RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10748
(98 letters)
>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 = 151 bits (385), Expect = 5e-50
Identities = 60/79 (75%), Positives = 71/79 (89%)
Query: 12 QKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKT 71
QKVMVQPINLIFR+LQN+SRVQIWLYE ++RIEG I+GFDEYMN+VL+ AEE ++K+ T
Sbjct: 1 QKVMVQPINLIFRYLQNKSRVQIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNT 60
Query: 72 RKALGTIMLKGDNITLIQN 90
RK LG I+LKGDNITLIQN
Sbjct: 61 RKPLGRILLKGDNITLIQN 79
>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional.
Length = 89
Score = 127 bits (322), Expect = 3e-40
Identities = 55/79 (69%), Positives = 64/79 (81%)
Query: 10 KVQKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKS 69
K+QK+M QPIN IFRF ++RVQIWLY++ NLRIEG ILGFDEYMN+VL+ AEE K
Sbjct: 7 KLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKK 66
Query: 70 KTRKALGTIMLKGDNITLI 88
TRK LG I+LKGDNITLI
Sbjct: 67 NTRKDLGRILLKGDNITLI 85
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 64.1 bits (157), Expect = 2e-15
Identities = 19/66 (28%), Positives = 35/66 (53%)
Query: 24 RFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGD 83
+FL+ ++ + G + GFD++MN+VLE EE + ++ LG + ++G+
Sbjct: 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGN 60
Query: 84 NITLIQ 89
NI I
Sbjct: 61 NIVYII 66
>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 = 61.0 bits (149), Expect = 3e-14
Identities = 22/65 (33%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 24 RFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGD 83
+FLQ ++ + + G + GFD++MN+VL+ EE K K LG ++++G+
Sbjct: 1 KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNK-LGLVLIRGN 59
Query: 84 NITLI 88
NI LI
Sbjct: 60 NIVLI 64
>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 = 50.7 bits (122), Expect = 3e-10
Identities = 17/57 (29%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 33 QIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQ 89
+ + + G ++ FD+YMN+VL+ E K R LG ++++G NI I+
Sbjct: 8 TVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRV-LGLVLIRGSNIVSIR 63
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 49.2 bits (118), Expect = 2e-09
Identities = 24/80 (30%), Positives = 42/80 (52%), Gaps = 7/80 (8%)
Query: 12 QKVMVQPINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEY---NIK 68
+ P++ + + L RV + L G ++GFD+YMN+VL+ EE + +
Sbjct: 2 SMLGPLPLSFLKKLLN--KRVLVKLKNGR--EYRGTLVGFDQYMNLVLDDVEEIISHDGE 57
Query: 69 SKTRKALGTIMLKGDNITLI 88
R+ G ++++GDNI LI
Sbjct: 58 KNVRRLGGEVLIRGDNIVLI 77
>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 = 48.0 bits (115), Expect = 6e-09
Identities = 23/57 (40%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 34 IWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKA--LGTIMLKGDNITLI 88
IW+ + G +LGFD+Y+N+VLE EY I + RK L I+L G+NI ++
Sbjct: 16 IWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNIAML 72
>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 = 46.4 bits (111), Expect = 2e-08
Identities = 20/48 (41%), Positives = 32/48 (66%), Gaps = 1/48 (2%)
Query: 41 NLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLI 88
+ G + GFD+++N+VLE+AEE RK LGT++++GDN+ I
Sbjct: 21 GKEVRGVLKGFDQHLNLVLENAEEIIEGESVRK-LGTVLVRGDNVVFI 67
>gnl|CDD|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein. The archaeal
Sm-like (LSm): The Sm proteins are conserved in all
three domains of life and are always associated with
U-rich RNA sequences. They function to mediate RNA-RNA
interactions and RNA biogenesis. All Sm proteins
contain a common sequence motif in two segments, Sm1
and Sm2, separated by a short variable linker.
Eukaryotic Sm proteins form part of specific small
nuclear ribonucleoproteins (snRNPs) that are involved
in the processing of pre-mRNAs to mature mRNAs, and are
a major component of the eukaryotic spliceosome. Most
snRNPs consist of seven Sm proteins (B/B', D1, D2, D3,
E, F and G) arranged in a ring on a uridine-rich
sequence (Sm site), plus a small nuclear RNA (snRNA)
(either U1, U2, U5 or U4/6). Since archaebacteria do
not have any splicing apparatus, their Sm proteins may
play a more general role. Archaeal LSm proteins are
likely to represent the ancestral Sm domain. Members of
this family share a highly conserved Sm fold containing
an N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm-like proteins
exist in archaea as well as prokaryotes that form
heptameric and hexameric ring structures similar to
those found in eukaryotes.
Length = 69
Score = 44.8 bits (106), Expect = 1e-07
Identities = 25/72 (34%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 18 PINLIFRFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGT 77
P + + +R RV++ EN +++G ++ D+YMN+ L E + K R +LGT
Sbjct: 1 PNKKVKSLVGSRIRVEMKGDEN---QLQGRLVAVDDYMNLHLTDTMECVGEEKVR-SLGT 56
Query: 78 IMLKGDNITLIQ 89
++L+G+NI LIQ
Sbjct: 57 VVLRGNNILLIQ 68
>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 = 39.8 bits (94), Expect = 8e-06
Identities = 19/52 (36%), Positives = 29/52 (55%), Gaps = 10/52 (19%)
Query: 44 IEGHILGFDEYMNIVLESAEEY-NIKSKTRKA---------LGTIMLKGDNI 85
G L FD++MN+VL EE+ IK K +K LG ++L+G+N+
Sbjct: 23 FVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKKGEEREEKRVLGLVLLRGENV 74
>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 = 39.0 bits (92), Expect = 2e-05
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 52 DEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLI 88
D YMN+VLE EEY K G ++G+N+ I
Sbjct: 32 DGYMNLVLEDTEEYVDGQLVAK-YGDAFIRGNNVLYI 67
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 38.1 bits (89), Expect = 4e-05
Identities = 15/43 (34%), Positives = 29/43 (67%), Gaps = 1/43 (2%)
Query: 46 GHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLI 88
G + G+D +MN+VL++AEE + + LG ++++GDN+ +
Sbjct: 29 GELQGYDIHMNLVLDNAEEI-QDGEVVRKLGKVVIRGDNVVYV 70
>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 = 37.5 bits (88), Expect = 5e-05
Identities = 18/68 (26%), Positives = 41/68 (60%), Gaps = 5/68 (7%)
Query: 24 RFLQNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGD 83
+++ R +++ N N ++ G + GFD +MN+VL+ A E + + +G ++++G+
Sbjct: 7 KYMDKRLSLKL----NGNRKVSGVLRGFDPFMNLVLDDAVEE-VGDGEKTPIGMVVIRGN 61
Query: 84 NITLIQNL 91
+I +I+ L
Sbjct: 62 SIIMIEAL 69
>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 = 38.0 bits (89), Expect = 5e-05
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 9/51 (17%)
Query: 46 GHILGFDEYMNIVLESAEEY--------NIKSKTRKALGTIMLKGDNITLI 88
G + G+D+ +N+VL+ EY + +TR LG ++ +G ++ LI
Sbjct: 27 GILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDETRS-LGLVVCRGTSVVLI 76
>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 = 37.2 bits (87), Expect = 7e-05
Identities = 15/45 (33%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 45 EGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQ 89
+G ++ D YMN+ L + EEY I K LG ++++ +N+ I+
Sbjct: 25 KGTLVSVDSYMNLQLANTEEY-IDGKFTGNLGEVLIRCNNVLYIR 68
>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 = 36.5 bits (85), Expect = 1e-04
Identities = 12/45 (26%), Positives = 31/45 (68%), Gaps = 2/45 (4%)
Query: 22 IFRFLQNRSRVQIWLYENVNLR--IEGHILGFDEYMNIVLESAEE 64
+ R++++R+RV++++ + +R EG+++ FD++ N+ L +E
Sbjct: 1 LHRWMRDRTRVKVYIRKAKGIRGSCEGYLVAFDKHWNLALVDVDE 45
>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 = 36.7 bits (86), Expect = 2e-04
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 44 IEGHILGFDEYMNIVLESAEEYNIKSK---TRKALGTIMLKGDNITLI 88
I G + GFD+ N++L + E S LG +L+GDN+ +I
Sbjct: 22 IVGTLKGFDQTTNLILSNCHERVYSSDEGVEEVPLGLYLLRGDNVAVI 69
>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 = 32.2 bits (74), Expect = 0.007
Identities = 16/70 (22%), Positives = 33/70 (47%), Gaps = 14/70 (20%)
Query: 31 RVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEY------------NIKSKTRKALGTI 78
RV + L + LR G + +D+++N++L EE I T++ + +
Sbjct: 13 RVYVKLRGDRELR--GRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTKRNIPML 70
Query: 79 MLKGDNITLI 88
++GD + L+
Sbjct: 71 FVRGDGVILV 80
>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 = 31.8 bits (73), Expect = 0.010
Identities = 20/70 (28%), Positives = 34/70 (48%), Gaps = 10/70 (14%)
Query: 25 FLQNRSRVQIWLYENVNLRI-EGHILGFDEYMNIVLESAEEYNIKS----KTRKALGTIM 79
L RV + + R+ G + D+ NI+L +AEEY S + ++LG +M
Sbjct: 7 LLGRTLRVTL-----TDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLGAEEPRSLGLVM 61
Query: 80 LKGDNITLIQ 89
+ G +I I+
Sbjct: 62 VPGKHIVSIE 71
>gnl|CDD|178145 PLN02530, PLN02530, histidine-tRNA ligase.
Length = 487
Score = 32.4 bits (74), Expect = 0.019
Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 14/56 (25%)
Query: 31 RVQIWLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNIT 86
R++ WL+++ R + GF+E VLES E Y RKA G+ IT
Sbjct: 85 RLRNWLFDH--FREVSRLFGFEEVDAPVLESEELY-----IRKA-------GEEIT 126
>gnl|CDD|216596 pfam01600, Corona_S1, Coronavirus S1 glycoprotein. The coronavirus
spike glycoprotein forms the characteristic 'corona'
after which the group is named. The Spike glycoprotein
is translated as a large polypeptide that is
subsequently cleaved to S1 and S2 pfam01601.
Length = 512
Score = 30.5 bits (69), Expect = 0.10
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 43 RIEGHILGFDEYMNIVLESAEEYNI 67
+ G +Y NI L+ +YNI
Sbjct: 397 GTPPPVEGQHDYSNITLDKCTDYNI 421
>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 = 28.3 bits (64), Expect = 0.21
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 51 FDEYMNIVLESAEEYNIKSK--TRKALGTIMLKGDNITLI 88
FD++ N+VLE E I G +++G+N+ L+
Sbjct: 32 FDQFANLVLEDTVERIIVGNQYGDIPRGLFIIRGENVVLL 71
>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 = 28.3 bits (64), Expect = 0.26
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 5/54 (9%)
Query: 40 VNLR----IEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGDNITLIQ 89
V LR + G I D +MNI L A + + K ++G NI +
Sbjct: 24 VELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQHH-FDEFFVQGRNIRYVH 76
>gnl|CDD|212463 cd01716, Hfq, bacterial Hfq-like. Hfq, an abundant, ubiquitous
RNA-binding protein, functions as a pleiotropic
regulator of RNA metabolism in prokaryotes, required
for transcription of some transcripts and degradation
of others. Hfq binds small RNA molecules called
riboregulators that modulate the stability or
translation efficiency of RNA transcripts. Hfq binds
preferentially to unstructured A/U-rich RNA sequences
and is similar to the eukaryotic Sm proteins in both
sequence and structure. Hfq forms a homo-hexameric ring
similar to the heptameric ring of the Sm proteins.
Length = 60
Score = 25.6 bits (57), Expect = 1.6
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 7/46 (15%)
Query: 20 NLIFRFL----QNRSRVQIWLYENVNLRIEGHILGFDEYMNIVLES 61
NL +FL + + V I+L V R++G I FD + ++LES
Sbjct: 1 NLQDQFLNTLRKEKKPVTIYLVNGV--RLKGKIKSFDNFT-VLLES 43
>gnl|CDD|221927 pfam13116, DUF3971, Protein of unknown function. Some members of
this family are related to the AsmA family proteins.
Length = 289
Score = 26.8 bits (60), Expect = 1.7
Identities = 18/77 (23%), Positives = 30/77 (38%), Gaps = 9/77 (11%)
Query: 28 NRSRVQI--WLYENVNLRIEGHILGFDEYMNIVLESAEEYNIKSKTRKALGTIMLKGD-- 83
+ S V I E L I+G G E + L++ +K +AL + + G
Sbjct: 105 DGSTVVIPDLFGEKSVLEIDGDASGPGEAILDYLKA---SPLKDSVGEALPVLQVSGKVD 161
Query: 84 -NITL-IQNLNPDEVKV 98
++ L I + VK
Sbjct: 162 GDLNLDIPLDGEEVVKA 178
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 26.0 bits (58), Expect = 3.4
Identities = 9/35 (25%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 39 NVNLRI-EGHILGFDEYMNIVLESAEEYNIKSKTR 72
N+ L + +G + +Y+ + + AEEY + T+
Sbjct: 1062 NLILTVHKGSVE---KYLEVSKKLAEEYGVSDYTK 1093
>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 = 25.4 bits (56), Expect = 3.6
Identities = 14/60 (23%), Positives = 28/60 (46%), Gaps = 12/60 (20%)
Query: 41 NLRIEGHILGFDEYMNIVLESA----EEYNIKSKTRKA--------LGTIMLKGDNITLI 88
N ++ + FD + N+VLE+ E K +K+ + + L+GD++ L+
Sbjct: 26 NKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKGKKSKPVNKDRFISKMFLRGDSVILV 85
>gnl|CDD|185219 PRK15319, PRK15319, AIDA autotransporter-like protein ShdA;
Provisional.
Length = 2039
Score = 26.2 bits (57), Expect = 4.0
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 59 LESAEEYNIKSKTRKALGTIMLKGDN 84
L+ ++ KS T++ GT++L GDN
Sbjct: 1224 LDPGSRWDGKSLTKEGAGTLILSGDN 1249
>gnl|CDD|116012 pfam07389, DUF1500, Protein of unknown function (DUF1500). This
family consists of several Orthopoxvirus specific
proteins of around 100 residues in length. The function
of this family is unknown.
Length = 100
Score = 25.3 bits (55), Expect = 4.2
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 13 KVMVQPINLIFRFLQNRSRVQIWLYENVN 41
+ V P + I R + N S V+ W+ + +N
Sbjct: 45 RCAVIPFDDIVRIMPNESCVKQWVIDTLN 73
>gnl|CDD|224844 COG1933, COG1933, Archaeal DNA polymerase II, large subunit [DNA
replication, recombination, and repair].
Length = 253
Score = 25.9 bits (57), Expect = 4.4
Identities = 6/22 (27%), Positives = 11/22 (50%)
Query: 54 YMNIVLESAEEYNIKSKTRKAL 75
Y+ EY +K+ TR+ +
Sbjct: 205 YLGTAKMLVTEYKVKNYTRQRI 226
>gnl|CDD|225380 COG2824, PhnA, Uncharacterized Zn-ribbon-containing protein
involved in phosphonate metabolism [Inorganic ion
transport and metabolism].
Length = 112
Score = 25.1 bits (55), Expect = 6.0
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 60 ESAEEYNIKSKTRKALGTIMLKGDNITLIQNL 91
E+AEE + + + G ++ GD++TLI++L
Sbjct: 34 EAAEEADEALIVKDSNGNLLADGDSVTLIKDL 65
>gnl|CDD|202780 pfam03831, PhnA, PhnA protein.
Length = 55
Score = 24.0 bits (53), Expect = 6.8
Identities = 7/22 (31%), Positives = 15/22 (68%)
Query: 71 TRKALGTIMLKGDNITLIQNLN 92
+ + G ++ GD++TLI++L
Sbjct: 2 VKDSNGNVLADGDSVTLIKDLK 23
>gnl|CDD|239231 cd02903, Macro_BAL_like, Macro domain, BAL_like family. The macro
domain is a high-affinity ADP-ribose binding module
found in a variety of proteins as a stand-alone domain
or in combination with other domains like in histone
macroH2A and some PARPs (poly ADP-ribose polymerases).
Some macro domains recognize poly ADP-ribose as a
ligand. Previously identified as displaying an Appr-1"-p
(ADP-ribose-1"-monophosphate) processing activity, the
macro domain may play roles in distinct ADP-ribose
pathways, such as the ADP-ribosylation of proteins, an
important post-translational modification which occurs
in DNA repair, transcription, chromatin biology, and
long-term memory formation, among other processes.
Members of this family show similarity to BAL
(B-aggressive lymphoma) proteins, which contain one to
three macro domains. Most BAL family macro domains
belong to this family except for the most N-terminal
domain in multiple-domain containing proteins. Most BAL
proteins also contain a C-terminal PARP active site and
are also named as PARPs. Human BAL1 (or PARP-9) was
originally identified as a risk-related gene in diffuse
large B-cell lymphoma that promotes malignant B-cell
migration. Some BAL family proteins exhibit PARP
activity. Poly (ADP-ribosyl)ation is an immediate
DNA-damage-dependent post-translational modification of
histones and other nuclear proteins. BAL proteins may
also function as transcription repressors.
Length = 137
Score = 24.5 bits (54), Expect = 9.3
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 58 VLESAEEYNIKSKTRKALGT 77
LE EE + S + A+GT
Sbjct: 97 CLEKCEELSYTSISFPAIGT 116
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.321 0.139 0.391
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: 4,919,973
Number of extensions: 410147
Number of successful extensions: 399
Number of sequences better than 10.0: 1
Number of HSP's gapped: 387
Number of HSP's successfully gapped: 46
Length of query: 98
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 34
Effective length of database: 8,098,946
Effective search space: 275364164
Effective search space used: 275364164
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)