RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3154
(101 letters)
>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 = 158 bits (403), Expect = 1e-52
Identities = 73/82 (89%), Positives = 80/82 (97%)
Query: 13 EPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIY 72
EPLDLIRLSLDERV+VK+R +R LRG+LHAYDQHLNM+LGDVEET+TTVEIDEETYEEIY
Sbjct: 1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIY 60
Query: 73 KTTKRSIPMLFVRGDGVILVSP 94
KTTKR+IPMLFVRGDGVILVSP
Sbjct: 61 KTTKRNIPMLFVRGDGVILVSP 82
>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 = 70.7 bits (174), Expect = 6e-18
Identities = 30/81 (37%), Positives = 46/81 (56%), Gaps = 13/81 (16%)
Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
PLD++ SL++ V VK++ + +RG L +DQHLN+VL + E EI E
Sbjct: 2 PLDVLNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAE------EIIEG------- 48
Query: 74 TTKRSIPMLFVRGDGVILVSP 94
+ R + + VRGD V+ +SP
Sbjct: 49 ESVRKLGTVLVRGDNVVFISP 69
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 66.7 bits (164), Expect = 2e-16
Identities = 25/79 (31%), Positives = 43/79 (54%), Gaps = 12/79 (15%)
Query: 16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTT 75
++ + +RV V+++N R RG L +DQ +N+VL DVEETV E
Sbjct: 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGE------------K 48
Query: 76 KRSIPMLFVRGDGVILVSP 94
KR + ++F+RG+ ++ +
Sbjct: 49 KRKLGLVFIRGNNIVYIIL 67
>gnl|CDD|201787 pfam01423, LSM, LSM domain. The LSM domain contains Sm proteins
as well as other related LSM (Like Sm) proteins. The
U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein
particles (snRNPs) involved in pre-mRNA splicing
contain seven Sm proteins (B/B', D1, D2, D3, E, F and
G) in common, which assemble around the Sm site present
in four of the major spliceosomal small nuclear RNAs.
The U6 snRNP binds to the LSM (Like Sm) proteins. Sm
proteins are also found in archaebacteria, which do not
have any splicing apparatus suggesting a more general
role for Sm proteins. All Sm proteins contain a common
sequence motif in two segments, Sm1 and Sm2, separated
by a short variable linker. This family also includes
the bacterial Hfq (host factor Q) proteins. Hfq are
also RNA-binding proteins, that form hexameric rings.
Length = 66
Score = 66.0 bits (162), Expect = 5e-16
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 13/79 (16%)
Query: 16 DLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTT 75
++ L +RV V+++N R LRG L +DQ +N+VL DVEET I
Sbjct: 1 KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEET-------------IKDGK 47
Query: 76 KRSIPMLFVRGDGVILVSP 94
+ ++ +RG+ ++L+SP
Sbjct: 48 VNKLGLVLIRGNNIVLISP 66
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 64.2 bits (157), Expect = 3e-15
Identities = 31/81 (38%), Positives = 49/81 (60%), Gaps = 9/81 (11%)
Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
PL ++ L++RV VK++N R RG L +DQ++N+VL DVEE ++ D E K
Sbjct: 8 PLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIIS---HDGE------K 58
Query: 74 TTKRSIPMLFVRGDGVILVSP 94
+R + +RGD ++L+SP
Sbjct: 59 NVRRLGGEVLIRGDNIVLISP 79
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 56.2 bits (136), Expect = 3e-12
Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 13/84 (15%)
Query: 11 VKEPLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEE 70
+ PLD++ +L+ V V+++ R RG+L YD H+N+VL + EE D E
Sbjct: 2 AQRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEI-----QDGE---- 52
Query: 71 IYKTTKRSIPMLFVRGDGVILVSP 94
R + + +RGD V+ VSP
Sbjct: 53 ----VVRKLGKVVIRGDNVVYVSP 72
>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 = 54.6 bits (132), Expect = 2e-11
Identities = 29/84 (34%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 14 PLDLIRLSL--DERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEI 71
PL L+ S+ + +V + RN + L ++ A+D+H NMVL +V+E T V + +
Sbjct: 5 PLSLLTQSVKNNTQVLINCRNNKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKGKKSK 64
Query: 72 YKTTKRSIPMLFVRGDGVILVSPP 95
R I +F+RGD VILV
Sbjct: 65 PVNKDRFISKMFLRGDSVILVLRN 88
>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 = 53.4 bits (129), Expect = 4e-11
Identities = 19/73 (26%), Positives = 38/73 (52%), Gaps = 13/73 (17%)
Query: 21 SLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIP 80
+ + V V++++ RVL G L A+D+++N+VL DV ET + R +
Sbjct: 4 FIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGK-------------VRVLG 50
Query: 81 MLFVRGDGVILVS 93
++ +RG ++ +
Sbjct: 51 LVLIRGSNIVSIR 63
>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 = 46.0 bits (110), Expect = 4e-08
Identities = 20/72 (27%), Positives = 41/72 (56%), Gaps = 2/72 (2%)
Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
++ R+ V +++ R G A+D+H+N+VL D EE ++ EE + KR + +
Sbjct: 9 INYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKKGEE--REEKRVLGL 66
Query: 82 LFVRGDGVILVS 93
+ +RG+ V+ ++
Sbjct: 67 VLLRGENVVSMT 78
>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 = 43.7 bits (104), Expect = 3e-07
Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 15 LDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKT 74
LDL + +D+++ VK + R + G L YDQ LN+VL D E + E + +E
Sbjct: 5 LDLSKY-VDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDE---- 59
Query: 75 TKRSIPMLFVRGDGVILVSP 94
RS+ ++ RG V+L+SP
Sbjct: 60 -TRSLGLVVCRGTSVVLISP 78
>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 = 39.1 bits (92), Expect = 2e-05
Identities = 12/46 (26%), Positives = 21/46 (45%)
Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEET 67
L + V + + RVL G D+ N++L + EE ++ E
Sbjct: 8 LGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLGAEE 53
>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 = 5e-05
Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 13/71 (18%)
Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
+D+R+ +K+ R + G L +D +N+VL ++ EE+ K I M
Sbjct: 9 MDKRLSLKLNGNRKVSGVLRGFDPFMNLVL-------------DDAVEEVGDGEKTPIGM 55
Query: 82 LFVRGDGVILV 92
+ +RG+ +I++
Sbjct: 56 VVIRGNSIIMI 66
>gnl|CDD|212473 cd01726, LSm6, Like-Sm protein 6. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. LSm657 is
believed to be an assembly intermediate for both the
LSm1-7 and LSm2-8 rings. Members of this family share a
highly conserved Sm fold containing an N-terminal helix
followed by a strongly bent five-stranded antiparallel
beta-sheet.
Length = 68
Score = 37.9 bits (89), Expect = 5e-05
Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 13/80 (16%)
Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYK 73
P ++ + + V VK++N RG L D ++N+VL D EE V
Sbjct: 2 PSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQ------------ 49
Query: 74 TTKRSIPMLFVRGDGVILVS 93
F+RG+ V+ +S
Sbjct: 50 -LVAKYGDAFIRGNNVLYIS 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 = 37.6 bits (88), Expect = 5e-05
Identities = 17/39 (43%), Positives = 24/39 (61%), Gaps = 4/39 (10%)
Query: 25 RVHVKMRNERVLRGK----LHAYDQHLNMVLGDVEETVT 59
RV V +R + +RG L A+D+H N+ L DV+ET T
Sbjct: 10 RVKVYIRKAKGIRGSCEGYLVAFDKHWNLALVDVDETWT 48
>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 = 37.6 bits (88), Expect = 7e-05
Identities = 18/54 (33%), Positives = 31/54 (57%)
Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEET 67
PL+LI + ++ + M++++ G L +D ++NMVL DV E T E + T
Sbjct: 4 PLELIDKCIGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKIT 57
>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 = 36.0 bits (84), Expect = 3e-04
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 10/71 (14%)
Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
LD+++ V +R+ R L G L ++DQ N+VL D E + + ++
Sbjct: 11 LDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLF--------- 61
Query: 82 LFVRGDGVILV 92
+RG+ V+L+
Sbjct: 62 -IIRGENVVLL 71
>gnl|CDD|212472 cd01725, LSm2, Like-Sm protein 2. The eukaryotic LSm proteins
(LSm2-8 or LSm1-7) assemble into a hetero-heptameric
ring around the 3'-terminus uridylation tag of the
gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA.
LSm2-8 form the core of the snRNP particle that, in
turn, assembles with other components onto the pre-mRNA
to form the spliceosome which is responsible for the
excision of introns and the ligation of exons. LSm1-7
is involved in recognition of the 3' uridylation tag
and recruitment of the decapping machinery. Members of
this family share a highly conserved Sm fold containing
an N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet.
Length = 89
Score = 33.3 bits (77), Expect = 0.004
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 11/68 (16%)
Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
+ + V V+++N+ + G LH+ DQ+LN+ L ++ D E Y + S+
Sbjct: 10 VGKEVTVELKNDLSITGTLHSVDQYLNIKLTNISVN------DPEKYPHL-----LSVKN 58
Query: 82 LFVRGDGV 89
F+RG V
Sbjct: 59 CFIRGSVV 66
>gnl|CDD|212490 cd11679, archaeal_Sm_like, archaeal Sm-related protein. Archaeal
Sm-related proteins: The Sm proteins are conserved in
all three domains of life and are always associated
with U-rich RNA sequences. They function to mediate
RNA-RNA interactions and RNA biogenesis. All Sm
proteins contain a common sequence motif in two
segments, Sm1 and Sm2, separated by a short variable
linker. Eukaryotic Sm proteins form part of specific
small nuclear ribonucleoproteins (snRNPs) that are
involved in the processing of pre-mRNAs to mature
mRNAs, and are a major component of the eukaryotic
spliceosome. Most snRNPs consist of seven Sm proteins
(B/B', D1, D2, D3, E, F and G) arranged in a ring on a
uridine-rich sequence (Sm site), plus a small nuclear
RNA (snRNA) (either U1, U2, U5 or U4/6). Since
archaebacteria do not have any splicing apparatus,
their Sm proteins may play a more general role.
Archaeal Lsm proteins are likely to represent the
ancestral Sm domain.
Length = 65
Score = 32.2 bits (74), Expect = 0.006
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 5/56 (8%)
Query: 22 LDERVHVKMRNERVLRGKLHAYDQH-LNMVLGDVE----ETVTTVEIDEETYEEIY 72
LD+ V V + N + G+L +D LN+VL + + V I+ EI
Sbjct: 9 LDKEVIVTLSNGKTYTGQLVGFDPSSLNIVLTNAKDSSGNKFPKVIINGNRISEIL 64
>gnl|CDD|212489 cd11678, archaeal_LSm, archaeal Like-Sm protein. The archaeal
Sm-like (LSm): The Sm proteins are conserved in all
three domains of life and are always associated with
U-rich RNA sequences. They function to mediate RNA-RNA
interactions and RNA biogenesis. All Sm proteins
contain a common sequence motif in two segments, Sm1
and Sm2, separated by a short variable linker.
Eukaryotic Sm proteins form part of specific small
nuclear ribonucleoproteins (snRNPs) that are involved
in the processing of pre-mRNAs to mature mRNAs, and are
a major component of the eukaryotic spliceosome. Most
snRNPs consist of seven Sm proteins (B/B', D1, D2, D3,
E, F and G) arranged in a ring on a uridine-rich
sequence (Sm site), plus a small nuclear RNA (snRNA)
(either U1, U2, U5 or U4/6). Since archaebacteria do
not have any splicing apparatus, their Sm proteins may
play a more general role. Archaeal LSm proteins are
likely to represent the ancestral Sm domain. Members of
this family share a highly conserved Sm fold containing
an N-terminal helix followed by a strongly bent
five-stranded antiparallel beta-sheet. Sm-like proteins
exist in archaea as well as prokaryotes that form
heptameric and hexameric ring structures similar to
those found in eukaryotes.
Length = 69
Score = 32.1 bits (73), Expect = 0.007
Identities = 21/82 (25%), Positives = 42/82 (51%), Gaps = 14/82 (17%)
Query: 14 PLDLIRLSLDERVHVKMR-NERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIY 72
P ++ + R+ V+M+ +E L+G+L A D ++N+ L D E V ++
Sbjct: 1 PNKKVKSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKV--------- 51
Query: 73 KTTKRSIPMLFVRGDGVILVSP 94
RS+ + +RG+ ++L+ P
Sbjct: 52 ----RSLGTVVLRGNNILLIQP 69
>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional.
Length = 89
Score = 32.4 bits (74), Expect = 0.009
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 12/59 (20%)
Query: 35 VLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVS 93
+ GK+ +D+++NMVL D EE T K T++ + + ++GD + L+
Sbjct: 40 RIEGKILGFDEYMNMVLDDAEEVYTK------------KNTRKDLGRILLKGDNITLIM 86
>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 = 31.4 bits (72), Expect = 0.016
Identities = 14/44 (31%), Positives = 22/44 (50%)
Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEET 57
PL L+R + V V+++N G L D +N+ L +V T
Sbjct: 2 PLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICT 45
>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 = 29.0 bits (66), Expect = 0.13
Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 2/48 (4%)
Query: 25 RVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIY 72
V++RNE +RG + D +N+ L D T T + ++E +
Sbjct: 21 VTTVELRNETSVRGIIDNVDGFMNITLSDA--TFTDRRGKQHHFDEFF 66
>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 = 29.0 bits (66), Expect = 0.17
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 9/71 (12%)
Query: 22 LDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPM 81
L++RV V + RV+ G L +DQ N++L + E V + +E EE+ + +
Sbjct: 8 LNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHERVYS---SDEGVEEV------PLGL 58
Query: 82 LFVRGDGVILV 92
+RGD V ++
Sbjct: 59 YLLRGDNVAVI 69
>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 = 0.34
Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 16/68 (23%)
Query: 27 HVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRG 86
MR E + G +D+++N+VL D EE T++ + + ++G
Sbjct: 28 QTDMRIEGKIIG----FDEYMNLVLDDAEEVHLKTN------------TRKPLGRILLKG 71
Query: 87 DGVILVSP 94
D + L+
Sbjct: 72 DNITLIQN 79
>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 = 26.4 bits (59), Expect = 0.94
Identities = 10/32 (31%), Positives = 18/32 (56%)
Query: 25 RVHVKMRNERVLRGKLHAYDQHLNMVLGDVEE 56
V VK++ +G L + D ++N+ L + EE
Sbjct: 13 PVIVKLKWGMEYKGTLVSVDSYMNLQLANTEE 44
>gnl|CDD|233317 TIGR01218, Gpos_tandem_5TM, tandem five-transmembrane protein.
Members of this family of proteins, with average length
of 210, have no invariant residues but five predicted
transmembrane segments. Strangely, most members occur
in groups of consecutive paralogous genes. A striking
example is a set of eleven encoded consecutively,
head-to-tail, in Staphylococcus aureus strain COL.
Length = 208
Score = 26.8 bits (60), Expect = 2.0
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 57 TVTTVEIDEETYEEIYKT--TKRSIPMLFVRGDGVIL 91
EID + +E++ KT K S + +G V+L
Sbjct: 42 PKKLYEIDNDEFEKLKKTKKKKNSGLGILGQGISVLL 78
>gnl|CDD|222837 PHA01794, PHA01794, hypothetical protein.
Length = 134
Score = 26.1 bits (57), Expect = 2.6
Identities = 7/30 (23%), Positives = 16/30 (53%)
Query: 50 VLGDVEETVTTVEIDEETYEEIYKTTKRSI 79
+L + + V T E +E T E ++ ++ +
Sbjct: 55 ILDAIADFVETFEDEEGTTEGLFAELEKEM 84
>gnl|CDD|187603 cd05345, BKR_3_SDR_c, putative beta-ketoacyl acyl carrier protein
[ACP] reductase (BKR), subgroup 3, classical (c) SDR.
This subgroup includes the putative Brucella melitensis
biovar Abortus 2308 BKR, FabG, Mesorhizobium loti
MAFF303099 FabG, and other classical SDRs. BKR, a member
of the SDR family, catalyzes the NADPH-dependent
reduction of acyl carrier protein in the first reductive
step of de novo fatty acid synthesis (FAS). FAS
consists of 4 elongation steps, which are repeated to
extend the fatty acid chain thru the addition of
two-carbo units from malonyl acyl-carrier protein (ACP):
condensation, reduction, dehydration, and final
reduction. Type II FAS, typical of plants and many
bacteria, maintains these activities on discrete
polypeptides, while type I Fas utilizes one or 2
multifunctional polypeptides. BKR resembles enoyl
reductase, which catalyzes the second reduction step in
FAS. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold (alpha/beta folding
pattern with a central beta-sheet), an NAD(P)(H)-binding
region, and a structurally diverse C-terminal region.
Classical SDRs are typically about 250 residues long,
while extended SDRS are approximately 350 residues.
Sequence identity between different SDR enzymes are
typically in the 15-30% range, but the enzymes share the
Rossmann fold NAD-binding motif and characteristic
NAD-binding and catalytic sequence patterns. These
enzymes have a 3-glycine N-terminal NAD(P)(H)-binding
pattern (typically, TGxxxGxG in classical SDRs and
TGxxGxxG in extended SDRs), while substrate binding is
in the C-terminal region. A critical catalytic Tyr
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering), is often found in a
conserved YXXXK pattern. In addition to the Tyr and Lys,
there is often an upstream Ser (Ser-138, 15-PGDH
numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or
additional Ser, contributing to the active site.
Substrates for these enzymes include sugars, steroids,
alcohols, and aromatic compounds. The standard reaction
mechanism is a proton relay involving the conserved Tyr
and Lys, as well as Asn (or Ser). Some SDR family
members, including 17 beta-hydroxysteroid dehydrogenase
contain an additional helix-turn-helix motif that is not
generally found among SDRs.
Length = 248
Score = 26.2 bits (58), Expect = 3.3
Identities = 11/40 (27%), Positives = 21/40 (52%), Gaps = 8/40 (20%)
Query: 60 TVEIDEETYEE--------IYKTTKRSIPMLFVRGDGVIL 91
+E+DEE ++ IY + + +P + +G GVI+
Sbjct: 96 MLEVDEEEFDRVFAVNVKSIYLSAQALVPHMEEQGGGVII 135
>gnl|CDD|236612 PRK09685, PRK09685, DNA-binding transcriptional activator FeaR;
Provisional.
Length = 302
Score = 26.1 bits (58), Expect = 3.6
Identities = 20/74 (27%), Positives = 30/74 (40%), Gaps = 12/74 (16%)
Query: 17 LIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTK 76
L+R +L +R V+ R ER + + DQ + EE + I E +
Sbjct: 180 LLRPALHQRESVQPRRERQFQKVVALIDQSIQ------EEILRPEWIAGEL-----GISV 228
Query: 77 RSIPMLFVR-GDGV 89
RS+ LF G V
Sbjct: 229 RSLYRLFAEQGLVV 242
>gnl|CDD|221854 pfam12920, TcdA_TcdB_pore, TcdA/TcdB pore forming domain. This
family represents the most conserved region within the
C. difficile Toxin A and Toxin B pore forming region.
Length = 654
Score = 26.1 bits (58), Expect = 4.1
Identities = 14/56 (25%), Positives = 19/56 (33%), Gaps = 3/56 (5%)
Query: 39 KLHAYDQHLNMVLG---DVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVIL 91
K+ AY Q + LG D + V V+ T + G GVI
Sbjct: 133 KVQAYVQLAQIGLGLIQDASKLVNLVKTALREEINALPTLLKGFSATANEGVGVIF 188
>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 = 24.8 bits (55), Expect = 4.5
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 14 PLDLIRLSLDERVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIY 72
P+ L+ + V V+++ V RGKL + ++N L DV TVT + E++Y
Sbjct: 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDV--TVTARDGKVSKLEQVY 57
>gnl|CDD|233867 TIGR02436, TIGR02436, four helix bundle protein. This family
describes a protein of unknown function whose structure
is a bundle of four long alpha helices. Some of the
first members of this family were found encoded in the
(atypically large) intervening sequence (IVS) of
Leptospira 23S RNA, a region often present in the rRNA
gene and removed during rRNA processing without
re-ligation. However, this location is not conserved,
and naming this protein as a 23S RNA protein is both
confusing and inaccurate.
Length = 108
Score = 25.1 bits (56), Expect = 4.5
Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 45 QHLNMVLGDVEETVTTVE-------IDEETYEEIYKTTKRSIPML 82
+ L++ LG ET T +E IDEE YEE+ + + I ML
Sbjct: 56 RFLSIALGSAAETETQLELAKDLGYIDEEEYEELLEELEEIIKML 100
>gnl|CDD|147670 pfam05635, Ribosomal_S23p, S23 ribosomal protein. This family
consists of bacterial 23S rRNA proteins.
Length = 110
Score = 24.7 bits (55), Expect = 6.0
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 7/45 (15%)
Query: 45 QHLNMVLGDVEETVTTVE-------IDEETYEEIYKTTKRSIPML 82
+ LN+ G E T + I EE YEE+ + + ML
Sbjct: 63 RFLNIARGSAAELETQLIIAKDLGYISEEEYEELLEELEEISKML 107
>gnl|CDD|215172 PLN02303, PLN02303, urease.
Length = 837
Score = 25.5 bits (56), Expect = 6.2
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 17/49 (34%)
Query: 47 LNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP 95
L+M L D + + +D ETYE V DG +L P
Sbjct: 793 LDMKLND---ALPVITVDPETYE--------------VTADGEVLTCAP 824
>gnl|CDD|237305 PRK13207, ureC, urease subunit alpha; Reviewed.
Length = 568
Score = 25.1 bits (56), Expect = 6.8
Identities = 12/35 (34%), Positives = 15/35 (42%), Gaps = 14/35 (40%)
Query: 61 VEIDEETYEEIYKTTKRSIPMLFVRGDGVILVSPP 95
+E+D ETYE VR DG +L P
Sbjct: 535 IEVDPETYE--------------VRADGELLTCEP 555
>gnl|CDD|153307 cd07623, BAR_SNX1_2, The Bin/Amphiphysin/Rvs (BAR) domain of
Sorting Nexins 1 and 2. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions. Sorting
nexins (SNXs) are Phox homology (PX) domain containing
proteins that are involved in regulating membrane
traffic and protein sorting in the endosomal system.
SNXs differ from each other in their lipid-binding
specificity, subcellular localization and specific
function in the endocytic pathway. A subset of SNXs also
contain BAR domains. The PX-BAR structural unit
determines the specific membrane targeting of SNXs. This
subfamily consists of SNX1, SNX2, and similar proteins.
SNX1 and SNX2 are components of the retromer complex, a
membrane coat multimeric complex required for endosomal
retrieval of lysosomal hydrolase receptors to the Golgi.
The retromer consists of a cargo-recognition subcomplex
and a subcomplex formed by a dimer of sorting nexins
(SNX1 and/or SNX2), which ensures efficient cargo
sorting by facilitating proper membrane localization of
the cargo-recognition subcomplex. BAR domains form
dimers that bind to membranes, induce membrane bending
and curvature, and may also be involved in
protein-protein interactions.
Length = 224
Score = 24.9 bits (55), Expect = 7.1
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 47 LNMVLGDVEETVTTVEIDEETYEEIYKTTKRSI 79
L+ +++E V+ ++ +EEI KT K+ I
Sbjct: 151 LDQAQQEIKEWEAKVDRGQKEFEEISKTIKKEI 183
>gnl|CDD|233499 TIGR01631, Trypano_RHS, trypanosome RHS (retrotransposon hot spot)
family. This model describes full-length and
part-length members of the RHS (retrotransposon hot
spot) family in Trypanosoma brucei and Trypanosoma
cruzi. Members of this family are frequently interrupted
by non-LTR retrotransposons inserted at exactly the same
relative position.
Length = 760
Score = 25.2 bits (55), Expect = 7.3
Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 7/73 (9%)
Query: 25 RVHVKMRNERVLRGKLHAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSIPMLFV 84
R + ++ RVL Y+Q L+ + EI + Y +YK + P++
Sbjct: 594 RPGEQRQSHRVLL---AVYEQELSTRHHVLPPDEHFSEIIDIEYGVLYKPEVGNFPVV-- 648
Query: 85 RGDGVILVSPPNR 97
D V P
Sbjct: 649 --DAFFFVESPAI 659
>gnl|CDD|215793 pfam00213, OSCP, ATP synthase delta (OSCP) subunit. The ATP D
subunit from E. coli is the same as the OSCP subunit
which is this family. The ATP D subunit from metazoa are
found in family pfam00401.
Length = 171
Score = 24.8 bits (55), Expect = 7.7
Identities = 17/76 (22%), Positives = 31/76 (40%), Gaps = 11/76 (14%)
Query: 7 PTISVKEPLDLIRLSLDERVHVKMRN----------ERVLRGKLHAYDQHLNMVLGDVEE 56
P IS +E L++ ++ +N +L +++ N G VE
Sbjct: 46 PLISAEEKKALLKAVFGGKLSELTKNFLKLLAENGRLSLLPEIAEEFEELYNEHRGIVEA 105
Query: 57 TVTT-VEIDEETYEEI 71
TVT+ V + EE + +
Sbjct: 106 TVTSAVPLSEEQLKAL 121
>gnl|CDD|217047 pfam02455, Hex_IIIa, Hexon-associated protein (IIIa). The major
capsid protein of the adenovirus strain is also known as
a hexon. This is a family of hexon-associated proteins
(protein IIIa).
Length = 491
Score = 25.1 bits (55), Expect = 8.1
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 56 ETVTTVEIDEETYEEI 71
ET+ ++DEETY EI
Sbjct: 192 ETLGAADVDEETYAEI 207
>gnl|CDD|220003 pfam08752, Gamma-COP, Coatomer gamma subunit appendage domain.
COPI-coated vesicles function in retrograde transport
from the Golgi to the ER, and in intra-Golgi transport.
This domain corresponds to the coatomer gamma subunit
appendage domain. It contains a protein-protein
interaction site and a second proposed binding site
that interacts with the alpha, beta,epsilon COPI
subcomplex.
Length = 269
Score = 24.9 bits (55), Expect = 8.2
Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 12/59 (20%)
Query: 32 NERVLRGKLHAYDQHLNMVLG-DVEETVT---------TVEIDEETYEEIYKTTKRSIP 80
E V+ H + H +VL ++ T+ +E EE YEE++ +P
Sbjct: 35 TEYVVSVVKHIFKNH--IVLQFNITNTLNDQVLENVSVELEPSEEEYEELFIIPIDKLP 91
>gnl|CDD|224086 COG1164, COG1164, Oligoendopeptidase F [Amino acid transport and
metabolism].
Length = 598
Score = 25.0 bits (55), Expect = 9.0
Identities = 6/24 (25%), Positives = 12/24 (50%)
Query: 62 EIDEETYEEIYKTTKRSIPMLFVR 85
E+D E + + ++ K + L R
Sbjct: 257 EVDREVVDNLIESVKEAFLPLLHR 280
>gnl|CDD|222441 pfam13898, DUF4205, Domain of unknown function (DUF4205). The
proteins in this family are uncharacterized but often
named FAM188B.
Length = 341
Score = 25.0 bits (55), Expect = 9.4
Identities = 7/39 (17%), Positives = 11/39 (28%), Gaps = 2/39 (5%)
Query: 54 VEETVTTVEIDEETYEEIYKTTKRSIPMLFVRGDGVILV 92
+ E + EE+ + G G IL
Sbjct: 121 LTEKLMLFTFT--KLEELQAFLYEHLSQFETGGHGCILF 157
>gnl|CDD|219460 pfam07541, EIF_2_alpha, Eukaryotic translation initiation factor
2 alpha subunit. These proteins share a region of
similarity that falls towards the C terminus from
pfam00575.
Length = 112
Score = 24.4 bits (54), Expect = 9.6
Identities = 14/49 (28%), Positives = 22/49 (44%), Gaps = 3/49 (6%)
Query: 41 HAYDQHLNMVLGDVEETVTTVEIDEETYEEIYKTTKRSI--PMLFVRGD 87
HAYD + EE + + I EE E + + + I P + +R D
Sbjct: 15 HAYDAFEAAAI-PGEEVLDDLGIPEEWKEALLEIIRERITPPPVKIRAD 62
>gnl|CDD|153371 cd07320, Extradiol_Dioxygenase_3B_like, Subunit B of Class III
Extradiol ring-cleavage dioxygenases. Dioxygenases
catalyze the incorporation of both atoms of molecular
oxygen into substrates using a variety of reaction
mechanisms, resulting in the cleavage of aromatic
rings. Two major groups of dioxygenases have been
identified according to the cleavage site of the
aromatic ring. Intradiol enzymes cleave the aromatic
ring between two hydroxyl groups, whereas extradiol
enzymes cleave the aromatic ring between a hydroxylated
carbon and an adjacent non-hydroxylated carbon.
Extradiol dioxygenases can be further divided into
three classes. Class I and II enzymes are evolutionary
related and show sequence similarity, with the
two-domain class II enzymes evolving from the class I
enzyme through gene duplication. Class III enzymes are
different in sequence and structure and usually have
two subunits, designated A and B. This model represents
the catalytic subunit B of extradiol dioxygenase class
III enzymes. Enzymes belonging to this family include
Protocatechuate 4,5-dioxygenase (LigAB),
2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarB),
4,5-DOPA Dioxygenase, 2,3-dihydroxyphenylpropionate
1,2-dioxygenase, and 3,4-dihydroxyphenylacetate
(homoprotocatechuate) 2,3-dioxygenase (HPCD). There are
also some family members that do not show the typical
dioxygenase activity.
Length = 260
Score = 24.8 bits (54), Expect = 9.9
Identities = 7/26 (26%), Positives = 12/26 (46%)
Query: 56 ETVTTVEIDEETYEEIYKTTKRSIPM 81
V V+ D + EI + + IP+
Sbjct: 74 RPVYDVKGDPDLAWEIAEELIKEIPV 99
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
0.317 0.136 0.376
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: 5,288,233
Number of extensions: 453845
Number of successful extensions: 658
Number of sequences better than 10.0: 1
Number of HSP's gapped: 645
Number of HSP's successfully gapped: 62
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.0 bits)