 10/22 (45%)
Query: 16 GRPVVVKLVSGVDYRGVLSCLD 37
G+ V V L +G Y G+
Sbjct: 12 GQRVEVTLKNGSVYEGIFHTAS 33
>gnl|CDD|212465 cd01718, Sm_E, Sm protein E. The eukaryotic Sm proteins (B/B',
D1, D2, D3, E, F and G) assemble into a
hetero-heptameric ring around the Sm site of the
2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and
U5 snRNAs (Sm snRNAs) forming the core of the snRNP
particle. The snRNP particle, in turn, assembles with
other components onto the pre-mRNA to form the
spliceosome which is responsible for the excision of
introns and the ligation of exons. Members of this
family share a highly conserved Sm fold containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm subunit E
binds subunits F and G to form a trimer which then
assembles onto snRNA along with the D1/D2 and D3/B
heterodimers forming a seven-membered ring structure.
Length = 79
Score = 26.7 bits (60), Expect = 0.65
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 3/60 (5%)
Query: 18 PVVVKLVSGVDYR--GVLSCLDGYMNIALEQTEE-YINGQLKNKYGDTFIRGNNVLYIST 74
V + L D R G + D YMN+ L+ EE ++ + G ++G+N+ I
Sbjct: 20 RVQIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNTRKPLGRILLKGDNITLIQN 79
>gnl|CDD|236681 PRK10401, PRK10401, DNA-binding transcriptional regulator GalS;
Provisional.
Length = 346
Score = 27.4 bits (61), Expect = 0.74
Identities = 13/33 (39%), Positives = 21/33 (63%), Gaps = 2/33 (6%)
Query: 5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLD 37
+ L+QF+ QI G ++ ++V G +R V CLD
Sbjct: 129 DELAQFMDQIPGMVLINRVVPGYAHRCV--CLD 159
>gnl|CDD|233121 TIGR00768, rimK_fam, alpha-L-glutamate ligases, RimK family. This
family, related to bacterial glutathione synthetases,
contains at least two different alpha-L-glutamate
ligases. One is RimK, as in E. coli, which adds
additional Glu residues to the native Glu-Glu C-terminus
of ribosomal protein S6, but not to Lys-Glu mutants.
Most species with a member of this subfamily lack an S6
homolog ending in Glu-Glu, however. Members in
Methanococcus jannaschii act instead as a
tetrahydromethanopterin:alpha-l-glutamate ligase
(MJ0620) and a gamma-F420-2:alpha-l-glutamate ligase
(MJ1001).
Length = 277
Score = 26.9 bits (60), Expect = 0.95
Identities = 19/60 (31%), Positives = 26/60 (43%), Gaps = 1/60 (1%)
Query: 5 ESLSQFIQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFI 64
E + I++I G PVV+K V G R V D L + E +NG Y +I
Sbjct: 113 EEALKLIEEI-GFPVVLKPVFGSWGRLVSLARDKQAAETLLEHFEQLNGPQNLFYVQEYI 171
>gnl|CDD|223024 PHA03252, PHA03252, DNA packaging tegument protein UL25;
Provisional.
Length = 589
Score = 27.0 bits (60), Expect = 1.0
Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 3/42 (7%)
Query: 16 GRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKN 57
V+V+++ RGV+ L GY EE ++GQ+++
Sbjct: 314 DEHVLVRVLLK---RGVIQQLPGYKASTSRVVEERLSGQVRD 352
>gnl|CDD|130973 TIGR01918, various_sel_PB, selenoprotein B,
glycine/betaine/sarcosine/D-proline reductase family.
This model represents selenoprotein B of glycine
reductase, sarcosine reductase, betaine reductase,
D-proline reductase, and perhaps others. This model is
built in fragment mode to assist in recognizing
fragmentary translations. All members are expected to
contain an internal TGA codon, encoding selenocysteine,
which may be misinterpreted as a stop codon.
Length = 431
Score = 26.8 bits (59), Expect = 1.0
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 31 GVLSCLDGYMNIALEQTEEYINGQLKNKYGDTFIRG 66
+ C D + LE+ + LK+K D FI G
Sbjct: 48 HTVVCGDSFFGENLEEAVARVLEMLKDKEPDIFIAG 83
>gnl|CDD|110632 pfam01645, Glu_synthase, Conserved region in glutamate synthase.
This family represents a region of the glutamate
synthase protein. This region is expressed as a separate
subunit in the glutamate synthase alpha subunit from
archaebacteria, or part of a large multidomain enzyme in
other organisms. The aligned region of these proteins
contains a putative FMN binding site and Fe-S cluster.
Length = 367
Score = 26.9 bits (60), Expect = 1.1
Identities = 11/30 (36%), Positives = 15/30 (50%), Gaps = 4/30 (13%)
Query: 1 MSRKESLSQFIQQIH----GRPVVVKLVSG 26
+ E L+Q I + P+ VKLVSG
Sbjct: 183 IYSIEDLAQLIYDLKEINPKAPISVKLVSG 212
>gnl|CDD|163592 TIGR03880, KaiC_arch_3, KaiC domain protein, AF_0351 family.
This model represents a rather narrowly distributed
archaeal protein family in which members have a single
copy of the KaiC domain. This stands in contrast to the
circadian clock protein KaiC itself, with two copies of
the domain. Members are expected to have weak ATPase
activity, by homology to the
autokinase/autophosphorylase KaiC itself.
Length = 224
Score = 26.2 bits (58), Expect = 1.5
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 40 MNIALEQTEEYINGQLKNKYGDTFIRGNNVLYI 72
M I+LE+ EE I G K+K D + LYI
Sbjct: 48 MYISLEEREERILGYAKSKGWDLEDYIDKSLYI 80
>gnl|CDD|215314 PLN02576, PLN02576, protoporphyrinogen oxidase.
Length = 496
Score = 25.4 bits (56), Expect = 3.7
Identities = 11/30 (36%), Positives = 18/30 (60%), Gaps = 4/30 (13%)
Query: 2 SRKESLSQFIQQIHGRPVVVKL----VSGV 27
R+ES+ +F+++ G V +L VSGV
Sbjct: 143 GREESVGEFVRRHLGDEVFERLIDPFVSGV 172
>gnl|CDD|182468 PRK10446, PRK10446, ribosomal protein S6 modification protein;
Provisional.
Length = 300
Score = 24.9 bits (54), Expect = 5.0
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 8 SQFIQQIHGRPVVVKLVSGVDYRGVL 33
S I + G P+VVKLV G GV+
Sbjct: 127 SDLIDMVGGAPLVVKLVEGTQGIGVV 152
>gnl|CDD|237029 PRK12268, PRK12268, methionyl-tRNA synthetase; Reviewed.
Length = 556
Score = 24.8 bits (55), Expect = 5.7
Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 12/36 (33%)
Query: 50 YINGQLK--NKYG-----DTFIR-----GNNVLYIS 73
Y NG L + G D F R GN VL++S
Sbjct: 13 YANGPLHLGHLAGSGLPADVFARYQRLKGNEVLFVS 48
>gnl|CDD|223516 COG0439, AccC, Biotin carboxylase [Lipid metabolism].
Length = 449
Score = 24.9 bits (55), Expect = 5.7
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 3/51 (5%)
Query: 11 IQQIHGRPVVVKLVSGVDYRGVLSCLDGYMNIALEQTEEYINGQLKNKYGD 61
I + G PV+VK +G RG+ + LE E G+ + +G+
Sbjct: 147 IAEEIGYPVIVKAAAGGGGRGMRVVRNEE---ELEAAFEAARGEAEAAFGN 194
>gnl|CDD|225802 COG3263, COG3263, NhaP-type Na+/H+ and K+/H+ antiporters with a
unique C-terminal domain [Inorganic ion transport and
metabolism].
Length = 574
Score = 24.7 bits (54), Expect = 7.5
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 52 NGQLKNKYGDTFIRGNNVLYISTQKR 77
+GQL + G T +R +VL + +R
Sbjct: 447 DGQLIHPQGSTRLREGDVLCVIGSER 472
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
0.320 0.138 0.389
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: 3,969,041
Number of extensions: 309734
Number of successful extensions: 361
Number of sequences better than 10.0: 1
Number of HSP's gapped: 354
Number of HSP's successfully gapped: 43
Length of query: 80
Length of database: 10,937,602
Length adjustment: 49
Effective length of query: 31
Effective length of database: 8,764,256
Effective search space: 271691936
Effective search space used: 271691936
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 (21.8 bits)
S2: 53 (24.0 bits)