RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14196
(79 letters)
>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 = 100 bits (252), Expect = 4e-30
Identities = 35/48 (72%), Positives = 41/48 (85%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
PIKLLHEAEGHI+T E G+++RGKL+EAEDNMNC + DVTVT RDG
Sbjct: 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDG 48
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 48.6 bits (117), Expect = 1e-09
Identities = 16/46 (34%), Positives = 22/46 (47%)
Query: 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
K L + G + E NG +RG L + MN + DV T +DG
Sbjct: 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG 46
>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 = 46.8 bits (112), Expect = 6e-09
Identities = 17/49 (34%), Positives = 22/49 (44%)
Query: 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGTYY 56
K L + G +T E NG RG L + MN + DV T +DG
Sbjct: 1 KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVN 49
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 42.7 bits (101), Expect = 4e-07
Identities = 12/45 (26%), Positives = 20/45 (44%)
Query: 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVT 49
+P+ L + + + NG +RG LV + MN + DV
Sbjct: 7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEI 51
>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 = 41.5 bits (98), Expect = 7e-07
Identities = 15/44 (34%), Positives = 22/44 (50%)
Query: 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
L + G ++ E +G + G LV + MN + DV T RDG
Sbjct: 1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDG 44
>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 = 40.3 bits (95), Expect = 3e-06
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGT 54
P+ LL A+GH + E NG+ + G LV ++ MN + +V T +DG
Sbjct: 2 PLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGD 50
>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 = 39.8 bits (94), Expect = 4e-06
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 14 EGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGT 54
+G + T E N RG + + MN ++D T T R G
Sbjct: 18 QGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGK 58
>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 = 26.7 bits (60), Expect = 0.46
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG 53
P K L + G + + NG +RG L + MN + D T + DG
Sbjct: 2 PSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLED-TEEYVDG 48
>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 = 25.9 bits (57), Expect = 0.97
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 6 PIKLLHEAEGHIITCETT-NGDLFRGKLVEAEDNMNCAMADVT 47
P K + G I E + + +G+LV +D MN + D
Sbjct: 1 PNKKVKSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTM 43
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 26.6 bits (60), Expect = 1.2
Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 8/26 (30%)
Query: 17 IITCETTNG--------DLFRGKLVE 34
++TCET +G DL GKLV
Sbjct: 852 VLTCETRHGVCAKCYGRDLATGKLVN 877
>gnl|CDD|177942 PLN02307, PLN02307, phosphoglucomutase.
Length = 579
Score = 26.2 bits (58), Expect = 2.0
Identities = 9/13 (69%), Positives = 9/13 (69%)
Query: 62 PIAGMWNGTSGLR 74
PI G GTSGLR
Sbjct: 19 PIEGQKPGTSGLR 31
>gnl|CDD|131434 TIGR02381, cspD, cold shock domain protein CspD. This model
represents what appears to be a phylogenetically
distinct clade, containing E. coli CspD (SP|P24245) and
related proteobacterial proteins within the larger
family of cold shock domain proteins described by Pfam
model pfam00313. The gene symbol cspD may have been
used idependently for other subfamilies of cold shock
domain proteins, such as for B. subtilis CspD. These
proteins typically are shorter than 70 amino acids. In
E. coli, CspD is a stress response protein induced in
stationary phase. This homodimer binds single-stranded
DNA and appears to inhibit DNA replication [DNA
metabolism, DNA replication, recombination, and repair,
Cellular processes, Adaptations to atypical
conditions].
Length = 68
Score = 24.8 bits (54), Expect = 2.7
Identities = 12/29 (41%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 1 MSIGIPIKLLHEAEGH-IITCETTNGDLF 28
M+IGI +K + A+G I E +GD+F
Sbjct: 1 MAIGI-VKWFNNAKGFGFICPEGVDGDIF 28
>gnl|CDD|236887 PRK11259, solA, N-methyltryptophan oxidase; Provisional.
Length = 376
Score = 24.8 bits (55), Expect = 5.0
Identities = 13/25 (52%), Positives = 13/25 (52%)
Query: 46 VTVTFRDGTYYLPALVPIAGMWNGT 70
VTVT DGTY LV AG W
Sbjct: 182 VTVTTADGTYEAKKLVVSAGAWVKD 206
>gnl|CDD|197321 cd09087, Ape1-like_AP-endo, Human Ape1-like subfamily of the
ExoIII family purinic/apyrimidinic (AP) endonucleases.
This subfamily includes human Ape1 (also known as Apex,
Hap1, or Ref-1) and related proteins. These are
Escherichia coli exonuclease III (ExoIII)-like AP
endonucleases and they belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different
AP endonuclease enzymes catalyze the different
reactions with different efficiences. Many organisms
have two AP endonucleases, usually one is the dominant
AP endonuclease, the other has weak AP endonuclease
activity; for example, Ape1 and Ape2 in humans. Ape1 is
found in this subfamily, it exhibits strong
AP-endonuclease activity but shows weak 3'-5'
exonuclease and 3'-phosphodiesterase activities. Class
II AP endonucleases have been classified into two
families, designated ExoIII and EndoIV, based on their
homology to the Escherichia coli enzymes exonuclease
III (ExoIII) and endonuclease IV (EndoIV). This
subfamily belongs to the ExoIII family; the EndoIV
family belongs to a different superfamily.
Length = 253
Score = 24.4 bits (54), Expect = 7.7
Identities = 9/18 (50%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 4 GIPIKLLHEAEGHIITCE 21
GI I+ H+ EG +IT E
Sbjct: 83 GIGIEE-HDQEGRVITAE 99
>gnl|CDD|176226 cd08265, Zn_ADH3, Alcohol dehydrogenases of the MDR family. This
group resembles the zinc-dependent alcohol dehydrogenase
and has the catalytic and structural zinc-binding sites
characteristic of this group. The medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines. Other MDR members have only a catalytic zinc,
and some contain no coordinated zinc.
Length = 384
Score = 24.4 bits (53), Expect = 8.6
Identities = 11/42 (26%), Positives = 17/42 (40%)
Query: 4 GIPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMAD 45
P+ + HE G + + +G V AE+ M C M
Sbjct: 86 EFPVVIGHEFSGVVEKTGKNVKNFEKGDPVTAEEMMWCGMCR 127
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
0.320 0.136 0.428
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: 4,002,118
Number of extensions: 298838
Number of successful extensions: 271
Number of sequences better than 10.0: 1
Number of HSP's gapped: 271
Number of HSP's successfully gapped: 16
Length of query: 79
Length of database: 10,937,602
Length adjustment: 48
Effective length of query: 31
Effective length of database: 8,808,610
Effective search space: 273066910
Effective search space used: 273066910
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)