RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15782
(129 letters)
>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 = 176 bits (448), Expect = 8e-59
Identities = 64/88 (72%), Positives = 78/88 (88%)
Query: 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
+ FLMKLS+ETVTIELKNGT VHGTI GVDV+MNTHLK VK+T+KGK P +LD++S+RGN
Sbjct: 3 VRFLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLKGKNPVSLDTLSIRGN 62
Query: 61 NIRYYILPDSLPLETLLIDDAPRSKGKR 88
NIRY ILPDSL L+TLL+DD P++K K+
Sbjct: 63 NIRYIILPDSLNLDTLLVDDTPKAKAKK 90
>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 = 76.8 bits (190), Expect = 5e-20
Identities = 27/66 (40%), Positives = 38/66 (57%)
Query: 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNN 61
FL KL + VT+ELKNG ++ GT++G D MN L V+ T+K + L + +RGNN
Sbjct: 1 KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNN 60
Query: 62 IRYYIL 67
I
Sbjct: 61 IVLISP 66
>gnl|CDD|197820 smart00651, Sm, snRNP Sm proteins. small nuclear
ribonucleoprotein particles (snRNPs) involved in
pre-mRNA splicing.
Length = 67
Score = 74.1 bits (183), Expect = 7e-19
Identities = 31/67 (46%), Positives = 42/67 (62%), Gaps = 1/67 (1%)
Query: 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK-GKEPTTLDSISLRGN 60
FL KL + V +ELKNG + GT++G D MN L+ V+ TVK G++ L + +RGN
Sbjct: 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGN 60
Query: 61 NIRYYIL 67
NI Y IL
Sbjct: 61 NIVYIIL 67
>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 = 63.7 bits (156), Expect = 1e-14
Identities = 26/68 (38%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 6 KLSHE----TVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNN 61
KL HE VT+ELK G G + + MN LK V +T + + + L+ + +RG+
Sbjct: 3 KLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGKVSKLEQVYIRGSQ 62
Query: 62 IRYYILPD 69
IR+ ILPD
Sbjct: 63 IRFIILPD 70
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 61.2 bits (149), Expect = 1e-13
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 4/71 (5%)
Query: 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTT----LDSIS 56
++FL KL ++ V ++LKNG + GT+ G D MN L V+ + +
Sbjct: 9 LSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGEVL 68
Query: 57 LRGNNIRYYIL 67
+RG+NI
Sbjct: 69 IRGDNIVLISP 79
>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 = 59.2 bits (144), Expect = 5e-13
Identities = 20/63 (31%), Positives = 31/63 (49%)
Query: 4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIR 63
L +TV++ELK+G + GT+ D MN L V T + + L + +RG+NI
Sbjct: 1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIV 60
Query: 64 YYI 66
Sbjct: 61 SIR 63
>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 = 53.0 bits (128), Expect = 2e-10
Identities = 25/61 (40%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 12 VTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVK-GKEPTTLDSISLRGNNIRYYILPDS 70
V +ELKNG +G + D MN HLK V T K G + +RGN I+Y LPD
Sbjct: 14 VLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIRGNTIKYLRLPDE 73
Query: 71 L 71
+
Sbjct: 74 V 74
>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 = 51.8 bits (125), Expect = 6e-10
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 12 VTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEP--TTLDSISLRGNNIRYYILPD 69
VT+ELKN + GT+ VD +N L + + K P ++ + +RG+ +RY LP
Sbjct: 14 VTVELKNDLSITGTLHSVDQYLNIKLTNISVNDPEKYPHLLSVKNCFIRGSVVRYVQLPA 73
Query: 70 SLPLETLLIDDAPR 83
++T L+ DA R
Sbjct: 74 D-EVDTELLQDATR 86
>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 = 49.8 bits (120), Expect = 3e-09
Identities = 22/55 (40%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 11 TVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMT-VKGKEPTTLDSISLRGNNIRY 64
T+EL+N T V G I VD MN L T +GK+ D ++G NIRY
Sbjct: 21 VTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQ-HHFDEFFVQGRNIRY 74
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional.
Length = 293
Score = 52.0 bits (125), Expect = 5e-09
Identities = 25/41 (60%), Positives = 25/41 (60%)
Query: 85 KGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
G R RGGG GG RG GGRGG GG GRGRGG G G
Sbjct: 7 GGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRG 47
Score = 47.4 bits (113), Expect = 3e-07
Identities = 19/42 (45%), Positives = 19/42 (45%)
Query: 86 GKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPP 127
G G G G GG G GG GGRG G RGRGG
Sbjct: 2 MGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGG 43
Score = 46.6 bits (111), Expect = 5e-07
Identities = 24/43 (55%), Positives = 24/43 (55%)
Query: 83 RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
R G R GGG GG RG G GRGGG GGRG GG G G
Sbjct: 14 RGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56
Score = 46.3 bits (110), Expect = 7e-07
Identities = 24/39 (61%), Positives = 24/39 (61%)
Query: 91 RRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
GGG GG RG G GG GGGRGG GRGG RG G R
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGR 39
Score = 45.9 bits (109), Expect = 9e-07
Identities = 24/38 (63%), Positives = 24/38 (63%)
Query: 92 RGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
GGG GG RG GG GGRGGG G GRGG RGRG
Sbjct: 6 FGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGG 43
Score = 45.5 bits (108), Expect = 1e-06
Identities = 21/43 (48%), Positives = 21/43 (48%)
Query: 83 RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
G R GG GG G G GGRGGGRGG G G GG
Sbjct: 2 MGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGG 44
Score = 44.3 bits (105), Expect = 3e-06
Identities = 20/44 (45%), Positives = 20/44 (45%)
Query: 86 GKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
G R GGG GG GGRGG G G G GG G GG
Sbjct: 12 GGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPG 55
Score = 42.4 bits (100), Expect = 1e-05
Identities = 22/46 (47%), Positives = 22/46 (47%)
Query: 83 RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPR 128
G RGGG GG G G GG GG G GRG RG GG R
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGR 46
Score = 38.6 bits (90), Expect = 3e-04
Identities = 17/38 (44%), Positives = 18/38 (47%)
Query: 82 PRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGG 119
+G G G G RGRGG GG GG GG G G
Sbjct: 19 GGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56
Score = 37.8 bits (88), Expect = 5e-04
Identities = 19/40 (47%), Positives = 21/40 (52%)
Query: 82 PRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPR 121
G+ RGGG GG RGRG GG GG GG G G +
Sbjct: 17 GGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56
>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 = 41.4 bits (98), Expect = 4e-06
Identities = 21/63 (33%), Positives = 32/63 (50%)
Query: 2 NFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNN 61
FL L+ + V ++LK G + GT+ VD MN L + + GK L + +R NN
Sbjct: 4 PFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIRCNN 63
Query: 62 IRY 64
+ Y
Sbjct: 64 VLY 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 = 38.7 bits (91), Expect = 4e-05
Identities = 20/64 (31%), Positives = 32/64 (50%)
Query: 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGN 60
FL K+ + V ++LKNG + G + +D MN L+ + V G+ +RGN
Sbjct: 3 SKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIRGN 62
Query: 61 NIRY 64
N+ Y
Sbjct: 63 NVLY 66
>gnl|CDD|236941 PRK11634, PRK11634, ATP-dependent RNA helicase DeaD; Provisional.
Length = 629
Score = 40.6 bits (95), Expect = 6e-05
Identities = 21/70 (30%), Positives = 26/70 (37%), Gaps = 12/70 (17%)
Query: 72 PLETLLIDDA-PRSKGKR--------DSRRGGG---AGGARGRGGRGGRGGGRGGRGRGG 119
P+ L+ DA P + G+R RR GG +G R G GR R
Sbjct: 554 PMNMQLLGDAQPHTGGERRGGGRGFGGERREGGRNFSGERREGGRGDGRRFSGERREGRA 613
Query: 120 PRGRGGPPRR 129
PR RR
Sbjct: 614 PRRDDSTGRR 623
>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 = 37.6 bits (88), Expect = 1e-04
Identities = 15/52 (28%), Positives = 31/52 (59%)
Query: 11 TVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
V ++LK G +V G ++G D +N L+ + ++G+ L ++ +RG+N+
Sbjct: 13 NVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVRGDNV 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 = 36.7 bits (85), Expect = 3e-04
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 12 VTIELK-NGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
+ +E+K + Q+ G + VD MN HL V ++ +L ++ LRGNNI
Sbjct: 13 IRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLRGNNI 64
>gnl|CDD|218811 pfam05918, API5, Apoptosis inhibitory protein 5 (API5). This
family consists of apoptosis inhibitory protein 5 (API5)
sequences from several organisms. Apoptosis or
programmed cell death is a physiological form of cell
death that occurs in embryonic development and organ
formation. It is characterized by biochemical and
morphological changes such as DNA fragmentation and cell
volume shrinkage. API5 is an anti apoptosis gene located
in human chromosome 11, whose expression prevents the
programmed cell death that occurs upon the deprivation
of growth factors.
Length = 543
Score = 38.5 bits (89), Expect = 4e-04
Identities = 17/44 (38%), Positives = 20/44 (45%), Gaps = 8/44 (18%)
Query: 82 PRSKGKRDSRRGGGAGGARGRG-GRGGRGGGRGGRGRGGPRGRG 124
+G + G + G RGR GRG GGG GRG RG
Sbjct: 505 KSGEG---ISKVGQSYGGRGRTRGRGRGGGG----GRGRGYNRG 541
Score = 25.8 bits (56), Expect = 9.8
Identities = 10/22 (45%), Positives = 11/22 (50%)
Query: 104 GRGGRGGGRGGRGRGGPRGRGG 125
G G G+ GRG RGRG
Sbjct: 507 GEGISKVGQSYGGRGRTRGRGR 528
>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 = 35.7 bits (83), Expect = 7e-04
Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 14 IELKNGTQVHGTIQGVDVAMNTHLKTVK---MTVKGKEPTTLDSISLRGNNI 62
I +K+ + GT+ G D +N L+ V +T +G++ T LD I L GNNI
Sbjct: 18 IIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKITKLDQILLNGNNI 69
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 37.5 bits (87), Expect = 8e-04
Identities = 13/42 (30%), Positives = 16/42 (38%)
Query: 88 RDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
R R GGG G GRG + G+ G + P R
Sbjct: 391 RQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSR 432
Score = 33.2 bits (76), Expect = 0.022
Identities = 12/37 (32%), Positives = 15/37 (40%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
G G GRG GGRG +G RG + +
Sbjct: 390 GRQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKP 426
Score = 30.5 bits (69), Expect = 0.18
Identities = 11/52 (21%), Positives = 18/52 (34%)
Query: 78 IDDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
I + + +G +GGG G +G+ RG G R +
Sbjct: 387 IQNGRQQRGGGGRGQGGGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAK 438
Score = 30.5 bits (69), Expect = 0.19
Identities = 10/48 (20%), Positives = 15/48 (31%)
Query: 82 PRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
R + + RRG G + G G + R PR+
Sbjct: 404 GRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGDAKPAGEQQRRRRPRK 451
>gnl|CDD|179104 PRK00737, PRK00737, small nuclear ribonucleoprotein; Provisional.
Length = 72
Score = 35.0 bits (81), Expect = 0.001
Identities = 17/53 (32%), Positives = 27/53 (50%)
Query: 12 VTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNIRY 64
V + LK G + G +QG D+ MN L + G+ L + +RG+N+ Y
Sbjct: 17 VLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVY 69
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 36.9 bits (85), Expect = 0.001
Identities = 19/41 (46%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 89 DSRRGGG--AGGARGRGGRGGRGGGRGGRGR-GGPRGRGGP 126
+ RRGGG G R G G GG R G G G PR R P
Sbjct: 429 EQRRGGGRSGPGGGSRSGSVGGGGRRDGAGADGKPRPRRKP 469
Score = 31.8 bits (72), Expect = 0.085
Identities = 17/46 (36%), Positives = 18/46 (39%), Gaps = 1/46 (2%)
Query: 83 RSKGKRDSRRGGGAGGARGRGGRG-GRGGGRGGRGRGGPRGRGGPP 127
R G R GG G+ G GGR G G R R PR G
Sbjct: 431 RRGGGRSGPGGGSRSGSVGGGGRRDGAGADGKPRPRRKPRVEGEAD 476
Score = 31.1 bits (70), Expect = 0.12
Identities = 15/34 (44%), Positives = 15/34 (44%), Gaps = 4/34 (11%)
Query: 100 RGRGGRGGRGGGRGGRGRGGPRGRG----GPPRR 129
RG G G GG R G GG R G G PR
Sbjct: 432 RGGGRSGPGGGSRSGSVGGGGRRDGAGADGKPRP 465
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 34.9 bits (81), Expect = 0.006
Identities = 14/45 (31%), Positives = 18/45 (40%)
Query: 80 DAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRG 124
D R +G R+ R+ G RGR GR G R +G
Sbjct: 170 DERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDR 214
Score = 32.2 bits (74), Expect = 0.050
Identities = 16/51 (31%), Positives = 17/51 (33%), Gaps = 4/51 (7%)
Query: 83 RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGR----GGPRGRGGPPRR 129
R + G R GRGG RG R R G RG G R
Sbjct: 233 RDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNER 283
Score = 31.4 bits (72), Expect = 0.10
Identities = 14/50 (28%), Positives = 16/50 (32%)
Query: 80 DAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
+A +R RG RG RGR RGR G R
Sbjct: 155 EARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRD 204
Score = 31.0 bits (71), Expect = 0.16
Identities = 10/51 (19%), Positives = 13/51 (25%)
Query: 79 DDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
+ + + R G R G RG R G G R
Sbjct: 157 RADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRD 207
Score = 29.5 bits (67), Expect = 0.43
Identities = 13/41 (31%), Positives = 15/41 (36%)
Query: 83 RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGR 123
R + +R RR R G G G GR G R R
Sbjct: 227 RGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFR 267
Score = 29.5 bits (67), Expect = 0.51
Identities = 15/51 (29%), Positives = 16/51 (31%)
Query: 79 DDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
DA + D G G G RG R R RGR G G
Sbjct: 236 RDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNEREPE 286
Score = 29.1 bits (66), Expect = 0.56
Identities = 19/46 (41%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 86 GKRDSRRGGGAGGARGRGGRGGRGGGRG--GRGRGGPRGRGGPPRR 129
+R RR ARG R RG G G GRGG RGR R
Sbjct: 225 DRRGRRRRRDRRDARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRD 270
Score = 29.1 bits (66), Expect = 0.65
Identities = 12/51 (23%), Positives = 16/51 (31%)
Query: 79 DDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
++ + +R R A RG GR G G R G R
Sbjct: 166 EEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRRE 216
Score = 29.1 bits (66), Expect = 0.67
Identities = 10/51 (19%), Positives = 12/51 (23%)
Query: 79 DDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
A ++ R R R G RG G R G
Sbjct: 151 QPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGD 201
Score = 27.9 bits (63), Expect = 1.8
Identities = 13/51 (25%), Positives = 16/51 (31%)
Query: 79 DDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
D + +R+ G R G R GR R R G R R
Sbjct: 200 GDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDRGDR 250
Score = 26.0 bits (58), Expect = 7.2
Identities = 12/47 (25%), Positives = 15/47 (31%), Gaps = 1/47 (2%)
Query: 80 DAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRG-GRGRGGPRGRGG 125
+ R + G G R GR G R R +G R G
Sbjct: 173 RRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERG 219
Score = 25.6 bits (57), Expect = 8.2
Identities = 15/51 (29%), Positives = 17/51 (33%)
Query: 79 DDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
++ R R G G GR GR R R GR G P R
Sbjct: 238 ARGDDNREDRGDRDGDDGEGRGGRRGRRFRDRDRRGRRGGDGGNEREPELR 288
>gnl|CDD|236092 PRK07772, PRK07772, single-stranded DNA-binding protein;
Provisional.
Length = 186
Score = 34.6 bits (80), Expect = 0.006
Identities = 22/41 (53%), Positives = 23/41 (56%)
Query: 88 RDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPR 128
R SR GGG GG G GG GG GG GG G GG GG +
Sbjct: 119 RASRGGGGGGGGGGFGGGGGGSGGGGGGGGGGGAPGGGGAQ 159
Score = 29.6 bits (67), Expect = 0.37
Identities = 20/47 (42%), Positives = 21/47 (44%), Gaps = 3/47 (6%)
Query: 81 APRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPP 127
A R G GGG GG G G GG GGG GG GG + P
Sbjct: 120 ASRGGGGGGG--GGGFGGG-GGGSGGGGGGGGGGGAPGGGGAQASAP 163
>gnl|CDD|221759 pfam12764, Gly-rich_Ago1, Glycine-rich region of argonaut. This
domain is often found at the very N-terminal of
argonaut-like proteins.
Length = 102
Score = 32.6 bits (74), Expect = 0.016
Identities = 16/32 (50%), Positives = 17/32 (53%)
Query: 98 GARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
RGRGG +GG GG G G GGPPR
Sbjct: 7 QGRGRGGPPQQGGRGGGGGGRGGGSTGGPPRP 38
Score = 30.3 bits (68), Expect = 0.11
Identities = 19/34 (55%), Positives = 20/34 (58%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGP 126
G G GG +GGRGG GGGRGG GGP P
Sbjct: 8 GRGRGGPPQQGGRGGGGGGRGGGSTGGPPRPSVP 41
>gnl|CDD|240255 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provisional.
Length = 257
Score = 33.5 bits (77), Expect = 0.017
Identities = 20/31 (64%), Positives = 20/31 (64%)
Query: 96 AGGARGRGGRGGRGGGRGGRGRGGPRGRGGP 126
A ARG GRG GRGGRGRG RGRGG
Sbjct: 1 AAAARGGEGRGFGRRGRGGRGRGRGRGRGGE 31
Score = 32.7 bits (75), Expect = 0.027
Identities = 15/25 (60%), Positives = 15/25 (60%)
Query: 94 GGAGGARGRGGRGGRGGGRGGRGRG 118
GG G GR GRGGRG GRG G
Sbjct: 6 GGEGRGFGRRGRGGRGRGRGRGRGG 30
Score = 28.5 bits (64), Expect = 0.82
Identities = 12/24 (50%), Positives = 12/24 (50%)
Query: 91 RRGGGAGGARGRGGRGGRGGGRGG 114
RG G G GRG GRG G G
Sbjct: 9 GRGFGRRGRGGRGRGRGRGRGGEG 32
Score = 28.5 bits (64), Expect = 0.86
Identities = 15/26 (57%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 104 GRGGRGGGRGGRG-RGGPRGRGGPPR 128
G GRG GR GRG RG RGRG
Sbjct: 6 GGEGRGFGRRGRGGRGRGRGRGRGGE 31
Score = 27.3 bits (61), Expect = 2.1
Identities = 20/29 (68%), Positives = 21/29 (72%), Gaps = 2/29 (6%)
Query: 90 SRRGGGAG-GARGRGGRG-GRGGGRGGRG 116
+R G G G G RGRGGRG GRG GRGG G
Sbjct: 4 ARGGEGRGFGRRGRGGRGRGRGRGRGGEG 32
>gnl|CDD|218425 pfam05091, eIF-3_zeta, Eukaryotic translation initiation factor 3
subunit 7 (eIF-3). This family is made up of eukaryotic
translation initiation factor 3 subunit 7 (eIF-3
zeta/eIF3 p66/eIF3d). Eukaryotic initiation factor 3 is
a multi-subunit complex that is required for binding of
mRNA to 40 S ribosomal subunits, stabilisation of
ternary complex binding to 40 S subunits, and
dissociation of 40 and 60 S subunits. These functions
and the complex nature of eIF3 suggest multiple
interactions with many components of the translational
machinery. The gene coding for the protein has been
implicated in cancer in mammals.
Length = 517
Score = 33.4 bits (77), Expect = 0.018
Identities = 19/55 (34%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 77 LIDDAPRSK------GKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
L+DD R K GKR R RG+G +G RG RGG R +
Sbjct: 79 LVDDRSRLKARTTKHGKRKRRGKQTRTQRRGQGPQGKRGMTSRRAKRGGQRKQKR 133
Score = 30.4 bits (69), Expect = 0.25
Identities = 23/53 (43%), Positives = 23/53 (43%), Gaps = 5/53 (9%)
Query: 82 PRSKGKRDSRRGGGAGGARG----RGGRGG-RGGGRGGRGRGGPRGRGGPPRR 129
R K R RRG G G RG R RGG R R GRGG RG R
Sbjct: 98 RRGKQTRTQRRGQGPQGKRGMTSRRAKRGGQRKQKRFQTGRGGRRGARHRRLR 150
>gnl|CDD|224429 COG1512, COG1512, Beta-propeller domains of methanol dehydrogenase
type [General function prediction only].
Length = 271
Score = 33.5 bits (77), Expect = 0.018
Identities = 16/35 (45%), Positives = 18/35 (51%)
Query: 91 RRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
RR G+GG+ G GG GG GG G G G G
Sbjct: 235 RRSSGSGGSGGSGGGSSGGGFSGGGGSSGGGGASG 269
Score = 29.2 bits (66), Expect = 0.53
Identities = 16/38 (42%), Positives = 16/38 (42%)
Query: 88 RDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
D G G R G GG GG GG GG G GG
Sbjct: 223 PDRWLNGVLGRRRRSSGSGGSGGSGGGSSGGGFSGGGG 260
Score = 29.2 bits (66), Expect = 0.53
Identities = 15/34 (44%), Positives = 17/34 (50%)
Query: 92 RGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
R + G+ G GG GG G G G GG G GG
Sbjct: 233 RRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGGGG 266
Score = 28.9 bits (65), Expect = 0.73
Identities = 16/38 (42%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 86 GKRDSRRGGGAGGARGRGGRGG--RGGGR--GGRGRGG 119
G+R G G G G G GG GGG GG G G
Sbjct: 232 GRRRRSSGSGGSGGSGGGSSGGGFSGGGGSSGGGGASG 269
Score = 28.1 bits (63), Expect = 1.1
Identities = 14/35 (40%), Positives = 14/35 (40%)
Query: 83 RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGR 117
RS G S GG G G GG GG G G
Sbjct: 236 RSSGSGGSGGSGGGSSGGGFSGGGGSSGGGGASGS 270
>gnl|CDD|220915 pfam10961, DUF2763, Protein of unknown function (DUF2763). This
eukaryotic family of proteins has no known function.
Length = 91
Score = 32.0 bits (73), Expect = 0.023
Identities = 18/43 (41%), Positives = 19/43 (44%)
Query: 87 KRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
R + G R GGRGG G GGR G G GGP R
Sbjct: 44 VTKRYRKNSSSGKRWDGGRGGPGPPGGGRRMGRIGGGGGPSRP 86
Score = 27.0 bits (60), Expect = 1.5
Identities = 15/46 (32%), Positives = 15/46 (32%)
Query: 80 DAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
R R GG GG GG G GG G P GG
Sbjct: 46 KRYRKNSSSGKRWDGGRGGPGPPGGGRRMGRIGGGGGPSRPPMAGG 91
>gnl|CDD|234276 TIGR03601, B_an_ocin, probable heterocycle-containing bacteriocin,
BA_2677 family. Numerous bacteria encode systems for
producing bacteriocins by extensive modification of
ribosomally produced precursors. These proteins are
recognizable in part by proximity to the modification
proteins, and in part by small size, with leader
peptide-like N-terminal sequence followed by
low-complexity sequence rich in Cys, Gly, and/or Ser.
This protein family represents a probable member of the
class, though previously unrecognized because it is not
encoded adjacent to its modification proteins [Cellular
processes, Toxin production and resistance].
Length = 79
Score = 31.5 bits (71), Expect = 0.033
Identities = 15/26 (57%), Positives = 16/26 (61%)
Query: 89 DSRRGGGAGGARGRGGRGGRGGGRGG 114
D+RR GG GG GGR G GGR G
Sbjct: 38 DARRCGGCGGGGCCGGRCGGCGGRCG 63
Score = 25.7 bits (56), Expect = 3.2
Identities = 12/28 (42%), Positives = 12/28 (42%)
Query: 97 GGARGRGGRGGRGGGRGGRGRGGPRGRG 124
AR GG GG G G G G R G
Sbjct: 37 DDARRCGGCGGGGCCGGRCGGCGGRCGG 64
>gnl|CDD|184923 PRK14959, PRK14959, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 624
Score = 32.7 bits (74), Expect = 0.044
Identities = 19/62 (30%), Positives = 23/62 (37%), Gaps = 4/62 (6%)
Query: 67 LPDSLPLETLLIDDA--PRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRG 124
L ++ LE LL++ A PR R GG A G G GG G
Sbjct: 346 LEPAMALELLLLNLAMLPRLMPVESLRPSGGGASAPS--GSAAEGPASGGAATIPTPGTQ 403
Query: 125 GP 126
GP
Sbjct: 404 GP 405
>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein;
Provisional.
Length = 182
Score = 32.1 bits (73), Expect = 0.048
Identities = 19/40 (47%), Positives = 19/40 (47%)
Query: 86 GKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
G R GGG GG G G GG GGG G G G GG
Sbjct: 109 GGRGGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGG 148
Score = 31.7 bits (72), Expect = 0.056
Identities = 19/42 (45%), Positives = 19/42 (45%)
Query: 86 GKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPP 127
G GGG GG GG GGR G GG G GG R P
Sbjct: 127 GGGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGGASRPSAP 168
Score = 31.3 bits (71), Expect = 0.082
Identities = 18/37 (48%), Positives = 18/37 (48%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
GGG GG G GG GGG G GG G GG R
Sbjct: 128 GGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGGASR 164
Score = 31.3 bits (71), Expect = 0.095
Identities = 18/44 (40%), Positives = 19/44 (43%)
Query: 86 GKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
G + GGG GG G G R GG GGR GG G G
Sbjct: 120 GGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGGAS 163
Score = 30.9 bits (70), Expect = 0.11
Identities = 15/42 (35%), Positives = 16/42 (38%)
Query: 86 GKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPP 127
G GG G +R GG G GG GG GG P
Sbjct: 128 GGGGGGGGGYGGESRSGGGGGRASGGGGGGAGGGASRPSAPA 169
Score = 29.0 bits (65), Expect = 0.61
Identities = 18/37 (48%), Positives = 18/37 (48%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
GG GG GG GG GGG GG G R GG R
Sbjct: 114 SGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRA 150
Score = 27.8 bits (62), Expect = 1.3
Identities = 16/32 (50%), Positives = 16/32 (50%)
Query: 98 GARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
G RG G GG GG GG G GG G GG
Sbjct: 109 GGRGGSGGGGGGGDEGGYGGGGGGGGGGYGGE 140
Score = 25.5 bits (56), Expect = 7.8
Identities = 12/42 (28%), Positives = 12/42 (28%)
Query: 83 RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRG 124
G GG G GG G G G P G G
Sbjct: 131 GGGGGGYGGESRSGGGGGRASGGGGGGAGGGASRPSAPAGGG 172
>gnl|CDD|212463 cd01716, Hfq, bacterial Hfq-like. Hfq, an abundant, ubiquitous
RNA-binding protein, functions as a pleiotropic
regulator of RNA metabolism in prokaryotes, required
for transcription of some transcripts and degradation
of others. Hfq binds small RNA molecules called
riboregulators that modulate the stability or
translation efficiency of RNA transcripts. Hfq binds
preferentially to unstructured A/U-rich RNA sequences
and is similar to the eukaryotic Sm proteins in both
sequence and structure. Hfq forms a homo-hexameric ring
similar to the heptameric ring of the Sm proteins.
Length = 60
Score = 30.2 bits (69), Expect = 0.049
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 3/28 (10%)
Query: 12 VTIELKNGTQVHGTIQGVD---VAMNTH 36
VTI L NG ++ G I+ D V + +
Sbjct: 17 VTIYLVNGVRLKGKIKSFDNFTVLLESD 44
>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 = 30.6 bits (70), Expect = 0.064
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 8 SHETVTIEL--KNGTQVHGTIQGVDVAMNTHL-KTVKMTVKGKEPTTLDSISLRGNNI 62
+ V I L + ++ G I G D MN L ++ +K L I L+G+NI
Sbjct: 17 NKSRVQIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNTRKPLGRILLKGDNI 74
>gnl|CDD|222374 pfam13779, DUF4175, Domain of unknown function (DUF4175).
Length = 820
Score = 31.8 bits (73), Expect = 0.077
Identities = 15/51 (29%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 77 LIDDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGG-RGGRGRGGPRGRGGP 126
L D+ R ++ + + G G +G+GG+G G +G +G+G +G+ G
Sbjct: 603 LSDETFRDLQEQFNAQRGEQQGQQGQGGQGQGQPGQQGQQGQGQQQGQQGQ 653
Score = 29.9 bits (68), Expect = 0.38
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 92 RGGGAGGARGRGGRGGRGGGRGGRGRGGPRG 122
+G G G +G+ G+G + G +G G+GG
Sbjct: 631 QGQGQPGQQGQQGQGQQQGQQGQGGQGGQGS 661
Score = 27.6 bits (62), Expect = 2.5
Identities = 13/34 (38%), Positives = 21/34 (61%)
Query: 92 RGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
+GG G G+ G+ G+G +G +G+GG G+G
Sbjct: 628 QGGQGQGQPGQQGQQGQGQQQGQQGQGGQGGQGS 661
>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional.
Length = 346
Score = 31.7 bits (72), Expect = 0.088
Identities = 11/51 (21%), Positives = 17/51 (33%)
Query: 79 DDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
DD+ + + +GGG + R G R + R P R
Sbjct: 21 DDSDKRTHNPRTGKGGGRPSGKSRADGGRRPARDDRNSQSRDRKWEDSPWR 71
Score = 26.3 bits (58), Expect = 5.3
Identities = 13/40 (32%), Positives = 15/40 (37%), Gaps = 2/40 (5%)
Query: 92 RGGGAGGARGRGGRGGRGGGRG-GRGRG-GPRGRGGPPRR 129
R R R G+GGGR G+ R G R R
Sbjct: 18 RSDDDSDKRTHNPRTGKGGGRPSGKSRADGGRRPARDDRN 57
>gnl|CDD|221517 pfam12300, DUF3628, Protein of unknown function (DUF3628). This
domain family is found in bacteria, and is typically
between 153 and 183 amino acids in length. The family is
found in association with pfam00270, pfam00271.
Length = 180
Score = 30.8 bits (69), Expect = 0.11
Identities = 18/40 (45%), Positives = 19/40 (47%)
Query: 89 DSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPR 128
+ RRGGG G R GR G R G G GG R PR
Sbjct: 53 EWRRGGGRSGPGERSGRPVGKGPRDGDGGGGRRRGPRKPR 92
Score = 28.5 bits (63), Expect = 0.71
Identities = 18/52 (34%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 73 LETLLIDDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRG 124
E + R G+ S G +G G+G R G GGG RG PR G
Sbjct: 46 REVRAAQEWRRGGGR--SGPGERSGRPVGKGPRDGDGGGGRRRGPRKPRLEG 95
>gnl|CDD|235782 PRK06341, PRK06341, single-stranded DNA-binding protein;
Provisional.
Length = 166
Score = 30.9 bits (70), Expect = 0.11
Identities = 15/30 (50%), Positives = 15/30 (50%)
Query: 92 RGGGAGGARGRGGRGGRGGGRGGRGRGGPR 121
RG G GG G GG G G RGGPR
Sbjct: 117 RGEGGGGGGGGDDGGGGDFGSSGPSRGGPR 146
Score = 26.7 bits (59), Expect = 3.6
Identities = 17/42 (40%), Positives = 17/42 (40%)
Query: 88 RDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
R GGG GG G GG G G G R G GG R
Sbjct: 117 RGEGGGGGGGGDDGGGGDFGSSGPSRGGPRPASSGGGGNFSR 158
Score = 25.1 bits (55), Expect = 9.4
Identities = 15/35 (42%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 98 GARGRGGRGGRGG---GRGGRGRGGPRGRGGPPRR 129
RG GG GG GG G G G GP G P
Sbjct: 115 DGRGEGGGGGGGGDDGGGGDFGSSGPSRGGPRPAS 149
>gnl|CDD|237378 PRK13406, bchD, magnesium chelatase subunit D; Provisional.
Length = 584
Score = 31.1 bits (71), Expect = 0.13
Identities = 20/56 (35%), Positives = 23/56 (41%), Gaps = 6/56 (10%)
Query: 66 ILPDSLPLETLLIDDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPR 121
LP L L L + +R GGAG A+ RG G R G RGG R
Sbjct: 308 ALPPDL-LARLA-----AGGARARARSAGGAGAAQKGNRRGRPLGSRPGEPRGGAR 357
Score = 27.7 bits (62), Expect = 1.8
Identities = 13/34 (38%), Positives = 14/34 (41%), Gaps = 3/34 (8%)
Query: 96 AGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
AGGAR R G G +G RGR R
Sbjct: 319 AGGARARARSAGGAGAAQ---KGNRRGRPLGSRP 349
>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 = 29.0 bits (66), Expect = 0.17
Identities = 17/59 (28%), Positives = 29/59 (49%)
Query: 4 LMKLSHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKEPTTLDSISLRGNNI 62
L K + ++++L +V G ++G D MN L V E T + + +RGN+I
Sbjct: 5 LKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGEKTPIGMVVIRGNSI 63
>gnl|CDD|140324 PTZ00303, PTZ00303, phosphatidylinositol kinase; Provisional.
Length = 1374
Score = 30.8 bits (69), Expect = 0.17
Identities = 15/43 (34%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 83 RSKGKRDSRRGGGAGGARG-RGGRGGRGGGRGGRGRGGPRGRG 124
R +G+ S GG A + G G G G G G+G G R
Sbjct: 386 RLRGRPSSSIGGNANSSTGGNGAAGAGGAGAAGKGGGSAAARA 428
>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional.
Length = 796
Score = 30.6 bits (69), Expect = 0.20
Identities = 17/27 (62%), Positives = 17/27 (62%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRGG 119
GGG GG G GG GG GGG GG G G
Sbjct: 78 GGGGGGGGGFGGFGGGGGGGGGGGGGW 104
Score = 30.2 bits (68), Expect = 0.24
Identities = 16/30 (53%), Positives = 16/30 (53%)
Query: 94 GGAGGARGRGGRGGRGGGRGGRGRGGPRGR 123
GG G GG GG GGG GG G GG R
Sbjct: 76 ISGGGGGGGGGFGGFGGGGGGGGGGGGGWR 105
Score = 28.7 bits (64), Expect = 0.86
Identities = 14/23 (60%), Positives = 14/23 (60%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGR 115
GGG G G GG GG GGG G R
Sbjct: 83 GGGGFGGFGGGGGGGGGGGGGWR 105
Score = 28.7 bits (64), Expect = 0.89
Identities = 16/25 (64%), Positives = 16/25 (64%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGR 117
GGG GG G GG GG GGG GG R
Sbjct: 81 GGGGGGFGGFGGGGGGGGGGGGGWR 105
Score = 28.3 bits (63), Expect = 1.2
Identities = 16/45 (35%), Positives = 18/45 (40%)
Query: 81 APRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
S + + GG GG GGG GG G GG G GG
Sbjct: 56 TSSSASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGG 100
Score = 28.3 bits (63), Expect = 1.3
Identities = 15/26 (57%), Positives = 15/26 (57%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRG 118
GGG GG G G GG GGG GG G
Sbjct: 80 GGGGGGGFGGFGGGGGGGGGGGGGWR 105
Score = 27.9 bits (62), Expect = 2.0
Identities = 16/46 (34%), Positives = 17/46 (36%)
Query: 80 DAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
A + A G GG GG GG GG G GG G G
Sbjct: 59 SASLVANGAVALLSASAISGGGGGGGGGFGGFGGGGGGGGGGGGGW 104
>gnl|CDD|227244 COG4907, COG4907, Predicted membrane protein [Function unknown].
Length = 595
Score = 30.3 bits (68), Expect = 0.22
Identities = 14/28 (50%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 90 SRRGGGAGGARGRGGRGGRGGGRGGRGR 117
SRR +GG G G GG GG GG R
Sbjct: 570 SRRSSSSGG--GGGFSGGGSGGGGGGAR 595
Score = 29.5 bits (66), Expect = 0.41
Identities = 13/29 (44%), Positives = 13/29 (44%)
Query: 84 SKGKRDSRRGGGAGGARGRGGRGGRGGGR 112
R S GG GG G G GG GG R
Sbjct: 567 IASSRRSSSSGGGGGFSGGGSGGGGGGAR 595
Score = 28.4 bits (63), Expect = 1.2
Identities = 13/41 (31%), Positives = 14/41 (34%)
Query: 83 RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGR 123
RS + A R GG G GG G GG R
Sbjct: 555 RSFNNLNRAYSAIASSRRSSSSGGGGGFSGGGSGGGGGGAR 595
Score = 27.6 bits (61), Expect = 2.2
Identities = 10/28 (35%), Positives = 12/28 (42%)
Query: 81 APRSKGKRDSRRGGGAGGARGRGGRGGR 108
A + GG +GG G GG G R
Sbjct: 568 ASSRRSSSSGGGGGFSGGGSGGGGGGAR 595
>gnl|CDD|222425 pfam13865, FoP_duplication, C-terminal duplication domain of Friend
of PRMT1. Fop, or Friend of Prmt1, proteins are
conserved from fungi and plants to vertebrates. There is
little that is actually conserved except for this
C-terminal LDXXLDAYM region where X is any amino acid).
The Fop proteins themselves are nuclear proteins
localised to regions with low levels of DAPI, with a
punctate/speckle-like distribution. Fop is a
chromatin-associated protein and it colocalises with
facultative heterochromatin. It is is critical for
oestrogen-dependent gene activation.
Length = 76
Score = 28.6 bits (64), Expect = 0.28
Identities = 17/42 (40%), Positives = 18/42 (42%)
Query: 88 RDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
GG RGRG R GR GRGGR G + P R
Sbjct: 3 GRKGSRGGKFRPRGRGARRGRRRGRGGRKGKGGAAKPKPKTR 44
Score = 28.2 bits (63), Expect = 0.36
Identities = 15/38 (39%), Positives = 16/38 (42%)
Query: 90 SRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPP 127
R G GG GRG R G R GRG +G P
Sbjct: 2 GGRKGSRGGKFRPRGRGARRGRRRGRGGRKGKGGAAKP 39
Score = 26.3 bits (58), Expect = 2.5
Identities = 10/39 (25%), Positives = 11/39 (28%)
Query: 84 SKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRG 122
K G R GR GGR G+G
Sbjct: 2 GGRKGSRGGKFRPRGRGARRGRRRGRGGRKGKGGAAKPK 40
Score = 25.1 bits (55), Expect = 6.0
Identities = 14/31 (45%), Positives = 15/31 (48%)
Query: 82 PRSKGKRDSRRGGGAGGARGRGGRGGRGGGR 112
R R RG G RGRGGR G+GG
Sbjct: 7 SRGGKFRPRGRGARRGRRRGRGGRKGKGGAA 37
Score = 24.7 bits (54), Expect = 7.5
Identities = 12/38 (31%), Positives = 15/38 (39%)
Query: 83 RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGP 120
R + R G G RGR G G+GG + P
Sbjct: 4 RKGSRGGKFRPRGRGARRGRRRGRGGRKGKGGAAKPKP 41
Score = 24.7 bits (54), Expect = 7.6
Identities = 15/40 (37%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 90 SRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
S G+ G + R G GR RGRGG +G+GG +
Sbjct: 1 SGGRKGSRGGKFRPRGRGARRGR-RRGRGGRKGKGGAAKP 39
>gnl|CDD|222389 pfam13801, Metal_resist, Heavy-metal resistance. This is a
metal-binding protein which is involved in resistance to
heavy-metal ions. The protein forms a four-helix hooked
hairpin, consisting of two long alpha helices each
flanked by a shorter alpha helix. It binds a metal ion
in a type-2 like centre. It contains two copies of an
LTXXQ motif.
Length = 125
Score = 29.1 bits (66), Expect = 0.39
Identities = 13/37 (35%), Positives = 14/37 (37%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
G GA RG G GG R GP PP +
Sbjct: 10 AGVVAGAALRGPGGPGPGGPRRRPGLGPAALALPPEQ 46
>gnl|CDD|216868 pfam02084, Bindin, Bindin.
Length = 239
Score = 29.5 bits (66), Expect = 0.40
Identities = 18/37 (48%), Positives = 19/37 (51%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
GGG G G G GG GGG G G GP+G GG
Sbjct: 186 GGGGYGGGGGGMGGGGGGGMGEMGGMGPQGGGGGYGG 222
>gnl|CDD|225203 COG2321, COG2321, Predicted metalloprotease [General function
prediction only].
Length = 295
Score = 29.7 bits (67), Expect = 0.41
Identities = 14/32 (43%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 83 RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGG 114
R + RRG +G RG GG G R GG G
Sbjct: 7 RESDNVEDRRGRSSGSVRG-GGPGLRLGGGIG 37
Score = 29.3 bits (66), Expect = 0.54
Identities = 13/32 (40%), Positives = 13/32 (40%)
Query: 88 RDSRRGGGAGGARGRGGRGGRGGGRGGRGRGG 119
R R RGR RGGG G R GG
Sbjct: 4 RGRRESDNVEDRRGRSSGSVRGGGPGLRLGGG 35
>gnl|CDD|173331 PTZ00034, PTZ00034, 40S ribosomal protein S10; Provisional.
Length = 124
Score = 28.8 bits (65), Expect = 0.46
Identities = 13/36 (36%), Positives = 15/36 (41%)
Query: 82 PRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGR 117
P + K+ RGGRGGRG GRG
Sbjct: 89 PATHKKKSVNFERKTEEEGSRGGRGGRGRGRGYGRG 124
Score = 26.1 bits (58), Expect = 3.9
Identities = 13/18 (72%), Positives = 13/18 (72%)
Query: 107 GRGGGRGGRGRGGPRGRG 124
G GGRGGRGRG GRG
Sbjct: 107 GSRGGRGGRGRGRGYGRG 124
Score = 25.8 bits (57), Expect = 4.7
Identities = 14/24 (58%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 99 ARGRGGRGGRGGGRGGRGRGGPRG 122
G RGGRGG GRGRG RG
Sbjct: 103 TEEEGSRGGRGG--RGRGRGYGRG 124
>gnl|CDD|178439 PLN02847, PLN02847, triacylglycerol lipase.
Length = 633
Score = 29.1 bits (65), Expect = 0.61
Identities = 11/26 (42%), Positives = 11/26 (42%)
Query: 90 SRRGGGAGGARGRGGRGGRGGGRGGR 115
SRR G G GG G G G R
Sbjct: 21 SRRLAAEDGEDGGGGGDGSSGRSGRR 46
Score = 27.9 bits (62), Expect = 1.5
Identities = 12/30 (40%), Positives = 12/30 (40%)
Query: 100 RGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
R G GG GG G G GR RR
Sbjct: 22 RRLAAEDGEDGGGGGDGSSGRSGRRRIARR 51
>gnl|CDD|164795 PHA00370, III, attachment protein.
Length = 297
Score = 29.1 bits (65), Expect = 0.66
Identities = 14/42 (33%), Positives = 17/42 (40%)
Query: 84 SKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
G ++ G G G G GG G GGG G G + G
Sbjct: 99 DTGGGNTGGGSGGGDTGGSGGGGSDGGGSEGGSTGKSLTKEG 140
Score = 27.2 bits (60), Expect = 2.8
Identities = 15/44 (34%), Positives = 15/44 (34%)
Query: 82 PRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
G G GG G G GG GG G GG GG
Sbjct: 82 KDGDGGGTGEGGSDTGGDTGGGNTGGGSGGGDTGGSGGGGSDGG 125
>gnl|CDD|148592 pfam07073, ROF, Modulator of Rho-dependent transcription
termination (ROF). This family consists of several
bacterial modulator of Rho-dependent transcription
termination (ROF) proteins. ROF binds transcription
termination factor Rho and inhibits Rho-dependent
termination in vivo.
Length = 80
Score = 27.5 bits (62), Expect = 0.67
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 4 LMKLSHETVTIELKNGTQVHGT 25
+ L + +ELK+G QV G
Sbjct: 12 IACLHRYPLKLELKDGEQVEGK 33
>gnl|CDD|221518 pfam12301, CD99L2, CD99 antigen like protein 2. This family of
proteins is found in eukaryotes. Proteins in this family
are typically between 165 and 237 amino acids in length.
CD99L2 and CD99 are involved in trans-endothelial
migration of neutrophils in vitro and in the recruitment
of neutrophils into inflamed peritoneum.
Length = 154
Score = 28.6 bits (64), Expect = 0.76
Identities = 16/38 (42%), Positives = 17/38 (44%)
Query: 77 LIDDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGG 114
L D A K D +GGG GG G G GG GG
Sbjct: 73 LADVAGDGGYKPDKGKGGGGGGGGGGGTDGGPEGGAET 110
Score = 25.1 bits (55), Expect = 9.5
Identities = 19/58 (32%), Positives = 24/58 (41%), Gaps = 10/58 (17%)
Query: 80 DAPRSKGKRDSRRGGGAGG---------ARGRGG-RGGRGGGRGGRGRGGPRGRGGPP 127
P+ + + D GG GG G GG + +G G GG G GG GGP
Sbjct: 48 PKPKPRPQPDPGNPGGDGGGFSDSDLADVAGDGGYKPDKGKGGGGGGGGGGGTDGGPE 105
>gnl|CDD|235529 PRK05601, PRK05601, DNA polymerase III subunit epsilon; Validated.
Length = 377
Score = 28.6 bits (64), Expect = 0.81
Identities = 19/52 (36%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 75 TLLIDDAPRSKG------KRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGP 120
TL++ +APR+ G KR A R RG R RGG R R G
Sbjct: 127 TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNR--RGGRGRRRQRVGH 176
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 28.7 bits (65), Expect = 0.92
Identities = 16/45 (35%), Positives = 17/45 (37%), Gaps = 5/45 (11%)
Query: 90 SRRGGGAG-----GARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
+ GGA GA G G G G GG R G P RR
Sbjct: 314 AAAAGGASSAYSAGAAGGSGAAGVAAGLGGVARAGASAAASPLRR 358
Score = 25.6 bits (57), Expect = 9.6
Identities = 12/33 (36%), Positives = 12/33 (36%), Gaps = 2/33 (6%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
GAG A G G G RGG GG
Sbjct: 289 AAGAGLAAGGGAAAAGGAAAA--ARGGAAAAGG 319
>gnl|CDD|237539 PRK13878, PRK13878, conjugal transfer relaxase TraI; Provisional.
Length = 746
Score = 28.5 bits (64), Expect = 1.00
Identities = 12/49 (24%), Positives = 16/49 (32%), Gaps = 1/49 (2%)
Query: 80 DAPRSKGKRDSRRGG-GAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPP 127
+ P +G+ RGG G A + G R G GR
Sbjct: 520 ERPEHRGRTGRGRGGPGQRPAADQHAAGAAAVARAGDGRPAAGRGDRAG 568
>gnl|CDD|217975 pfam04228, Zn_peptidase, Putative neutral zinc metallopeptidase.
Members of this family have a predicted zinc binding
motif characteristic of neutral zinc metallopeptidases
(Prosite:PDOC00129).
Length = 292
Score = 28.2 bits (63), Expect = 1.1
Identities = 15/38 (39%), Positives = 15/38 (39%)
Query: 88 RDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
R R RG G GG GGG G R GG G
Sbjct: 4 RGRRESDNVEDRRGSSGGGGNGGGGGFRLGGGKTGLVV 41
>gnl|CDD|219133 pfam06682, DUF1183, Protein of unknown function (DUF1183). This
family consists of several eukaryotic proteins of around
360 residues in length. The function of this family is
unknown.
Length = 317
Score = 28.2 bits (63), Expect = 1.2
Identities = 19/38 (50%), Positives = 19/38 (50%)
Query: 90 SRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPP 127
S G G R G GG GGG GG G GG G G PP
Sbjct: 179 SCGGVRGGPRPERAGYGGGGGGGGGGGGGGGSGPGPPP 216
>gnl|CDD|224834 COG1923, Hfq, Uncharacterized host factor I protein [General
function prediction only].
Length = 77
Score = 27.0 bits (60), Expect = 1.4
Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 2 NFL--MKLSHETVTIELKNGTQVHGTIQGVD 30
FL ++ VTI L NG ++ G ++ D
Sbjct: 10 PFLNALRKEKIPVTIFLVNGFKLQGQVESFD 40
>gnl|CDD|219320 pfam07172, GRP, Glycine rich protein family. This family of
proteins includes several glycine rich proteins as well
as two nodulins 16 and 24. The family also contains
proteins that are induced in response to various
stresses.
Length = 91
Score = 26.6 bits (59), Expect = 1.8
Identities = 20/33 (60%), Positives = 20/33 (60%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
GGG GG G GG G GGG GG G G P G GG
Sbjct: 53 GGGGGGGYGGGGYYGGGGGYGGGGGGYPGGGGG 85
Score = 26.3 bits (58), Expect = 2.5
Identities = 17/33 (51%), Positives = 17/33 (51%)
Query: 92 RGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRG 124
GG G G GG GG GGG G G GG G G
Sbjct: 59 GYGGGGYYGGGGGYGGGGGGYPGGGGGGYGGGG 91
Score = 25.1 bits (55), Expect = 6.1
Identities = 18/33 (54%), Positives = 18/33 (54%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
GG GG G GG GG GGG G GG G GG
Sbjct: 45 YGGGGGGYGGGGGGGYGGGGYYGGGGGYGGGGG 77
Score = 25.1 bits (55), Expect = 6.6
Identities = 20/39 (51%), Positives = 21/39 (53%)
Query: 89 DSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPP 127
D + GGG GG G GG G GGG G G G G GG P
Sbjct: 42 DDKYGGGGGGYGGGGGGGYGGGGYYGGGGGYGGGGGGYP 80
Score = 24.7 bits (54), Expect = 9.2
Identities = 17/33 (51%), Positives = 17/33 (51%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
GGG GG G G GG GG GG G G GG
Sbjct: 54 GGGGGGYGGGGYYGGGGGYGGGGGGYPGGGGGG 86
Score = 24.7 bits (54), Expect = 9.4
Identities = 19/33 (57%), Positives = 19/33 (57%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
GGG GG GG GG GGG GG GG G GG
Sbjct: 57 GGGYGGGGYYGGGGGYGGGGGGYPGGGGGGYGG 89
>gnl|CDD|219420 pfam07466, DUF1517, Protein of unknown function (DUF1517). This
family consists of several hypothetical glycine rich
plant and bacterial proteins of around 300 residues in
length. The function of this family is unknown.
Length = 280
Score = 27.3 bits (61), Expect = 2.2
Identities = 14/44 (31%), Positives = 14/44 (31%), Gaps = 8/44 (18%)
Query: 91 RRGGGAGGARGR-------GGRGGRGGGRGGRGRGGPRGRGGPP 127
GG GG R R GG G G G G G P
Sbjct: 3 ASGGRIGGGSFRAPSRSSSSPRSSSPGGGGYYGSPGG-GFGFPF 45
>gnl|CDD|218797 pfam05890, Ebp2, Eukaryotic rRNA processing protein EBP2. This
family consists of several Eukaryotic rRNA processing
protein EBP2 sequences. Ebp2p is required for the
maturation of 25S rRNA and 60S subunit assembly. Ebp2p
may be one of the target proteins of Rrs1p for executing
the signal to regulate ribosome biogenesis. This family
also plays a role in chromosome segregation.
Length = 270
Score = 27.3 bits (61), Expect = 2.3
Identities = 13/42 (30%), Positives = 17/42 (40%), Gaps = 5/42 (11%)
Query: 87 KRDSRRG-----GGAGGARGRGGRGGRGGGRGGRGRGGPRGR 123
KR S+ G + +GG G G+GG R G R
Sbjct: 229 KRGSKSNTAESSNDLSGFSVKKMKGGGGAGKGGNKRPGKSRR 270
>gnl|CDD|234526 TIGR04260, Cyano_gly_rpt, rSAM-associated Gly-rich repeat protein.
Members of this protein family average 125 in length,
roughly half of which is the repetitive and extremely
Gly-rich C-terminal region. Virtually all members occur
in the Cyanobacteria, in a neighborhood that includes a
radical SAM/SPASM domain, often a marker of peptide
modification systems.
Length = 119
Score = 26.6 bits (59), Expect = 2.4
Identities = 15/36 (41%), Positives = 16/36 (44%)
Query: 90 SRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGG 125
RG G GG+ G GG G G GG GG G
Sbjct: 77 GGRGWGNGGSGGGWVNGGGGWGNGGWVNGGGWRNGY 112
>gnl|CDD|217348 pfam03064, U79_P34, HSV U79 / HCMV P34. This family represents
herpes virus protein U79 and cytomegalovirus early
phosphoprotein P34 (UL112).
Length = 238
Score = 27.1 bits (60), Expect = 2.7
Identities = 7/38 (18%), Positives = 11/38 (28%)
Query: 83 RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGP 120
+ K++ +R G GG G P
Sbjct: 181 DRRKKQEEKRRNDEDKRPGGGGGSSGGQSGLSTKDEPP 218
Score = 26.0 bits (57), Expect = 7.2
Identities = 7/24 (29%), Positives = 8/24 (33%)
Query: 100 RGRGGRGGRGGGRGGRGRGGPRGR 123
+ R R GG GG G
Sbjct: 189 KRRNDEDKRPGGGGGSSGGQSGLS 212
>gnl|CDD|236757 PRK10767, PRK10767, chaperone protein DnaJ; Provisional.
Length = 371
Score = 27.0 bits (61), Expect = 2.8
Identities = 17/39 (43%), Positives = 18/39 (46%), Gaps = 9/39 (23%)
Query: 93 GGGAGGARGRGGRGGR---------GGGRGGRGRGGPRG 122
GGG GG G GG G GGGRGG + RG
Sbjct: 77 GGGGGGFGGGGGFGDIFGDIFGDIFGGGRGGGRQRARRG 115
>gnl|CDD|132472 TIGR03431, PhnD, phosphonate ABC transporter, periplasmic
phosphonate binding protein. This model is a subset of
the broader subfamily of phosphate/phosphonate binding
protein ABC transporter components, TIGR01098. In this
model all members of the seed have support from genomic
context for association with pathways for the metabolims
of phosphonates, particularly the C-P lyase system,
GenProp0232. This model includes the characterized phnD
gene from E. coli. Note that this model does not
identify all phnD-subfamily genes with evident
phosphonate context, but all sequences above the trusted
context may be inferred to bind phosphonate compounds
even in the absence of such context. Furthermore, there
is ample evidence to suggest that many other members of
the TIGR01098 subfamily have a different primary
function.
Length = 288
Score = 26.9 bits (60), Expect = 3.1
Identities = 12/39 (30%), Positives = 15/39 (38%), Gaps = 8/39 (20%)
Query: 8 SHETVTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKG 46
SHE + + NGT VD A +M KG
Sbjct: 176 SHEAAILAVANGT--------VDAATTNDENLDRMIRKG 206
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 27.2 bits (61), Expect = 3.1
Identities = 15/50 (30%), Positives = 17/50 (34%)
Query: 79 DDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPR 128
D+A R + GGG GG G GG G G G P
Sbjct: 381 DEALRRLQEGPPSPGGGGGGPPGGGGAPGAPAAAAAPGAAAAAPAAGGPA 430
>gnl|CDD|223046 PHA03328, PHA03328, nuclear egress lamina protein UL31;
Provisional.
Length = 316
Score = 27.0 bits (60), Expect = 3.4
Identities = 14/51 (27%), Positives = 15/51 (29%), Gaps = 2/51 (3%)
Query: 79 DDAPRSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
DD + RR A R GR G G R R R R
Sbjct: 2 DDLALRRSSSSLRRSRRAARRSRRDGRVGSRGRS--RYRSRRRSSRRSSTR 50
>gnl|CDD|223278 COG0200, RplO, Ribosomal protein L15 [Translation, ribosomal
structure and biogenesis].
Length = 152
Score = 26.5 bits (59), Expect = 3.4
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 83 RSKGKRDSRRGGGAGGARGRGGRGGRGGGRGGRGRGG 119
++G + +R+ G G G G GGR G +G + R G
Sbjct: 8 PARGSKKTRKRVGRGIGSGLGKTGGR-GHKGQKARSG 43
>gnl|CDD|240227 PTZ00009, PTZ00009, heat shock 70 kDa protein; Provisional.
Length = 653
Score = 26.7 bits (59), Expect = 4.9
Identities = 14/34 (41%), Positives = 14/34 (41%), Gaps = 4/34 (11%)
Query: 93 GGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGP 126
GG GG G G GG GG G G GP
Sbjct: 618 GGMPGGMPG----GMPGGMPGGAGPAGAGASSGP 647
>gnl|CDD|179001 PRK00395, hfq, RNA-binding protein Hfq; Provisional.
Length = 79
Score = 25.3 bits (56), Expect = 5.0
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 1 MNFLMKLSHETVTIELKNGTQVHGTIQGVD 30
+N L K VTI L NG ++ G I+ D
Sbjct: 12 LNALRK-ERVPVTIYLVNGIKLQGQIESFD 40
>gnl|CDD|223029 PHA03264, PHA03264, envelope glycoprotein D; Provisional.
Length = 416
Score = 26.5 bits (58), Expect = 5.4
Identities = 12/49 (24%), Positives = 15/49 (30%), Gaps = 1/49 (2%)
Query: 81 APRSKGKRDSR-RGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPR 128
+P G + G GR G G G G GG P+
Sbjct: 274 SPAPPGDDRPEAKPEPGPVEDGAPGRETGGEGEGPEPAGRDGAAGGEPK 322
>gnl|CDD|173589 PTZ00398, PTZ00398, phosphoenolpyruvate carboxylase; Provisional.
Length = 974
Score = 26.3 bits (58), Expect = 6.1
Identities = 8/12 (66%), Positives = 8/12 (66%)
Query: 116 GRGGPRGRGGPP 127
GRGG RGG P
Sbjct: 664 GRGGSVSRGGGP 675
>gnl|CDD|177862 PLN02214, PLN02214, cinnamoyl-CoA reductase.
Length = 342
Score = 25.9 bits (56), Expect = 7.5
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 3/37 (8%)
Query: 12 VTIELKNGTQVHGTIQGVDVAMNTHLKTVKMTVKGKE 48
V I L+ G V GT++ D NTHL+ ++ GKE
Sbjct: 27 VKILLERGYTVKGTVRNPDDPKNTHLRELE---GGKE 60
>gnl|CDD|112890 pfam04094, DUF390, Protein of unknown function (DUF390). This is a
family of long proteins currently only found in the rice
genome. They have no known function. However they may be
some kind of transposable element.
Length = 843
Score = 25.9 bits (56), Expect = 7.9
Identities = 20/45 (44%), Positives = 21/45 (46%), Gaps = 3/45 (6%)
Query: 86 GKRDSRRG--GGAGGARGRGGR-GGRGGGRGGRGRGGPRGRGGPP 127
G SRRG GG R G R GG GG R RG + G PP
Sbjct: 70 GAGGSRRGEQSTPGGGRASGPRDGGPGGSRPADARGKRKQEGTPP 114
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 25.9 bits (57), Expect = 8.0
Identities = 10/52 (19%), Positives = 13/52 (25%), Gaps = 2/52 (3%)
Query: 80 DAPRSKGKRDSRRGGGAGGARGRGGRGGRG--GGRGGRGRGGPRGRGGPPRR 129
P ++ S+ A G R RG G R G
Sbjct: 844 RPPPARSSESSKSKPAAAGGRARGKNGRRRPRPPEPRARPGAAAPPKAAAAA 895
>gnl|CDD|221999 pfam13236, CLU, Clustered mitochondria. The CLU domain (CLUstered
mitochondria) is a eukaryotic domain found in proteins
from fungi, protozoa, plants to humans. It is required
for correct functioning of the mitochondria and
mitochondrial transport although the exact function of
the domain is unknown. In Dictyostelium the full-length
protein is required for a very late step in fission of
the outer mitochondrial membrane suggesting that
mitochondria are transported along microtubules, as in
mammalian cells, rather than along actin filaments, as
in budding yeast. Disruption of the protein-impaired
cytokinesis and caused mitochondria to cluster at the
cell centre. It is likely that CLU functions in a novel
pathway that positions mitochondria within the cell
based on their physiological state. Disruption of the
CLU pathway may enhance oxidative damage, alter gene
expression, cause mitochondria to cluster at microtubule
plus ends, and lead eventually to mitochondrial failure.
Length = 222
Score = 25.6 bits (57), Expect = 8.2
Identities = 11/36 (30%), Positives = 17/36 (47%), Gaps = 4/36 (11%)
Query: 36 HLKTVKMTVKGKEPTTL----DSISLRGNNIRYYIL 67
HLK ++ K + L DS + G + R Y+L
Sbjct: 174 HLKPHEVGDKDDQEVELCGSSDSKGILGTDGRKYVL 209
>gnl|CDD|223010 PHA03215, PHA03215, nuclear protein UL24; Provisional.
Length = 262
Score = 25.6 bits (56), Expect = 8.4
Identities = 15/42 (35%), Positives = 16/42 (38%)
Query: 88 RDSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
R +RRG G R R R RGG G P PP
Sbjct: 194 RTTRRGRRRGARRPRSRRRPRGGAAGPPVPAEPAAPERPPAD 235
>gnl|CDD|223023 PHA03249, PHA03249, DNA packaging tegument protein UL25;
Provisional.
Length = 653
Score = 25.7 bits (56), Expect = 8.8
Identities = 9/29 (31%), Positives = 9/29 (31%), Gaps = 3/29 (10%)
Query: 101 GRGGRGGRGGGRGGRGRGGPRGRGGPPRR 129
G RG G GR P RR
Sbjct: 71 GSEAEAERGRRAGMGGRNKA---TKPSRR 96
>gnl|CDD|218967 pfam06273, eIF-4B, Plant specific eukaryotic initiation factor 4B.
This family consists of several plant specific
eukaryotic initiation factor 4B proteins.
Length = 496
Score = 25.8 bits (56), Expect = 8.9
Identities = 12/27 (44%), Positives = 12/27 (44%)
Query: 100 RGRGGRGGRGGGRGGRGRGGPRGRGGP 126
G G GG GGG GG R R P
Sbjct: 182 SGGGAFGGGGGGGGGGERRSGGFRDSP 208
>gnl|CDD|215852 pfam00311, PEPcase, Phosphoenolpyruvate carboxylase.
Length = 794
Score = 25.6 bits (57), Expect = 9.1
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 101 GRGGRGGRGGG 111
GRGG GRGGG
Sbjct: 484 GRGGSVGRGGG 494
>gnl|CDD|193258 pfam12782, Innate_immun, Invertebrate innate immunity transcript
family. The immune response of the purple sea urchin
appears to be more complex than previously believed in
that it uses immune-related gene families homologous to
vertebrate Toll-like and NOD/NALP-like receptor families
as well as C-type lectins and a rudimentary complement
system. In addition, the species also produces this
unusual family of mRNAs, also known as 185/333, which is
strongly upregulated in response to pathogen challenge.
Length = 312
Score = 25.8 bits (56), Expect = 9.4
Identities = 19/38 (50%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 89 DSRRGGGAGGARGRGGRGGRGGGRGGRGRGGPRGRGGP 126
+ RRG G RG+G GGR GG GGPR GGP
Sbjct: 26 NERRGNENGRERGQGRFGGR---PGGMQMGGPRQDGGP 60
>gnl|CDD|236799 PRK10930, PRK10930, FtsH protease regulator HflK; Provisional.
Length = 419
Score = 25.6 bits (56), Expect = 9.4
Identities = 19/55 (34%), Positives = 23/55 (41%), Gaps = 19/55 (34%)
Query: 90 SRRGGGAGGARGRGGR------------------GGRGGGRGGRGRGGPRGRGGP 126
S+ GG +GG +GGR GG GGG+G G GG GP
Sbjct: 19 SKPGGNSGGNGNKGGRDQGPPDLDDIFRKLSKKLGGLGGGKGT-GSGGGSSSQGP 72
>gnl|CDD|237653 PRK14276, PRK14276, chaperone protein DnaJ; Provisional.
Length = 380
Score = 25.4 bits (56), Expect = 9.6
Identities = 12/26 (46%), Positives = 12/26 (46%)
Query: 94 GGAGGARGRGGRGGRGGGRGGRGRGG 119
G AG G GG G GG G G G
Sbjct: 69 GAAGANGGFGGGAGGFGGFDGSGGFG 94
>gnl|CDD|234570 PRK00009, PRK00009, phosphoenolpyruvate carboxylase; Reviewed.
Length = 911
Score = 25.5 bits (57), Expect = 9.8
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 101 GRGGRGGRGGG 111
GRGG GRGGG
Sbjct: 607 GRGGTVGRGGG 617
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 0.141 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: 6,725,914
Number of extensions: 611450
Number of successful extensions: 1967
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1290
Number of HSP's successfully gapped: 336
Length of query: 129
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 43
Effective length of database: 7,123,158
Effective search space: 306295794
Effective search space used: 306295794
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: 42 (22.0 bits)
S2: 53 (24.0 bits)