RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1084
(110 letters)
>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 = 179 bits (457), Expect = 1e-60
Identities = 79/90 (87%), Positives = 84/90 (93%), Gaps = 1/90 (1%)
Query: 16 FATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKG 75
F TGPLS+LT SVK+NTQVLINCRNNKKLL RVKAFDRHCNMVLENVKEMWTE P+ GKG
Sbjct: 1 FNTGPLSLLTQSVKNNTQVLINCRNNKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKG 60
Query: 76 KKKSKPVNKDRFISKMFLRGDSVILILKNP 105
KKSKPVNKDRFISKMFLRGDSVIL+L+NP
Sbjct: 61 -KKSKPVNKDRFISKMFLRGDSVILVLRNP 89
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear ribonucleoprotein
particles (snRNPs) involved in pre-mRNA splicing.
Length = 67
Score = 68.3 bits (168), Expect = 8e-17
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 13/71 (18%)
Query: 31 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISK 90
+VL+ +N ++ G +K FD+ N+VLE+V+E + K R +
Sbjct: 8 GKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD-------------GEKKRKLGL 54
Query: 91 MFLRGDSVILI 101
+F+RG++++ I
Sbjct: 55 VFIRGNNIVYI 65
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 64.6 bits (158), Expect = 3e-15
Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 12/82 (14%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 79
PLS L + N +VL+ +N ++ G + FD++ N+VL++V+E+ +
Sbjct: 8 PLSFLKKLL--NKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISH----------D 55
Query: 80 KPVNKDRFISKMFLRGDSVILI 101
N R ++ +RGD+++LI
Sbjct: 56 GEKNVRRLGGEVLIRGDNIVLI 77
>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 = 63.7 bits (156), Expect = 5e-15
Identities = 17/71 (23%), Positives = 36/71 (50%), Gaps = 14/71 (19%)
Query: 31 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISK 90
+V + +N ++L G +K FD+ N+VL++V+E + K +
Sbjct: 8 GKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKD--------------GKVNKLGL 53
Query: 91 MFLRGDSVILI 101
+ +RG++++LI
Sbjct: 54 VLIRGNNIVLI 64
>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 = 64.2 bits (157), Expect = 5e-15
Identities = 24/69 (34%), Positives = 41/69 (59%), Gaps = 1/69 (1%)
Query: 33 QVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMF 92
+V + R +++L GR+ A+D+H NM+L +V+E T + ++ K R I +F
Sbjct: 13 RVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTK-RNIPMLF 71
Query: 93 LRGDSVILI 101
+RGD VIL+
Sbjct: 72 VRGDGVILV 80
>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 = 55.7 bits (135), Expect = 6e-12
Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 16/82 (19%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 79
PL +L +S N VL+ + K++ G +K FD+H N+VLEN +E+ G+ +K
Sbjct: 2 PLDVLNES--LNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEI-----IEGESVRK- 53
Query: 80 KPVNKDRFISKMFLRGDSVILI 101
+ + +RGD+V+ I
Sbjct: 54 --------LGTVLVRGDNVVFI 67
>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 = 51.5 bits (124), Expect = 3e-10
Identities = 18/78 (23%), Positives = 36/78 (46%), Gaps = 16/78 (20%)
Query: 24 LTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVN 83
L D + V + ++ + L G + AFD++ N+VL++V E +
Sbjct: 1 LKDFI--GKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRD--------------G 44
Query: 84 KDRFISKMFLRGDSVILI 101
K R + + +RG +++ I
Sbjct: 45 KVRVLGLVLIRGSNIVSI 62
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 41.1 bits (97), Expect = 3e-06
Identities = 22/85 (25%), Positives = 47/85 (55%), Gaps = 16/85 (18%)
Query: 17 ATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGK 76
A PL +L +++ N+ VL+ + ++ G ++ +D H N+VL+N +E+ + G+
Sbjct: 2 AQRPLDVLNNAL--NSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEI-----QDGEVV 54
Query: 77 KKSKPVNKDRFISKMFLRGDSVILI 101
+K + K+ +RGD+V+ +
Sbjct: 55 RK---------LGKVVIRGDNVVYV 70
>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 = 35.7 bits (83), Expect = 3e-04
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 46 GRVKAFDRHCNMVLENVKEMWTE 68
G + AFD+H N+ L +V E WT
Sbjct: 27 GYLVAFDKHWNLALVDVDETWTR 49
>gnl|CDD|185472 PTZ00138, PTZ00138, small nuclear ribonucleoprotein; Provisional.
Length = 89
Score = 34.3 bits (79), Expect = 0.002
Identities = 17/61 (27%), Positives = 36/61 (59%), Gaps = 13/61 (21%)
Query: 41 NKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVIL 100
N ++ G++ FD + NMVL++ +E++T KK ++ + + ++ L+GD++ L
Sbjct: 38 NLRIEGKILGFDEYMNMVLDDAEEVYT--------KKNTR-----KDLGRILLKGDNITL 84
Query: 101 I 101
I
Sbjct: 85 I 85
>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 = 34.1 bits (79), Expect = 0.002
Identities = 18/71 (25%), Positives = 41/71 (57%), Gaps = 11/71 (15%)
Query: 31 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISK 90
+++ I +++K+ +G + FD + NMVLE+V TE+ +G+K +K + +
Sbjct: 13 GSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDV----TEYEITPEGRKITK-------LDQ 61
Query: 91 MFLRGDSVILI 101
+ L G+++ ++
Sbjct: 62 ILLNGNNIAML 72
>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 = 33.6 bits (78), Expect = 0.003
Identities = 19/69 (27%), Positives = 37/69 (53%), Gaps = 11/69 (15%)
Query: 33 QVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMF 92
++L+ R+ +KL+G +++FD+ N+VLE+ E R G + D
Sbjct: 14 KILVVLRDGRKLIGILRSFDQFANLVLEDTVE------RIIVGNQYG-----DIPRGLFI 62
Query: 93 LRGDSVILI 101
+RG++V+L+
Sbjct: 63 IRGENVVLL 71
>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 = 32.1 bits (74), Expect = 0.012
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 44 LLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVI 99
+G AFD+H N+VL + +E P K KKK + + R + + LRG++V+
Sbjct: 23 FVGTFLAFDKHMNLVLSDCEEFRKIKP---KKKKKGEEREEKRVLGLVLLRGENVV 75
>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 = 29.1 bits (66), Expect = 0.15
Identities = 20/81 (24%), Positives = 36/81 (44%), Gaps = 19/81 (23%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 79
PLS+L + VL+ +N + G + D N+ L+NV S
Sbjct: 2 PLSLLRTA--QGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICT-------------S 46
Query: 80 KPVNKDRF--ISKMFLRGDSV 98
K + DRF + + ++RG+++
Sbjct: 47 K--DGDRFWKMPECYIRGNTI 65
>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 = 27.5 bits (62), Expect = 0.54
Identities = 6/34 (17%), Positives = 11/34 (32%)
Query: 30 HNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVK 63
+ RN + G + D N+ L +
Sbjct: 18 QGRVTTVELRNETSVRGIIDNVDGFMNITLSDAT 51
>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 = 27.2 bits (61), Expect = 0.74
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 46 GRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILI 101
G +K +D+ N+VL++ E + + K ++ R + + RG SV+LI
Sbjct: 27 GILKGYDQLLNLVLDDTVEYLRDP------EDPYKLTDETRSLGLVVCRGTSVVLI 76
>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 = 26.8 bits (60), Expect = 0.92
Identities = 10/47 (21%), Positives = 19/47 (40%), Gaps = 6/47 (12%)
Query: 31 NTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMW------TEHPR 71
+ + + + L+G D+ N++L N +E E PR
Sbjct: 9 GRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLGAEEPR 55
>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 = 25.9 bits (58), Expect = 1.6
Identities = 18/82 (21%), Positives = 32/82 (39%), Gaps = 16/82 (19%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKS 79
P L V++ +N + G + D + N+VLE+ +E
Sbjct: 2 PSKFLKKI--IGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEY-----------VDG 48
Query: 80 KPVNKDRFISKMFLRGDSVILI 101
+ V K F+RG++V+ I
Sbjct: 49 QLVAK---YGDAFIRGNNVLYI 67
>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 = 26.0 bits (58), Expect = 2.3
Identities = 15/69 (21%), Positives = 36/69 (52%), Gaps = 13/69 (18%)
Query: 33 QVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMF 92
Q+ + + + ++ G++ FD + N+VL++ +E+ + KP+ ++
Sbjct: 22 QIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLK-------TNTRKPLG------RIL 68
Query: 93 LRGDSVILI 101
L+GD++ LI
Sbjct: 69 LKGDNITLI 77
>gnl|CDD|234031 TIGR02840, spore_YtaF, putative sporulation protein YtaF. This
protein family was identified, at the time of the
publication of the Carboxydothermus hydrogenoformans
genome, as having a phylogenetic profile that exactly
matches the subset of the Firmicutes capable of forming
endospores. The species include Bacillus anthracis,
Clostridium tetani, Thermoanaerobacter tengcongensis,
Geobacillus kaustophilus, etc. This protein, previously
named YtaF, is therefore a putative sporulation protein
[Cellular processes, Sporulation and germination].
Length = 206
Score = 26.5 bits (59), Expect = 3.0
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 74 KGKKKSKPVNKDRFISKMFLRGDSVILILKNP 105
+ KK+ K + + +K VI IL+NP
Sbjct: 84 RPKKEVKDRSSEPDSTKELKSFGFVIQILRNP 115
>gnl|CDD|198185 cd09931, SH2_C-SH2_SHP_like, C-terminal Src homology 2 (C-SH2)
domain found in SH2 domain Phosphatases (SHP) proteins.
The SH2 domain phosphatases (SHP-1, SHP-2/Syp,
Drosophila corkscrew (csw), and Caenorhabditis elegans
Protein Tyrosine Phosphatase (Ptp-2)) are cytoplasmic
signaling enzymes. They are both targeted and regulated
by interactions of their SH2 domains with
phosphotyrosine docking sites. These proteins contain
two SH2 domains (N-SH2, C-SH2) followed by a tyrosine
phosphatase (PTP) domain, and a C-terminal extension.
Shp1 and Shp2 have two tyrosyl phosphorylation sites in
their C-tails, which are phosphorylated differentially
by receptor and nonreceptor PTKs. Csw retains the
proximal tyrosine and Ptp-2 lacks both sites.
Shp-binding proteins include receptors, scaffolding
adapters, and inhibitory receptors. Some of these bind
both Shp1 and Shp2 while others bind only one. Most
proteins that bind a Shp SH2 domain contain one or more
immuno-receptor tyrosine-based inhibitory motifs
(ITIMs): [SIVL]xpYxx[IVL]. Shp1 N-SH2 domain blocks
the catalytic domain and keeps the enzyme in the
inactive conformation, and is thus believed to regulate
the phosphatase activity of SHP-1. Its C-SH2 domain is
thought to be involved in searching for phosphotyrosine
activators. The SHP2 N-SH2 domain is a conformational
switch; it either binds and inhibits the phosphatase,
or it binds phosphoproteins and activates the enzyme.
The C-SH2 domain contributes binding energy and
specificity, but it does not have a direct role in
activation. Csw SH2 domain function is essential, but
either SH2 domain can fulfill this requirement. The
role of the csw SH2 domains during Sevenless receptor
tyrosine kinase (SEV) signaling is to bind Daughter of
Sevenless rather than activated SEV. Ptp-2 acts in
oocytes downstream of sheath/oocyte gap junctions to
promote major sperm protein (MSP)-induced MAP Kinase
(MPK-1) phosphorylation. Ptp-2 functions in the oocyte
cytoplasm, not at the cell surface to inhibit multiple
RasGAPs, resulting in sustained Ras activation. It is
thought that MSP triggers PTP-2/Ras activation and ROS
production to stimulate MPK-1 activity essential for
oocyte maturation and that secreted MSP domains and
Cu/Zn superoxide dismutases function antagonistically
to control ROS and MAPK signaling. In general SH2
domains are involved in signal transduction. They
typically bind pTyr-containing ligands via two surface
pockets, a pTyr and hydrophobic binding pocket,
allowing proteins with SH2 domains to localize to
tyrosine phosphorylated sites.
Length = 99
Score = 25.3 bits (56), Expect = 5.0
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 6/50 (12%)
Query: 21 LSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEHP 70
LS+ TD K T ++I C+ K +G + FD L ++ E + ++P
Sbjct: 39 LSVRTDDDK-VTHIMIRCQGGKYDVGGGEEFDS-----LTDLVEHYKKNP 82
>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 = 24.4 bits (53), Expect = 6.7
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 14/60 (23%)
Query: 42 KKLLGRVKAFDRHCNMVLENVKEMWTEHPRAGKGKKKSKPVNKDRFISKMFLRGDSVILI 101
+L GR+ A D + N+ L + E G+ K R + + LRG++++LI
Sbjct: 22 NQLQGRLVAVDDYMNLHLTDTMEC--------VGE------EKVRSLGTVVLRGNNILLI 67
>gnl|CDD|220419 pfam09814, DUF2351, Uncharacterized conserved protein (DUF2351).
Members of this family of proteins have no known
function.
Length = 350
Score = 25.2 bits (55), Expect = 8.5
Identities = 21/105 (20%), Positives = 36/105 (34%), Gaps = 19/105 (18%)
Query: 11 EEEESFATGPLSILTDSVKHNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEM---WT 67
+ P S +K + C+N ++ + + FDR ++ EN E+ W
Sbjct: 84 LRTSNDPDVPWS--AKDLKKEPCFTLYCQNCGGVIIKSRNFDRVLDLPSENWAELMDFWH 141
Query: 68 EHP--------RAGKGKKKSKPVNKDRFISKMFLRGDSVILILKN 104
H K KP D + GD+ L+ K+
Sbjct: 142 CHKPPFAEAHKDDTPAKNSLKPTEGDLLV------GDTYFLVNKS 180
>gnl|CDD|223858 COG0787, Alr, Alanine racemase [Cell envelope biogenesis, outer
membrane].
Length = 360
Score = 25.2 bits (56), Expect = 8.6
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 21 LSILTDSVKHNTQVLINCRNNKKLLGRVKA 50
I +++HN + L KL+ VKA
Sbjct: 7 AEIDLGALRHNLRALRELAGPAKLMAVVKA 36
>gnl|CDD|100095 cd05802, GlmM, GlmM is a bacterial phosphoglucosamine mutase (PNGM)
that belongs to the alpha-D-phosphohexomutase
superfamily. It is required for the interconversion of
glucosamine-6-phosphate and glucosamine-1-phosphate in
the biosynthetic pathway of UDP-N-acetylglucosamine, an
essential precursor to components of the cell envelope.
In order to be active, GlmM must be phosphorylated,
which can occur via autophosphorylation or by the
Ser/Thr kinase StkP. GlmM functions in a classical
ping-pong bi-bi mechanism with
glucosamine-1,6-diphosphate as an intermediate. Other
members of the alpha-D-phosphohexomutase superfamily
include phosphoglucosamine mutase (PNGM),
phosphoacetylglucosamine mutase (PAGM), the bacterial
phosphomannomutase ManB, and the bifunctional
phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of
these enzymes has four domains with a centrally located
active site formed by four loops, one from each domain.
All four domains are included in this alignment model.
Length = 434
Score = 25.1 bits (56), Expect = 9.8
Identities = 10/24 (41%), Positives = 12/24 (50%)
Query: 20 PLSILTDSVKHNTQVLINCRNNKK 43
LS L +K QVL+N R K
Sbjct: 354 SLSELASDMKLYPQVLVNVRVKDK 377
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
0.316 0.132 0.377
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: 5,351,006
Number of extensions: 432036
Number of successful extensions: 332
Number of sequences better than 10.0: 1
Number of HSP's gapped: 323
Number of HSP's successfully gapped: 29
Length of query: 110
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 36
Effective length of database: 7,655,406
Effective search space: 275594616
Effective search space used: 275594616
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)