RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy800
(204 letters)
>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 = 150 bits (380), Expect = 2e-47
Identities = 59/72 (81%), Positives = 66/72 (91%)
Query: 115 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLD 174
+LPLEL+DKCIGS+I IIMK+DKE VGTL GFDD+VNM+LEDVTEYE TPEGR+ITKLD
Sbjct: 1 QILPLELIDKCIGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLD 60
Query: 175 QILLNGNNITML 186
QILLNGNNI ML
Sbjct: 61 QILLNGNNIAML 72
Score = 96.5 bits (241), Expect = 2e-26
Identities = 35/45 (77%), Positives = 41/45 (91%)
Query: 12 TLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
+LPLEL+DKCIGS+I IIMK+DKE VGTL GFDD+VNM+LEDVT
Sbjct: 1 QILPLELIDKCIGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVT 45
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear ribonucleoprotein
particles (snRNPs) involved in pre-mRNA splicing.
Length = 67
Score = 72.5 bits (179), Expect = 2e-17
Identities = 28/68 (41%), Positives = 41/68 (60%), Gaps = 2/68 (2%)
Query: 121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNG 180
+ K IG R+ + +KN +E GTL GFD F+N++LEDV E +G + KL + + G
Sbjct: 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEET--VKDGEKKRKLGLVFIRG 59
Query: 181 NNITMLGL 188
NNI + L
Sbjct: 60 NNIVYIIL 67
Score = 51.0 bits (123), Expect = 3e-09
Identities = 19/39 (48%), Positives = 27/39 (69%)
Query: 18 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
+ K IG R+ + +KN +E GTL GFD F+N++LEDV
Sbjct: 2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVE 40
>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 = 70.7 bits (174), Expect = 1e-16
Identities = 25/69 (36%), Positives = 42/69 (60%), Gaps = 3/69 (4%)
Query: 120 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLN 179
+ + K +G R+ + +KN +E+ GTL GFD F+N++L+DV E + KL +L+
Sbjct: 1 KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVN---KLGLVLIR 57
Query: 180 GNNITMLGL 188
GNNI ++
Sbjct: 58 GNNIVLISP 66
Score = 51.8 bits (125), Expect = 2e-09
Identities = 17/40 (42%), Positives = 29/40 (72%)
Query: 17 ELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
+ + K +G R+ + +KN +E+ GTL GFD F+N++L+DV
Sbjct: 1 KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVE 40
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 65.0 bits (159), Expect = 2e-14
Identities = 25/78 (32%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 112 NPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRIT 171
+ LPL + K + R+ + +KN +E GTL GFD ++N++L+DV E S + +
Sbjct: 2 SMLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVR 61
Query: 172 KL-DQILLNGNNITMLGL 188
+L ++L+ G+NI ++
Sbjct: 62 RLGGEVLIRGDNIVLISP 79
Score = 51.1 bits (123), Expect = 4e-09
Identities = 18/48 (37%), Positives = 30/48 (62%)
Query: 9 NPSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
+ LPL + K + R+ + +KN +E GTL GFD ++N++L+DV
Sbjct: 2 SMLGPLPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVE 49
>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 = 63.4 bits (155), Expect = 7e-14
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 3/65 (4%)
Query: 122 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGN 181
+ IG + + +K+ + + GTL FD ++N++L+DV E T ++ L +L+ G+
Sbjct: 1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVE---TGRDGKVRVLGLVLIRGS 57
Query: 182 NITML 186
NI +
Sbjct: 58 NIVSI 62
Score = 49.2 bits (118), Expect = 1e-08
Identities = 12/43 (27%), Positives = 25/43 (58%)
Query: 19 VDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS 61
+ IG + + +K+ + + GTL FD ++N++L+DV +
Sbjct: 1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRD 43
>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 = 50.7 bits (122), Expect = 5e-09
Identities = 21/68 (30%), Positives = 40/68 (58%), Gaps = 3/68 (4%)
Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
PL+++++ + + + +K KE+ G L GFD +N++LE+ E EG + KL +L
Sbjct: 2 PLDVLNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEE---IIEGESVRKLGTVL 58
Query: 178 LNGNNITM 185
+ G+N+
Sbjct: 59 VRGDNVVF 66
Score = 40.3 bits (95), Expect = 3e-05
Identities = 13/40 (32%), Positives = 27/40 (67%)
Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLED 54
PL+++++ + + + +K KE+ G L GFD +N++LE+
Sbjct: 2 PLDVLNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLEN 41
>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 = 49.0 bits (117), Expect = 2e-08
Identities = 24/67 (35%), Positives = 35/67 (52%), Gaps = 4/67 (5%)
Query: 118 PLELVDKCIGSRIHIIMKND-KEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQI 176
P + V +GSRI + MK D ++ G L DD++N+ L D E + R L +
Sbjct: 1 PNKKVKSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVR---SLGTV 57
Query: 177 LLNGNNI 183
+L GNNI
Sbjct: 58 VLRGNNI 64
Score = 38.6 bits (90), Expect = 1e-04
Identities = 17/45 (37%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 15 PLELVDKCIGSRIHIIMKND-KEIVGTLNGFDDFVNMLLEDVTDC 58
P + V +GSRI + MK D ++ G L DD++N+ L D +C
Sbjct: 1 PNKKVKSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMEC 45
>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 = 49.1 bits (118), Expect = 2e-08
Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 2/58 (3%)
Query: 129 RIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITML 186
+I + + D I G + GFD+++N++L+D E R+ L +ILL G+NIT++
Sbjct: 22 QIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNTRK--PLGRILLKGDNITLI 77
Score = 28.3 bits (64), Expect = 0.75
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 26 RIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCH 59
+I + + D I G + GFD+++N++L+D + H
Sbjct: 22 QIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVH 55
>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 = 48.8 bits (117), Expect = 3e-08
Identities = 22/69 (31%), Positives = 38/69 (55%)
Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
PL+L+ + R+++ ++ D+E+ G L+ +D +NM+L DV E +T E T +
Sbjct: 2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYK 61
Query: 178 LNGNNITML 186
NI ML
Sbjct: 62 TTKRNIPML 70
Score = 43.4 bits (103), Expect = 3e-06
Identities = 14/41 (34%), Positives = 28/41 (68%)
Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV 55
PL+L+ + R+++ ++ D+E+ G L+ +D +NM+L DV
Sbjct: 2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDV 42
>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional.
Length = 89
Score = 44.7 bits (106), Expect = 1e-06
Identities = 21/62 (33%), Positives = 37/62 (59%), Gaps = 4/62 (6%)
Query: 127 GSRIHIIM--KNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNIT 184
+R+ I + + I G + GFD+++NM+L+D E + R+ L +ILL G+NIT
Sbjct: 26 KTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRK--DLGRILLKGDNIT 83
Query: 185 ML 186
++
Sbjct: 84 LI 85
Score = 29.7 bits (67), Expect = 0.26
Identities = 11/38 (28%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 24 GSRIHIIM--KNDKEIVGTLNGFDDFVNMLLEDVTDCH 59
+R+ I + + I G + GFD+++NM+L+D + +
Sbjct: 26 KTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVY 63
>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 = 44.0 bits (105), Expect = 1e-06
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
P + + K IG + + +KN E G L D ++N++LED EY +G+ + K
Sbjct: 2 PSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEY---VDGQLVAKYGDAF 58
Query: 178 LNGNNI 183
+ GNN+
Sbjct: 59 IRGNNV 64
Score = 30.2 bits (69), Expect = 0.14
Identities = 16/49 (32%), Positives = 26/49 (53%)
Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHL 63
P + + K IG + + +KN E G L D ++N++LED + D L
Sbjct: 2 PSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQL 50
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 42.7 bits (101), Expect = 5e-06
Identities = 17/66 (25%), Positives = 41/66 (62%), Gaps = 3/66 (4%)
Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
PL++++ + S + + +K +E G L G+D +N++L++ E + +G + KL +++
Sbjct: 5 PLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQ---DGEVVRKLGKVV 61
Query: 178 LNGNNI 183
+ G+N+
Sbjct: 62 IRGDNV 67
Score = 32.3 bits (74), Expect = 0.025
Identities = 13/58 (22%), Positives = 32/58 (55%)
Query: 15 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDSHLLSYFASDLI 72
PL++++ + S + + +K +E G L G+D +N++L++ + D ++ +I
Sbjct: 5 PLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVI 62
>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 = 4e-05
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 5/73 (6%)
Query: 117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYE-STPEGRRITKLDQ 175
L + ++K R+ +I + + IVGTL GFD N++L + E S+ EG L
Sbjct: 3 LLEDYLNK----RVVVITTDGRVIVGTLKGFDQTTNLILSNCHERVYSSDEGVEEVPLGL 58
Query: 176 ILLNGNNITMLGL 188
LL G+N+ ++G
Sbjct: 59 YLLRGDNVAVIGE 71
Score = 32.9 bits (76), Expect = 0.019
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 4/44 (9%)
Query: 14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTD 57
L + ++K R+ +I + + IVGTL GFD N++L + +
Sbjct: 3 LLEDYLNK----RVVVITTDGRVIVGTLKGFDQTTNLILSNCHE 42
>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 = 2e-04
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 3/48 (6%)
Query: 139 EIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITML 186
++ G L GFD F+N++L+D E E T + +++ GN+I M+
Sbjct: 22 KVSGVLRGFDPFMNLVLDDAVEEVGDGEK---TPIGMVVIRGNSIIMI 66
Score = 30.6 bits (70), Expect = 0.11
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 36 EIVGTLNGFDDFVNMLLEDVTD 57
++ G L GFD F+N++L+D +
Sbjct: 22 KVSGVLRGFDPFMNLVLDDAVE 43
>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 = 37.5 bits (88), Expect = 3e-04
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 14/72 (19%)
Query: 124 KCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTE-------YESTPEGRRITKLDQI 176
+ + +I +++++ ++++G L FD F N++LED E Y P G
Sbjct: 9 EELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRG-------LF 61
Query: 177 LLNGNNITMLGL 188
++ G N+ +LG
Sbjct: 62 IIRGENVVLLGE 73
Score = 31.3 bits (72), Expect = 0.049
Identities = 10/37 (27%), Positives = 25/37 (67%)
Query: 21 KCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTD 57
+ + +I +++++ ++++G L FD F N++LED +
Sbjct: 9 EELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVE 45
>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 = 4e-04
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 126 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNI 183
G + + +K E GTL D ++N+ L + EY +G+ L ++L+ NN+
Sbjct: 10 TGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI---DGKFTGNLGEVLIRCNNV 64
Score = 25.6 bits (57), Expect = 5.6
Identities = 9/32 (28%), Positives = 16/32 (50%)
Query: 23 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLED 54
G + + +K E GTL D ++N+ L +
Sbjct: 10 TGKPVIVKLKWGMEYKGTLVSVDSYMNLQLAN 41
>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 = 36.8 bits (86), Expect = 8e-04
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 119 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPE 166
L+L K + +I + + +E+ G L G+D +N++L+D EY PE
Sbjct: 5 LDL-SKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPE 51
Score = 31.4 bits (72), Expect = 0.064
Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 5/54 (9%)
Query: 16 LELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT----DCHDSHLLS 65
L+L K + +I + + +E+ G L G+D +N++L+D D D + L+
Sbjct: 5 LDL-SKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLT 57
>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 = 36.4 bits (85), Expect = 0.001
Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 3/63 (4%)
Query: 121 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNG 180
L+ G + ++N+ + G ++ D F+N+ L D T G++ D+ + G
Sbjct: 13 LLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFT--DRRGKQ-HHFDEFFVQG 69
Query: 181 NNI 183
NI
Sbjct: 70 RNI 72
Score = 30.2 bits (69), Expect = 0.17
Identities = 10/39 (25%), Positives = 20/39 (51%)
Query: 18 LVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
L+ G + ++N+ + G ++ D F+N+ L D T
Sbjct: 13 LLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDAT 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 = 35.2 bits (82), Expect = 0.002
Identities = 13/63 (20%), Positives = 24/63 (38%), Gaps = 11/63 (17%)
Query: 126 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNITM 185
+G + + + + + +VGT D N++L + EY + L
Sbjct: 8 LGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSD-----------LGAEEPRS 56
Query: 186 LGL 188
LGL
Sbjct: 57 LGL 59
Score = 28.7 bits (65), Expect = 0.49
Identities = 7/34 (20%), Positives = 17/34 (50%)
Query: 23 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
+G + + + + + +VGT D N++L +
Sbjct: 8 LGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAE 41
>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 = 34.1 bits (79), Expect = 0.006
Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 117 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQI 176
LPL L+ G + + +KN + G L D+++N+ L++V ++ +G R K+ +
Sbjct: 1 LPLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVI--CTSKDGDRFWKMPEC 58
Query: 177 LLNGNNI 183
+ GN I
Sbjct: 59 YIRGNTI 65
Score = 26.0 bits (58), Expect = 4.9
Identities = 13/43 (30%), Positives = 24/43 (55%)
Query: 14 LPLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 56
LPL L+ G + + +KN + G L D+++N+ L++V
Sbjct: 1 LPLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVI 43
>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 = 33.6 bits (78), Expect = 0.008
Identities = 18/69 (26%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 118 PLELVDKCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQIL 177
P++L+ + G + + +K + G L +D +N L+DVT + +G +++KL+Q+
Sbjct: 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVT--VTARDG-KVSKLEQVY 57
Query: 178 LNGNNITML 186
+ G+ I +
Sbjct: 58 IRGSQIRFI 66
>gnl|CDD|212472 cd01725, LSm2, Like-Sm protein 2. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. Members of
this family share a highly conserved Sm fold containing
an N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet.
Length = 89
Score = 34.1 bits (79), Expect = 0.009
Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 5/47 (10%)
Query: 23 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTDCHDS----HLLS 65
+G + + +KND I GTL+ D ++N+ L +++ +D HLLS
Sbjct: 10 VGKEVTVELKNDLSITGTLHSVDQYLNIKLTNIS-VNDPEKYPHLLS 55
Score = 34.1 bits (79), Expect = 0.009
Identities = 11/34 (32%), Positives = 22/34 (64%)
Query: 126 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVT 159
+G + + +KND I GTL+ D ++N+ L +++
Sbjct: 10 VGKEVTVELKNDLSITGTLHSVDQYLNIKLTNIS 43
>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 = 32.3 bits (74), Expect = 0.037
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 15/71 (21%)
Query: 118 PLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV----TEYESTPEG---- 167
PL L+ + + +++ I +N+K+++ + FD NM+LE+V TE T +G
Sbjct: 5 PLSLLTQSVKNNTQVLINCRNNKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKGKKSK 64
Query: 168 -----RRITKL 173
R I+K+
Sbjct: 65 PVNKDRFISKM 75
Score = 30.4 bits (69), Expect = 0.16
Identities = 13/43 (30%), Positives = 27/43 (62%), Gaps = 2/43 (4%)
Query: 15 PLELVDKCI--GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDV 55
PL L+ + + +++ I +N+K+++ + FD NM+LE+V
Sbjct: 5 PLSLLTQSVKNNTQVLINCRNNKKLLARVKAFDRHCNMVLENV 47
>gnl|CDD|151890 pfam11451, DUF3202, Protein of unknown function (DUF3202). This
archaeal family of proteins has no known function.
Length = 67
Score = 31.0 bits (70), Expect = 0.059
Identities = 22/70 (31%), Positives = 34/70 (48%), Gaps = 9/70 (12%)
Query: 121 LVDKCI----GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQI 176
L+DK + G ++ + + D G L FD+ V +LL+DVT+ I +D I
Sbjct: 3 LLDKTLEEWKGHKVAVGIGGDHSFSGILEDFDEEV-ILLKDVTDVAGNKAKELIIGIDDI 61
Query: 177 LLNGNNITML 186
N IT+L
Sbjct: 62 ----NWITLL 67
Score = 26.8 bits (59), Expect = 2.0
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 5/44 (11%)
Query: 18 LVDKCI----GSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTD 57
L+DK + G ++ + + D G L FD+ V +LL+DVTD
Sbjct: 3 LLDKTLEEWKGHKVAVGIGGDHSFSGILEDFDEEV-ILLKDVTD 45
>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 = 31.4 bits (72), Expect = 0.060
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 8/66 (12%)
Query: 126 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEY------ESTPEGRRITK--LDQIL 177
I R+ + +++ ++ VGT FD +N++L D E+ + R K L +L
Sbjct: 9 INYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKKGEEREEKRVLGLVL 68
Query: 178 LNGNNI 183
L G N+
Sbjct: 69 LRGENV 74
Score = 28.7 bits (65), Expect = 0.53
Identities = 10/32 (31%), Positives = 20/32 (62%)
Query: 23 IGSRIHIIMKNDKEIVGTLNGFDDFVNMLLED 54
I R+ + +++ ++ VGT FD +N++L D
Sbjct: 9 INYRMRVTLQDGRQFVGTFLAFDKHMNLVLSD 40
>gnl|CDD|214711 smart00537, DCX, Domain in the Doublecortin (DCX) gene product.
Tandemly-repeated domain in doublin, the Doublecortin
gene product. Proposed to bind tubulin. Doublecortin
(DCX) is mutated in human X-linked neuronal migration
defects.
Length = 89
Score = 29.9 bits (68), Expect = 0.25
Identities = 11/39 (28%), Positives = 20/39 (51%), Gaps = 11/39 (28%)
Query: 154 LLEDVTEYES-----------TPEGRRITKLDQILLNGN 181
LL+D+TE T +G+++T LD++ G+
Sbjct: 36 LLQDLTEVVKLDLPHGVRKLYTLDGKKVTSLDELEDGGS 74
>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 = 29.9 bits (68), Expect = 0.30
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 124 KCIGSRIHIIMKNDKEIVGTLNGFDDFVNMLLEDVTEYESTPEGRRITKLDQILLNGNNI 183
K + I +KN + GT+ G D +N L++V + T +G+ LD + + GNNI
Sbjct: 8 KLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNV---KLTLKGKNPVSLDTLSIRGNNI 64
>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 = 28.4 bits (64), Expect = 0.58
Identities = 9/21 (42%), Positives = 10/21 (47%)
Query: 140 IVGTLNGFDDFVNMLLEDVTE 160
G L FD N+ L DV E
Sbjct: 25 CEGYLVAFDKHWNLALVDVDE 45
>gnl|CDD|188679 cd08724, RGS_GRK-like, Regulator of G protein signaling domain
(RGS) found in G protein-coupled receptor kinase (GRK).
The RGS domain is found in G protein-coupled receptor
kinases (GRKs). These proteins play a key role in
phosphorylation-dependent
desensitization/resensitization of GPCRs (G
protein-coupled receptors), intracellular trafficking,
endocytosis, as well as in the modulation of important
intracellular signaling cascades by GPCR. GRKs also
modulate cellular response in
phosphorylation-independent manner using their ability
to interact with multiple signaling proteins involved in
many essential cellular pathways. The RGS domain of the
GRKs has very little sequence similarity with the
canonical RGS domain of the RGS proteins and therefore
is often refered to as the RH (RGS Homology) domain.
Based on sequence homology the GRK family consists of
three major subfamilies: the GRK4 subfamily (GRK4, GRK5
and GRK6), the rhodopsin kinase or visual GRK subfamily
(GRK1 and GRK7), and the beta-adrenergic receptor
kinases subfamily (GRK2/GRK3). RGS proteins regulate
many aspects of embryonic development such as glial
differentiation, embryonic axis formation, skeletal and
muscle development, cell migration during early
embryogenesis, as well as apoptosis, cell proliferation,
and modulation of cardiac development.
Length = 114
Score = 28.7 bits (65), Expect = 1.0
Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 3/39 (7%)
Query: 154 LLEDVTEYESTPEGRRITKLDQILLNGNNITMLGLHTHC 192
L+++ EYE + R K +I + M H
Sbjct: 28 FLDEIKEYEVAEDEERAKKAREIY---DKYIMKESLAHS 63
>gnl|CDD|217637 pfam03607, DCX, Doublecortin.
Length = 60
Score = 27.5 bits (62), Expect = 1.2
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 9/34 (26%)
Query: 153 MLLEDVTE---------YESTPEGRRITKLDQIL 177
LL+D+TE T +G R+T LD++
Sbjct: 13 ALLDDLTEKVKLPSGVRKLYTLDGHRVTSLDELE 46
>gnl|CDD|212483 cd01736, LSm14_N, Like-Sm protein 14, N-terminal domain. LSm14
(also known as RAP55) belongs to a family of Sm-like
proteins that 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, that associates
with other Sm proteins to form hexameric and heptameric
ring structures. In addition to the N-terminal Sm-like
domain, LSm14 has an uncharacterized C-terminal domain
containing a conserved DFDF box. In Xenopus laevis,
LSm14 is an oocyte-specific constituent of
ribonucleoprotein particles.
Length = 74
Score = 26.8 bits (60), Expect = 2.0
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 7/68 (10%)
Query: 126 IGSRIHIIMKNDKEIVGTLNGFDDFVNML-LEDVTEY--ESTPEGRRITKLDQ----ILL 178
IGS+I +I K+D G L D + + L++V + E P GR I D+ I+
Sbjct: 5 IGSKISLISKSDIRYEGILYTIDTEDSTIALKNVRSFGTEGRPTGRPIPPSDEVYDYIVF 64
Query: 179 NGNNITML 186
G++I L
Sbjct: 65 RGSDIKDL 72
>gnl|CDD|213787 TIGR03222, benzo_boxC, benzoyl-CoA-dihydrodiol lyase. In the
presence of O2, the benzoyl-CoA oxygenase/reductase
BoxBA BoxAB converts benzoyl-CoA to
2,3-dihydro-2,3-dihydroxybenzoyl-CoA. Members of this
family, BoxC, homologous to enoyl-CoA
hydratases/isomerases, hydrolyze this compound to
3,4-dehydroadipyl-CoA semialdehyde + HCOOH.
Length = 546
Score = 28.6 bits (64), Expect = 2.2
Identities = 20/54 (37%), Positives = 30/54 (55%), Gaps = 7/54 (12%)
Query: 144 LNGFDDFVNMLLEDVTE---YESTPEGRRI---TKLDQILLNGNNITMLGLHTH 191
LN +D V++ L D + +E PE R + + D++ +G NI MLGL TH
Sbjct: 42 LNSYDLGVDIELHDAVQRIRFEH-PEVRTVVMTSGKDRVFCSGANIFMLGLSTH 94
>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit
clpA. [Protein fate, Degradation of proteins, peptides,
and glycopeptides].
Length = 730
Score = 28.8 bits (65), Expect = 2.4
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 85 TCAYSRSHQYRTLTHLLYTMTAPSVATN 112
A R H++ TL HLL + + A
Sbjct: 14 EEAKERRHEFVTLEHLLLALLDDNEAIE 41
>gnl|CDD|173955 cd08196, DHQS-like1, Dehydroquinate synthase (DHQS)-like. DHQS
catalyzes the conversion of DAHP to DHQ in shikimate
pathway for aromatic compounds synthesis.
Dehydroquinate synthase-like proteins. Dehydroquinate
synthase (DHQS) catalyzes the conversion of
3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to
dehydroquinate (DHQ) in the second step of the shikimate
pathway. This pathway involves seven sequential
enzymatic steps in the conversion of erythrose
4-phosphate and phosphoenolpyruvate into chorismate for
subsequent synthesis of aromatic compounds. The activity
of DHQS requires NAD as cofactor. Proteins of this
family share sequence similarity and functional motifs
with that of dehydroquinate synthase, but the specific
function has not been characterized.
Length = 346
Score = 28.5 bits (64), Expect = 2.6
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 10 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLN 42
P+TLL VD CIGS+ I + K +VG
Sbjct: 109 PTTLL--AQVDSCIGSKSSINVGPYKNLVGNFY 139
Score = 28.5 bits (64), Expect = 2.6
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 113 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLN 145
P+TLL VD CIGS+ I + K +VG
Sbjct: 109 PTTLL--AQVDSCIGSKSSINVGPYKNLVGNFY 139
>gnl|CDD|179358 PRK02001, PRK02001, hypothetical protein; Validated.
Length = 152
Score = 26.9 bits (60), Expect = 6.3
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 21 KCIGSRIHIIMKNDKEIVGTLNGFDD 46
K IG + ++ KN K+I G L D+
Sbjct: 87 KNIGRELEVLTKNGKKIEGELKSADE 112
Score = 26.9 bits (60), Expect = 6.3
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 124 KCIGSRIHIIMKNDKEIVGTLNGFDD 149
K IG + ++ KN K+I G L D+
Sbjct: 87 KNIGRELEVLTKNGKKIEGELKSADE 112
>gnl|CDD|221846 pfam12909, DUF3832, Protein of unknown function (DUF3832). This is
a family of proteins from bacteria and archaea of
unknwon function. The N-terminal part of the structure
from Syntropomonas wolfei Swol_0700 shows remote
homology to the N-terminus of the bacterial
toxin/antitoxin 'addiction module', and the C-terminus
is distantly related to the TTHA1013/TTHA0281
superfamily.
Length = 89
Score = 25.7 bits (57), Expect = 6.4
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 9/40 (22%)
Query: 131 HIIMKNDKEIVGTLNGFDDFVNM---------LLEDVTEY 161
I + D + TL+ D +VN L+ED+ +Y
Sbjct: 10 EWIEEEDGSVTVTLDELDLYVNGPTEEEALDDLVEDLRDY 49
>gnl|CDD|200442 cd11286, ADF_cofilin_like, Cofilin, Destrin, and related actin
depolymerizing factors. Actin depolymerization
factor/cofilin-like domains (ADF domains) are present in
a family of essential eukaryotic actin regulatory
proteins. These proteins enhance the turnover rate of
actin, and interact with actin monomers (G-actin) as
well as actin filaments (F-actin), typically with a
preference for ADP-G-actin subunits. The basic function
of cofilin is to promote disassembly of aged actin
filaments. Vertebrates have three isoforms of cofilin:
cofilin-1 (Cfl1, non-muscle cofilin), cofilin-2 (muscle
cofilin), and ADF (destrin). When bound to actin
monomers, cofilins inhibit their spontaneous exchange of
nucleotides. The cooperative binding to (aged)
ADP-F-actin induces a local change in the actin filament
structure and further promotes aging.
Length = 133
Score = 26.4 bits (59), Expect = 6.6
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 14/56 (25%)
Query: 132 IIMK---NDKEIV----GTLNG-FDDFVNMLLED-----VTEYE-STPEGRRITKL 173
II K + KEIV G + +DDF+ L E+ V ++E T +G + +KL
Sbjct: 25 IIFKISDDKKEIVVEKVGERDASYDDFLEKLPENECRYAVYDFEYETKDGGKRSKL 80
>gnl|CDD|223283 COG0205, PfkA, 6-phosphofructokinase [Carbohydrate transport and
metabolism].
Length = 347
Score = 27.2 bits (61), Expect = 7.1
Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 5/44 (11%)
Query: 23 IGSRIHIIMKNDKEIVGTLNGF-----DDFVNMLLEDVTDCHDS 61
I + + +K E+ G NG+ D + EDV D +
Sbjct: 21 IRAVVRTAIKEGLEVFGIYNGYLGLLEGDIKPLTREDVDDLINR 64
>gnl|CDD|178810 PRK00034, gatC, aspartyl/glutamyl-tRNA amidotransferase subunit
C; Reviewed.
Length = 95
Score = 25.5 bits (57), Expect = 8.6
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 25 SRIHIIMKNDKEIVGTLNGFDDFVNMLLE-DVTD 57
+R+ + + ++ G LN DFV L E D
Sbjct: 15 ARLELSEEELEKFAGQLNKILDFVEQLNEVDTEG 48
>gnl|CDD|172457 PRK13951, PRK13951, bifunctional shikimate kinase/3-dehydroquinate
synthase; Provisional.
Length = 488
Score = 26.8 bits (59), Expect = 8.7
Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 12/76 (15%)
Query: 113 PSTLLPLELVDKCIGSRIHIIMKNDKEIVGTLNG-----FDDFVNMLLEDVTEYESTPEG 167
P+TLL VD +G + I K +VGT D V + +++ E E
Sbjct: 270 PTTLL--AQVDASVGGKNAIDFAGVKNVVGTFRMPDYVIIDPTVTLSMDEGRFEEGVVEA 327
Query: 168 RRITKLDQILLNGNNI 183
++T +L+G +
Sbjct: 328 FKMT-----ILSGRGV 338
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 0.138 0.417
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: 10,352,274
Number of extensions: 963105
Number of successful extensions: 804
Number of sequences better than 10.0: 1
Number of HSP's gapped: 794
Number of HSP's successfully gapped: 72
Length of query: 204
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 112
Effective length of database: 6,857,034
Effective search space: 767987808
Effective search space used: 767987808
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: 57 (25.5 bits)