RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17123
(105 letters)
>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 = 98.0 bits (245), Expect = 2e-28
Identities = 38/48 (79%), Positives = 43/48 (89%)
Query: 20 KESILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
KESILDLSK++DK IRVKF GGRE +GILKG+D LLNLVLD+T EYLR
Sbjct: 1 KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLR 48
>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 = 62.1 bits (152), Expect = 2e-14
Identities = 20/41 (48%), Positives = 30/41 (73%)
Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
+L K++DK + +K G R+ SG+L+GFDP +NLVLD+ E
Sbjct: 4 ELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEE 44
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 53.7 bits (130), Expect = 3e-11
Identities = 18/52 (34%), Positives = 29/52 (55%)
Query: 24 LDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQV 75
L K + K + V+ GRE G LKGFD +NLVL++ E ++ + ++
Sbjct: 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKL 52
>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 = 3e-10
Identities = 20/49 (40%), Positives = 27/49 (55%)
Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSV 73
L K L K + V+ GRE G LKGFD +NLVLD+ E ++ +
Sbjct: 2 FLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNK 50
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 45.8 bits (109), Expect = 5e-08
Identities = 20/40 (50%), Positives = 24/40 (60%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
L K L+K + VK GRE G L GFD +NLVLD+ E
Sbjct: 12 LKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEI 51
>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 = 45.6 bits (109), Expect = 5e-08
Identities = 21/39 (53%), Positives = 28/39 (71%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTE 64
L++ L+K + VK GG+E G+LKGFD LNLVL+N E
Sbjct: 6 LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEE 44
>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 = 44.5 bits (106), Expect = 1e-07
Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
L F+ K + V+ GR +G L FD +NLVLD+ E R
Sbjct: 1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGR 42
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 43.4 bits (103), Expect = 3e-07
Identities = 20/42 (47%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 24 LD-LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTE 64
LD L+ L+ + V+ GGRE G L+G+D +NLVLDN E
Sbjct: 6 LDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEE 47
>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 = 40.6 bits (96), Expect = 7e-06
Identities = 20/50 (40%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQV 75
L +L+K + V GR G LKGFD NL+L N E RV V
Sbjct: 4 LEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHE--RVYSSDEGV 51
>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 = 39.8 bits (94), Expect = 1e-05
Identities = 15/45 (33%), Positives = 20/45 (44%)
Query: 23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
L L K L + +RV GR G D N++L N EY +
Sbjct: 1 RLKLRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRK 45
>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 = 38.0 bits (89), Expect = 5e-05
Identities = 17/40 (42%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPL-LNLVLDNTT 63
+L+ LDK + V + G+ +G L GFDP LN+VL N
Sbjct: 4 ELNSLLDKEVIVTLSNGKTYTGQLVGFDPSSLNIVLTNAK 43
>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 = 37.6 bits (88), Expect = 8e-05
Identities = 16/40 (40%), Positives = 19/40 (47%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
L+ K + VK G E G L D +NL L NT EY
Sbjct: 6 LNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEY 45
>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 = 37.2 bits (87), Expect = 1e-04
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 24 LDLSKF-LDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
LDL + LD+ + VK G RE G L +D LN++L + E
Sbjct: 3 LDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEET 45
>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 = 36.8 bits (86), Expect = 1e-04
Identities = 13/32 (40%), Positives = 19/32 (59%)
Query: 34 IRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
I + +E G L GFD +N+VL++ TEY
Sbjct: 16 IWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEY 47
>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 = 35.9 bits (83), Expect = 3e-04
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 5/58 (8%)
Query: 28 KFLDKVIRVKFAG-GRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIVRR 84
+ IRV+ G + G L D +NL L +T E + +VRS ++V R
Sbjct: 7 SLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVG----EEKVRSLGTVVLR 60
>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 = 34.8 bits (81), Expect = 7e-04
Identities = 17/40 (42%), Positives = 23/40 (57%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
L K + K + VK G E G+L D +NLVL++T EY
Sbjct: 6 LKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEY 45
>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 = 32.5 bits (75), Expect = 0.007
Identities = 23/61 (37%), Positives = 31/61 (50%)
Query: 23 ILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVRSWCSIV 82
L + LDK I V GR+ GIL+ FD NLVL++T E + V Q + I+
Sbjct: 4 TASLEEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLFII 63
Query: 83 R 83
R
Sbjct: 64 R 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 = 31.0 bits (71), Expect = 0.022
Identities = 12/43 (27%), Positives = 24/43 (55%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRV 68
+ ++++ +RV GR+ G FD +NLVL + E+ ++
Sbjct: 5 MLQYINYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRKI 47
>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional.
Length = 89
Score = 31.2 bits (71), Expect = 0.028
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 46 GILKGFDPLLNLVLDNTTEY 65
G + GFD +N+VLD+ E
Sbjct: 43 GKILGFDEYMNMVLDDAEEV 62
>gnl|CDD|236627 PRK09824, PRK09824, PTS system beta-glucoside-specific transporter
subunits IIABC; Provisional.
Length = 627
Score = 30.5 bits (69), Expect = 0.13
Identities = 12/51 (23%), Positives = 24/51 (47%), Gaps = 4/51 (7%)
Query: 3 AVNTTTDAGAETKDRKRKESILDLSKFLDKV--IRVKFAGGRECSGILKGF 51
+V + + + +K ++L ++F+D + I G +GILKG
Sbjct: 78 SVAGLGEKAQQAPENDKKGNLL--NRFIDVISGIFTPLIGVMAATGILKGM 126
>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 = 27.9 bits (63), Expect = 0.35
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 46 GILKGFDPLLNLVLDNTTEY 65
G + GFD +NLVLD+ E
Sbjct: 35 GKIIGFDEYMNLVLDDAEEV 54
>gnl|CDD|227376 COG5043, MRS6, Vacuolar protein sorting-associated protein
[Intracellular trafficking and secretion].
Length = 2552
Score = 28.7 bits (64), Expect = 0.62
Identities = 15/87 (17%), Positives = 24/87 (27%), Gaps = 19/87 (21%)
Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSV--------QVRS 77
L + + KF R S + E+ + V +
Sbjct: 299 LDYLQVVMKQQKFLKYRPKSTPK-----------EKPLEWFKYIILVVLDSIHEKRYHWT 347
Query: 78 WCSIVRRQESRRNVHRRDHKEYEDSNL 104
W R E RR + K+Y + L
Sbjct: 348 WKYFKERCEDRRAYMKIIRKKYLNEQL 374
>gnl|CDD|188420 TIGR03905, TIGR03905_4_Cys, uncharacterized protein TIGR03905.
This model describes a family of conserved hypothetical
proteins of small size, typically ~85 residues, with
four invariant Cys residues. This small protein is
distantly homologous to a C-terminal domain found in
proteins identified by N-terminal homology as
ribonucleotide reductases. The rare and sporadic
distribution of this protein family falls mostly within
the subset of bacterial genomes containing the
uncharacterized radical SAM protein modeled by
TIGR03904 [Unknown function, General].
Length = 78
Score = 25.9 bits (57), Expect = 2.2
Identities = 12/25 (48%), Positives = 15/25 (60%), Gaps = 2/25 (8%)
Query: 31 DKVIRVKFAGGRECSGILKGFDPLL 55
DKV V+F+GG C G LK L+
Sbjct: 20 DKVKEVRFSGG--CDGNLKAISKLV 42
>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 = 25.6 bits (57), Expect = 2.7
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTT 63
+ K + V+ +G L D LN+ L N +
Sbjct: 9 LVGKEVTVELKNDLSITGTLHSVDQYLNIKLTNIS 43
>gnl|CDD|222077 pfam13365, Trypsin_2, Trypsin-like peptidase domain. This family
includes trypsin like peptidase domains.
Length = 138
Score = 25.6 bits (56), Expect = 4.6
Identities = 8/26 (30%), Positives = 10/26 (38%)
Query: 34 IRVKFAGGRECSGILKGFDPLLNLVL 59
I V G + DP L+L L
Sbjct: 27 IEVVLPDGGRVPAEVVAADPDLDLAL 52
>gnl|CDD|131901 TIGR02854, spore_II_GA, sigma-E processing peptidase SpoIIGA.
Members of this protein family are the stage II
sporulation protein SpoIIGA. This protein acts as an
activating protease for Sigma-E, one of several
specialized sigma factors of the sporulation process in
Bacillus subtilis and related endospore-forming bacteria
[Cellular processes, Sporulation and germination].
Length = 288
Score = 25.8 bits (57), Expect = 4.6
Identities = 13/60 (21%), Positives = 27/60 (45%), Gaps = 14/60 (23%)
Query: 20 KESILDLSKFLDKVIRVKFAG-GRECSGILKGFDPLLNLVLDNTTEYLRVTY--QSVQVR 76
+ ILD ++ ++ + F G G SG L G P + +++ Y + ++V+
Sbjct: 214 GKMILDPERWQSRIRLIPFRGVGGG-SGFLLGIKP----------DRVKIRYEGEWIEVK 262
>gnl|CDD|239209 cd02843, PAZ_dicer_like, PAZ domain, dicer_like subfamily. Dicer
is an RNAse involved in cleaving dsRNA in the RNA
interference pathway. It generates dsRNAs which are
approximately 20 bp long (siRNAs), which in turn target
hydrolysis of homologous RNAs. PAZ domains are named
after the proteins Piwi Argonaut and Zwille. PAZ is
found in two families of proteins that are essential
components of RNA-mediated gene-silencing pathways,
including RNA interference, the piwi and Dicer
families. PAZ functions as a nucleic-acid binding
domain, with a strong preference for single-stranded
nucleic acids (RNA or DNA) or RNA duplexes with
single-stranded 3' overhangs. It has been suggested
that the PAZ domain provides a unique mode for the
recognition of the two 3'-terminal nucleotides in
single-stranded nucleic acids and buries the 3' OH
group, and that it might recognize characteristic 3'
overhangs in siRNAs within RISC (RNA-induced silencing)
and other complexes.
Length = 122
Score = 25.5 bits (56), Expect = 5.1
Identities = 6/23 (26%), Positives = 9/23 (39%)
Query: 12 AETKDRKRKESILDLSKFLDKVI 34
T D R+ D + D V+
Sbjct: 24 RATPDEARQPFKFDAEDYQDAVV 46
>gnl|CDD|218442 pfam05116, S6PP, Sucrose-6F-phosphate phosphohydrolase. This
family consists of Sucrose-6F-phosphate phosphohydrolase
proteins found in plants and cyanobacteria.
Sucrose-6(F)-phosphate phosphohydrolase catalyzes the
final step in the pathway of sucrose biosynthesis.
Length = 247
Score = 25.3 bits (56), Expect = 6.8
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 19 RKESILDLSKFLDKVIRVKFAGGRECSGILKG 50
+ E + + R+ FA GR +GIL+G
Sbjct: 210 QPELLQWYLENARDNPRIYFASGRCAAGILEG 241
>gnl|CDD|212485 cd01739, LSm11_M, Like-Sm protein 11, middle domain. The
eukaryotic Sm and Sm-like (LSm) proteins associate with
RNA to form the core domain of the ribonucleoprotein
particles involved in a variety of RNA processing
events including pre-mRNA splicing, telomere
replication, and mRNA degradation. Members of this
family share a highly conserved Sm fold containing an
N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. LSm11 is an
SmD2-like subunit which binds U7 snRNA along with LSm10
and five other Sm subunits to form a 7-membered ring
structure. LSm11 and the U7 snRNP of which it is a part
are thought to play an important role in histone mRNA
3' processing.
Length = 63
Score = 24.1 bits (53), Expect = 7.7
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 4/33 (12%)
Query: 44 CSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVR 76
C G L FD NL L + E T+ + +
Sbjct: 25 CEGYLVAFDKHWNLALVDVDE----TWTRRKYK 53
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
0.319 0.133 0.382
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: 5,050,354
Number of extensions: 413358
Number of successful extensions: 339
Number of sequences better than 10.0: 1
Number of HSP's gapped: 339
Number of HSP's successfully gapped: 38
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
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)