RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10177
(116 letters)
>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 = 115 bits (291), Expect = 2e-35
Identities = 47/59 (79%), Positives = 53/59 (89%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEV 59
+V+LRDGR LIG LRS DQFANLVL T+ERI VGNQYGDIPRG+FIIRGENVVL+GE+
Sbjct: 16 LVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLFIIRGENVVLLGEI 74
>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 = 62.2 bits (152), Expect = 4e-14
Identities = 26/77 (33%), Positives = 46/77 (59%), Gaps = 1/77 (1%)
Query: 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERI-HVGNQYGDIPRGIFIIRGENVVLMGEVD 60
V+ DGR ++G L+ DQ NL+L ER+ ++P G++++RG+NV ++GEVD
Sbjct: 14 VITTDGRVIVGTLKGFDQTTNLILSNCHERVYSSDEGVEEVPLGLYLLRGDNVAVIGEVD 73
Query: 61 KEKEHCPQLQQVSVEDI 77
+E + L ++ E +
Sbjct: 74 EELDGSIDLSKIRAEPL 90
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 57.9 bits (141), Expect = 1e-12
Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 58
+V L++GR G L+ DQF NLVL E + G + G+ IRG N+V +
Sbjct: 12 LVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEK--KRKLGLVFIRGNNIVYIIL 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 = 56.4 bits (137), Expect = 4e-12
Identities = 24/57 (42%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 58
V L++GR L G L+ DQF NLVL E I G G+ +IRG N+VL+
Sbjct: 13 VELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVN---KLGLVLIRGNNIVLISP 66
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 48.1 bits (115), Expect = 1e-08
Identities = 21/58 (36%), Positives = 29/58 (50%), Gaps = 1/58 (1%)
Query: 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGI-FIIRGENVVLMGE 58
V L++GR G L DQ+ NLVL E I + G +IRG+N+VL+
Sbjct: 22 VKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVLIRGDNIVLISP 79
>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 = 39.4 bits (93), Expect = 2e-05
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 3/56 (5%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLM 56
+ L R + G LR D F NLVL +E + G + P G+ +IRG +++++
Sbjct: 14 SLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGEK---TPIGMVVIRGNSIIMI 66
>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 = 38.7 bits (91), Expect = 3e-05
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 7/54 (12%)
Query: 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERI--HVGNQYGDIPRGIFIIRGENV 53
V L++G G L +D + NLVL T E + + +YGD IRG NV
Sbjct: 16 VKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDA-----FIRGNNV 64
>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 = 37.5 bits (88), Expect = 9e-05
Identities = 22/63 (34%), Positives = 31/63 (49%), Gaps = 8/63 (12%)
Query: 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIE--RIHVGNQYGDIPR------GIFIIRGENV 53
V L+DGR +G + D+ NLVL E +I + R G+ ++RGENV
Sbjct: 15 VTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKKGEEREEKRVLGLVLLRGENV 74
Query: 54 VLM 56
V M
Sbjct: 75 VSM 77
>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 = 35.3 bits (82), Expect = 6e-04
Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLM 56
V L+DGR L G L + D++ NLVL +E G G+ +IRG N+V +
Sbjct: 11 VELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKV---RVLGLVLIRGSNIVSI 62
>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 = 34.9 bits (81), Expect = 0.001
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVL 55
+V L+ G+ + G L+ DQ NLVL E + G ++RG+NVV
Sbjct: 15 LVKLKGGKEVRGVLKGFDQHLNLVLENAEE---IIEGESVRKLGTVLVRGDNVVF 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 = 32.5 bits (74), Expect = 0.009
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 6 DGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLM 56
D L G L +VD + NL L T+E VG + G ++RG N++L+
Sbjct: 20 DENQLQGRLVAVDDYMNLHLTDTME--CVGEEKVR-SLGTVVLRGNNILLI 67
>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 = 0.017
Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 58
+V L+ G G L SVD + NL L T E I G G++ G +IR NV+ + E
Sbjct: 15 IVKLKWGMEYKGTLVSVDSYMNLQLANTEEYID-GKFTGNL--GEVLIRCNNVLYIRE 69
>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 = 31.4 bits (72), Expect = 0.022
Identities = 10/28 (35%), Positives = 14/28 (50%)
Query: 4 LRDGRTLIGYLRSVDQFANLVLHKTIER 31
L DGR L+G D+ N++L E
Sbjct: 16 LTDGRVLVGTFVCTDKDGNIILSNAEEY 43
>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 = 0.15
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENV 53
+V L++G T G+L + D + N+ L I G+++ +P IRG +
Sbjct: 15 LVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPE--CYIRGNTI 65
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 28.8 bits (65), Expect = 0.19
Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 7/56 (12%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGDIPR--GIFIIRGENVV 54
+V L+ GR G L+ D NLVL E G++ R G +IRG+NVV
Sbjct: 18 LVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD-----GEVVRKLGKVVIRGDNVV 68
>gnl|CDD|190612 pfam03352, Adenine_glyco, Methyladenine glycosylase. The
DNA-3-methyladenine glycosylase I is constitutively
expressed and is specific for the alkylated
3-methyladenine DNA.
Length = 179
Score = 29.8 bits (68), Expect = 0.20
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 77 ILNAQRKEQEV--KQERSRMLAKRLKERGLSFV 107
I+N + EV K S ++K LK+RG FV
Sbjct: 120 IVNRWKSLAEVPAKTPLSDAISKDLKKRGFKFV 152
>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 = 28.3 bits (64), Expect = 0.31
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 9/61 (14%)
Query: 7 GRTLIGYLRSVDQFANLVLHKTIERI-------HVGNQYGDIPRGIFIIRGENVVLMGEV 59
GR + G L+ DQ NLVL T+E + + ++ + G+ + RG +VVL+ V
Sbjct: 22 GREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDETRSL--GLVVCRGTSVVLISPV 79
Query: 60 D 60
D
Sbjct: 80 D 80
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 28.8 bits (65), Expect = 0.60
Identities = 12/17 (70%), Positives = 13/17 (76%), Gaps = 1/17 (5%)
Query: 95 LAKRLKERGLSFVPDLI 111
LAKR RGLSF+ DLI
Sbjct: 287 LAKRYTNRGLSFL-DLI 302
>gnl|CDD|212467 cd01720, Sm_D2, Sm protein D2. 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 D2
heterodimerizes with subunit D1 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 D2,
D3, E, F, and G subunits.
Length = 89
Score = 26.9 bits (60), Expect = 1.1
Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 10/62 (16%)
Query: 4 LRDGRTLIGYLRSVDQFANLVLHKTIERIHVGNQYGD------IPRGIFI----IRGENV 53
R+ + L+ +++ D+ N+VL E + G + + FI +RG++V
Sbjct: 23 CRNNKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKGKKSKPVNKDRFISKMFLRGDSV 82
Query: 54 VL 55
+L
Sbjct: 83 IL 84
>gnl|CDD|225123 COG2213, MtlA, Phosphotransferase system, mannitol-specific IIBC
component [Carbohydrate transport and metabolism].
Length = 472
Score = 26.5 bits (59), Expect = 3.5
Identities = 7/31 (22%), Positives = 18/31 (58%)
Query: 59 VDKEKEHCPQLQQVSVEDILNAQRKEQEVKQ 89
D+ K P Q +S+ + L++ + ++ V++
Sbjct: 435 TDRAKRKVPDAQHISINNFLDSPKYDELVEK 465
>gnl|CDD|185175 PRK15272, PRK15272, pertussis toxin-like subunit ArtA;
Provisional.
Length = 242
Score = 26.5 bits (58), Expect = 3.8
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 2 VLLRDGRTLIGYLRSVDQF 20
V+ RDG +L+GY R+ QF
Sbjct: 32 VIFRDGFSLLGYNRNFQQF 50
>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 = 25.3 bits (56), Expect = 4.1
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 10/64 (15%)
Query: 2 VLLRDGRTLIGYLRSVDQFANLVLHKTIERIHV----GNQYGDIPR------GIFIIRGE 51
V LR R L G L + DQ N++L E I Y +I + + +RG+
Sbjct: 16 VKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTKRNIPMLFVRGD 75
Query: 52 NVVL 55
V+L
Sbjct: 76 GVIL 79
>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 = 24.9 bits (55), Expect = 4.7
Identities = 7/30 (23%), Positives = 15/30 (50%)
Query: 1 MVLLRDGRTLIGYLRSVDQFANLVLHKTIE 30
++++ + +G L D + N+VL E
Sbjct: 17 WIIMKSDKEFVGTLLGFDDYVNMVLEDVTE 46
>gnl|CDD|227038 COG4694, COG4694, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 758
Score = 26.4 bits (58), Expect = 4.8
Identities = 9/70 (12%), Positives = 27/70 (38%), Gaps = 5/70 (7%)
Query: 22 NLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGEVDKEKEHCPQLQQVSVEDILNAQ 81
+L + ++ + +GI + + +++K + + + + + I N
Sbjct: 83 SLKIEVYNKQFKHEQLWNSQVKGILTLGKKTN---DDLEKIESKKESINKKNEKKIKNE- 138
Query: 82 RKEQEVKQER 91
+VK +R
Sbjct: 139 -ASLQVKTQR 147
>gnl|CDD|129262 TIGR00158, L9, ribosomal protein L9. Ribosomal protein L9 appears
to be universal in, but restricted to, eubacteria and
chloroplast [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 148
Score = 25.8 bits (57), Expect = 5.0
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 77 ILNAQRKEQEVKQERSRMLAKRLKE 101
A+RK+ E K ++ A RLKE
Sbjct: 46 FFEARRKKLEEKLAANKAAAARLKE 70
>gnl|CDD|185750 cd09237, V_ScBro1_like, Protein-interacting V-domain of
Saccharomyces cerevisiae Bro1 and related domains. This
family contains the V-shaped (V) domain of Saccharomyces
cerevisiae Bro1, and related domains. It belongs to the
V_Alix_like superfamily which also includes the V-domain
of Saccharomyces cerevisiae Rim20 (also known as PalA),
mammalian Alix (apoptosis-linked gene-2 interacting
protein X), His-Domain type N23 protein tyrosine
phosphatase (HD-PTP, also known as PTPN23), and related
domains. Bro1 interacts with the ESCRT (Endosomal
Sorting Complexes Required for Transport) system, and
participates in endosomal trafficking. The mammalian
Alix V-domain (belonging to a different family) contains
a binding site, partially conserved in the superfamily,
for the retroviral late assembly (L) domain YPXnL motif.
The Alix V-domain is also a dimerization domain. Bro1
also has an N-terminal Bro1-like domain, which binds
Snf7, a component of the ESCRT-III complex, and a
C-terminal proline-rich region (PRR). The C-terminal
portion (V-domain and PRR) of S. cerevisiae Bro1
interacts with Doa4, a ubiquitin thiolesterase needed to
remove ubiquitin from MVB cargoes. It interacts with a
YPxL motif in the Doa4s catalytic domain to stimulate
its deubiquitination activity.
Length = 356
Score = 26.1 bits (58), Expect = 5.5
Identities = 13/46 (28%), Positives = 26/46 (56%), Gaps = 5/46 (10%)
Query: 58 EVDKEKEHCPQLQQV-SVEDILNAQRKEQEVKQERSRMLAKRLKER 102
++D + L+Q+ +E++L +K+ER R+L K LK++
Sbjct: 186 DLDDSQNEQTVLKQIKQLEELLEDLNL---IKEERQRVL-KDLKQK 227
>gnl|CDD|239631 cd03576, NTR_PCOLCE, NTR domain, PCOLCE subfamily; Procollagen
C-endopeptidase enhancers (PCOLCEs) are extracellular
matrix proteins that enhance the activity of
procollagen C-proteases, by binding to the procollagen
I C-peptide. They contain a C-terminal NTR domain,
which have been suggested to possess inhibitory
functions towards specific serine proteases but not
towards metzincins, which are inhibited by the related
TIMPs.
Length = 124
Score = 25.4 bits (56), Expect = 5.8
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 49 RGENVVLMGEVDKEK 63
RG N +LMG+VD+E
Sbjct: 81 RGLNYILMGQVDEEG 95
>gnl|CDD|236370 PRK09064, PRK09064, 5-aminolevulinate synthase; Validated.
Length = 407
Score = 25.6 bits (57), Expect = 6.9
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 73 SVEDILNAQRKEQEVKQERSRMLAKRLKERGLSFVP 108
S+ L +E+E QER+ L L G+ +P
Sbjct: 291 SIR-HLKESNEERERHQERAAKLKAALDAAGIPVMP 325
>gnl|CDD|234659 PRK00137, rplI, 50S ribosomal protein L9; Reviewed.
Length = 147
Score = 25.0 bits (56), Expect = 7.3
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 77 ILNAQRKEQEVKQERSRMLAKRLKER 102
L A+R E E K A+ L E+
Sbjct: 46 QLEARRAELEAKAAEELAEAEALAEK 71
>gnl|CDD|224995 COG2084, MmsB, 3-hydroxyisobutyrate dehydrogenase and related
beta-hydroxyacid dehydrogenases [Lipid metabolism].
Length = 286
Score = 25.6 bits (57), Expect = 7.6
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 90 ERSRMLAKRLKERGLSFV 107
E +R LA L +GL F+
Sbjct: 100 ETARELAAALAAKGLEFL 117
>gnl|CDD|193516 cd03896, M20_PAAh_like, M20 Peptidases, Poly(aspartic acid)
hydrolase-like proteins. Peptidase M20 family,
Poly(aspartic acid) hydrolase (PAA hydrolase)-like
subfamily. PAA hydrolase enzymes are involved in
alpha,beta-poly(D,L-aspartic acid) (tPAA)
biodegradation. PAA is being extensively studied as a
replacement for commercial polycarboxylate components
since it can be degraded by enzymes from isolated tPAA
degrading bacteria. Thus far, two types of PAA degrading
bacteria (Sphingomonas sp. KT-1 and Pedobacter sp. KP-2)
have been investigated in detail; the former can
completely degrade tPAA of low-molecular weights below
5000, while the latter can degrade high molecular weight
tPAA to release oligo(aspartic acid) (OAA) as a product,
suggesting two kinds of PAA degrading enzymes. It has
been shown that PAA hydrolase-1 from Sphingomonas sp.
KT-1 hydrolyzes beta,beta-aspartic acid units in tPAA to
produce OAA, and it is suggested that PAA hydrolase-2
hydrolyzes OAA to aspartic acid.
Length = 359
Score = 25.6 bits (57), Expect = 7.9
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 89 QERSRMLAKRLKERGLSFVP 108
R+ +A+RL+E GL V
Sbjct: 18 AARAEYVAERLRELGLEDVY 37
>gnl|CDD|184024 PRK13393, PRK13393, 5-aminolevulinate synthase; Provisional.
Length = 406
Score = 25.4 bits (56), Expect = 8.2
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 78 LNAQRKEQEVKQERSRMLAKRLKERGLSFVP 108
L A E+E Q+R L RL + G+ +P
Sbjct: 294 LKASSAERERHQDRVARLRARLDKAGIPHLP 324
>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 = 24.4 bits (54), Expect = 9.0
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 2/47 (4%)
Query: 12 GYLRSVDQFANLVLHKTIERIHVGNQYGDIPRGIFIIRGENVVLMGE 58
G + D++ NLVL E +H+ P G +++G+N+ L+
Sbjct: 35 GKIIGFDEYMNLVLDDAEE-VHLKTN-TRKPLGRILLKGDNITLIQN 79
>gnl|CDD|216234 pfam00998, RdRP_3, Viral RNA dependent RNA polymerase. This family
includes viral RNA dependent RNA polymerase enzymes from
hepatitis C virus and various plant viruses.
Length = 486
Score = 25.3 bits (56), Expect = 10.0
Identities = 13/47 (27%), Positives = 20/47 (42%), Gaps = 11/47 (23%)
Query: 70 QQVSVEDILNAQRKEQEV-------KQERSRMLAKRLKERGLSFVPD 109
Q VSVE + R E + +E +R+L +L G + D
Sbjct: 214 QHVSVEAL----RFEHSIYLAAFLGPEELARLLTWQLYNGGPMYASD 256
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
0.322 0.142 0.397
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: 6,073,770
Number of extensions: 542013
Number of successful extensions: 846
Number of sequences better than 10.0: 1
Number of HSP's gapped: 838
Number of HSP's successfully gapped: 72
Length of query: 116
Length of database: 10,937,602
Length adjustment: 79
Effective length of query: 37
Effective length of database: 7,433,636
Effective search space: 275044532
Effective search space used: 275044532
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)