RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17024
(132 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 = 141 bits (359), Expect = 2e-45
Identities = 49/70 (70%), Positives = 59/70 (84%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRG 65
PIKLLHEAEGHI+T E G+++RGKL+EAEDNMNC + DVTVT RDGKV + +YIRG
Sbjct: 1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTARDGKVSKLEQVYIRG 60
Query: 66 SKIRFLILPD 75
S+IRF+ILPD
Sbjct: 61 SQIRFIILPD 70
>gnl|CDD|201787 pfam01423, LSM, LSM domain. The LSM domain contains Sm proteins
as well as other related LSM (Like Sm) proteins. The
U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein
particles (snRNPs) involved in pre-mRNA splicing
contain seven Sm proteins (B/B', D1, D2, D3, E, F and
G) in common, which assemble around the Sm site present
in four of the major spliceosomal small nuclear RNAs.
The U6 snRNP binds to the LSM (Like Sm) proteins. Sm
proteins are also found in archaebacteria, which do not
have any splicing apparatus suggesting a more general
role for Sm proteins. All Sm proteins contain a common
sequence motif in two segments, Sm1 and Sm2, separated
by a short variable linker. This family also includes
the bacterial Hfq (host factor Q) proteins. Hfq are
also RNA-binding proteins, that form hexameric rings.
Length = 66
Score = 66.0 bits (162), Expect = 1e-15
Identities = 23/66 (34%), Positives = 32/66 (48%)
Query: 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSK 67
K L + G +T E NG RG L + MN + DV T +DGKV + + IRG+
Sbjct: 1 KFLQKLLGKRVTVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGKVNKLGLVLIRGNN 60
Query: 68 IRFLIL 73
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 = 65.2 bits (160), Expect = 2e-15
Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 1/67 (1%)
Query: 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYIRGS 66
K L + G + E NG +RG L + MN + DV T +DG K + + ++IRG+
Sbjct: 1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGN 60
Query: 67 KIRFLIL 73
I ++IL
Sbjct: 61 NIVYIIL 67
>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 = 61.4 bits (150), Expect = 1e-13
Identities = 18/61 (29%), Positives = 30/61 (49%)
Query: 14 EGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLIL 73
+G + T E N RG + + MN ++D T T R GK +++G IR++ +
Sbjct: 18 QGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQHHFDEFFVQGRNIRYVHI 77
Query: 74 P 74
P
Sbjct: 78 P 78
>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 = 58.8 bits (143), Expect = 7e-13
Identities = 22/63 (34%), Positives = 33/63 (52%)
Query: 10 LHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIR 69
L + G ++ E +G + G LV + MN + DV T RDGKV+ + + IRGS I
Sbjct: 1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIV 60
Query: 70 FLI 72
+
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 = 57.2 bits (139), Expect = 4e-12
Identities = 28/71 (39%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDG-KVKPMANIYIR 64
P+ LL A+GH + E NG+ + G LV ++ MN + +V T +DG + M YIR
Sbjct: 2 PLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSKDGDRFWKMPECYIR 61
Query: 65 GSKIRFLILPD 75
G+ I++L LPD
Sbjct: 62 GNTIKYLRLPD 72
>gnl|CDD|224869 COG1958, LSM1, Small nuclear ribonucleoprotein (snRNP) homolog
[Transcription].
Length = 79
Score = 52.7 bits (127), Expect = 2e-10
Identities = 18/73 (24%), Positives = 29/73 (39%), Gaps = 4/73 (5%)
Query: 5 IPIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVT-FRDG---KVKPMAN 60
+P+ L + + + NG +RG LV + MN + DV DG +
Sbjct: 7 LPLSFLKKLLNKRVLVKLKNGREYRGTLVGFDQYMNLVLDDVEEIISHDGEKNVRRLGGE 66
Query: 61 IYIRGSKIRFLIL 73
+ IRG I +
Sbjct: 67 VLIRGDNIVLISP 79
>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 = 44.5 bits (106), Expect = 5e-07
Identities = 24/89 (26%), Positives = 41/89 (46%), Gaps = 5/89 (5%)
Query: 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSK 67
KL +E +T E NG + G + + +MN + +V +T + + + IRG+
Sbjct: 8 KLSNET----VTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLKGKNPVSLDTLSIRGNN 63
Query: 68 IRFLILPDMLK-NAPMFKGKQGNKAGAAG 95
IR++ILPD L + + KA
Sbjct: 64 IRYIILPDSLNLDTLLVDDTPKAKAKKRA 92
>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 = 37.1 bits (86), Expect = 2e-04
Identities = 20/70 (28%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 6 PIKLLHEAEGHIITCETT-NGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIR 64
P K + G I E + + +G+LV +D MN + D + KV+ + + +R
Sbjct: 1 PNKKVKSLVGSRIRVEMKGDENQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLR 60
Query: 65 GSKIRFLILP 74
G+ I LI P
Sbjct: 61 GNNI-LLIQP 69
>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 = 37.3 bits (86), Expect = 3e-04
Identities = 18/23 (78%), Positives = 19/23 (82%)
Query: 109 GRGRGGPPQRGGRGGWGGPSRGG 131
GRGRGGPPQ+GGRGG GG GG
Sbjct: 8 GRGRGGPPQQGGRGGGGGGRGGG 30
Score = 27.2 bits (60), Expect = 1.5
Identities = 11/27 (40%), Positives = 12/27 (44%)
Query: 103 RAQAARGRGRGGPPQRGGRGGWGGPSR 129
R + GRGG G G GGP R
Sbjct: 11 RGGPPQQGGRGGGGGGRGGGSTGGPPR 37
>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 = 34.0 bits (79), Expect = 0.003
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 6/68 (8%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMAN---IY 62
P K L + G + + NG +RG L + MN + D T + DG++ A +
Sbjct: 2 PSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLED-TEEYVDGQLV--AKYGDAF 58
Query: 63 IRGSKIRF 70
IRG+ + +
Sbjct: 59 IRGNNVLY 66
>gnl|CDD|240291 PTZ00146, PTZ00146, fibrillarin; Provisional.
Length = 293
Score = 35.5 bits (82), Expect = 0.004
Identities = 15/50 (30%), Positives = 16/50 (32%)
Query: 83 FKGKQGNKAGAAGRGKSGILRAQAARGRGRGGPPQRGGRGGWGGPSRGGR 132
G GRG G G G + GRGG GG GG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGG 50
Score = 34.7 bits (80), Expect = 0.008
Identities = 20/50 (40%), Positives = 20/50 (40%)
Query: 82 MFKGKQGNKAGAAGRGKSGILRAQAARGRGRGGPPQRGGRGGWGGPSRGG 131
G G G G G R RG GRGG RG GG GG GG
Sbjct: 1 GMGGGFGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGG 50
Score = 33.2 bits (76), Expect = 0.027
Identities = 20/51 (39%), Positives = 21/51 (41%), Gaps = 2/51 (3%)
Query: 83 FKGKQGNKAGAAGRGKSGIL--RAQAARGRGRGGPPQRGGRGGWGGPSRGG 131
F G +G G G G G GRGRG GGRGG GG G
Sbjct: 6 FGGGRGGGRGGGGGGGRGGGGRGGGRGGGRGRGRGGGGGGRGGGGGGGPGK 56
>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 = 32.2 bits (74), Expect = 0.017
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 6/66 (9%)
Query: 15 GHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPM----ANIYIRGSKIRF 70
G +T E N G L + +N + +++V D + P N +IRGS +R+
Sbjct: 11 GKEVTVELKNDLSITGTLHSVDQYLNIKLTNISVN--DPEKYPHLLSVKNCFIRGSVVRY 68
Query: 71 LILPDM 76
+ LP
Sbjct: 69 VQLPAD 74
>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 = 29.9 bits (68), Expect = 0.078
Identities = 11/60 (18%), Positives = 26/60 (43%)
Query: 6 PIKLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRG 65
P+ +L+E+ + + G RG L + ++N + + V+ + + +RG
Sbjct: 2 PLDVLNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVRG 61
>gnl|CDD|180777 PRK06958, PRK06958, single-stranded DNA-binding protein;
Provisional.
Length = 182
Score = 29.8 bits (67), Expect = 0.30
Identities = 16/50 (32%), Positives = 20/50 (40%)
Query: 82 MFKGKQGNKAGAAGRGKSGILRAQAARGRGRGGPPQRGGRGGWGGPSRGG 131
M G+ G+ G G + G G G GG + GG GG GG
Sbjct: 107 MLGGRGGSGGGGGGGDEGGYGGGGGGGGGGYGGESRSGGGGGRASGGGGG 156
>gnl|CDD|223916 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related
3'-5' exonucleases [DNA replication, recombination, and
repair].
Length = 243
Score = 29.8 bits (67), Expect = 0.32
Identities = 16/81 (19%), Positives = 27/81 (33%), Gaps = 18/81 (22%)
Query: 12 EAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRD-------GKVKPMANIYIR 64
+I ETT + + +++E + VT+ V P I
Sbjct: 12 PTRFVVIDLETTGLNPKKDRIIE--------IGAVTLEDGRIVERSFHTLVNP--ERPIP 61
Query: 65 GSKIRFL-ILPDMLKNAPMFK 84
+ I +ML +AP F
Sbjct: 62 PEIFKIHGITDEMLADAPKFA 82
>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 = 29.6 bits (66), Expect = 0.47
Identities = 15/53 (28%), Positives = 17/53 (32%), Gaps = 1/53 (1%)
Query: 78 KNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRGGPPQRGGRGGWGGPSRG 130
N P K + N + GRG RG GG GG RG
Sbjct: 486 NNVPAKKSRPSNDQKQYVNKSGEGISKVGQSYGGRGRTRGRGRGGG-GGRGRG 537
>gnl|CDD|240255 PTZ00070, PTZ00070, 40S ribosomal protein S2; Provisional.
Length = 257
Score = 29.3 bits (66), Expect = 0.52
Identities = 16/30 (53%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 104 AQAARGRGRG-GPPQRGGRGGWGGPSRGGR 132
A A G GRG G RGGRG G RGG
Sbjct: 2 AAARGGEGRGFGRRGRGGRGRGRGRGRGGE 31
>gnl|CDD|236722 PRK10590, PRK10590, ATP-dependent RNA helicase RhlE; Provisional.
Length = 456
Score = 29.0 bits (65), Expect = 0.62
Identities = 15/56 (26%), Positives = 21/56 (37%), Gaps = 1/56 (1%)
Query: 77 LKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRGRGGPPQRGGRGGWGGPSRGGR 132
+K P+ G+Q G G+G G + Q RG GG + R G
Sbjct: 382 IKAEPIQNGRQQRGGGGRGQG-GGRGQQQGQPRRGEGGAKSASAKPAEKPSRRLGD 436
>gnl|CDD|240631 cd12154, FDH_GDH_like, Formate/glycerate dehydrogenases, D-specific
2-hydroxy acid dehydrogenases and related
dehydrogenases. The formate/glycerate dehydrogenase
like family contains a diverse group of enzymes such as
formate dehydrogenase (FDH), glycerate dehydrogenase
(GDH), D-lactate dehydrogenase, L-alanine dehydrogenase,
and S-Adenosylhomocysteine hydrolase, that share a
common 2-domain structure. Despite often low sequence
identity, these proteins typically have a characteristic
arrangement of 2 similar domains of the alpha/beta
Rossmann fold NAD+ binding form. The NAD(P) binding
domain is inserted within the linear sequence of the
mostly N-terminal catalytic domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD(P) is bound, primarily to
the C-terminal portion of the 2nd (internal) domain.
While many members of this family are dimeric, alanine
DH is hexameric and phosphoglycerate DH is tetrameric.
2-hydroxyacid dehydrogenases are enzymes that catalyze
the conversion of a wide variety of D-2-hydroxy acids to
their corresponding keto acids. The general mechanism is
(R)-lactate + acceptor to pyruvate + reduced acceptor.
Formate dehydrogenase (FDH) catalyzes the NAD+-dependent
oxidation of formate ion to carbon dioxide with the
concomitant reduction of NAD+ to NADH. FDHs of this
family contain no metal ions or prosthetic groups.
Catalysis occurs though direct transfer of a hydride ion
to NAD+ without the stages of acid-base catalysis
typically found in related dehydrogenases.
Length = 310
Score = 28.0 bits (62), Expect = 1.6
Identities = 22/109 (20%), Positives = 27/109 (24%), Gaps = 11/109 (10%)
Query: 8 KLLHEAEGHIITCETTNGDLFRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSK 67
L+ + ++ T D L EA V + S
Sbjct: 81 ALIQKLGDRLLFTYTIGAD--HRDLTEALARAGLTAIAVEGVELPLLT-SNSIGAGELSV 137
Query: 68 IRFLIL-----PDMLKNAPMFKGKQGNKAGAAGRGKSGILRAQAARGRG 111
P L AP GK G G G AQ RG G
Sbjct: 138 QFIARFLEVQQPGRLGGAPDVAGK---TVVVVGAGVVGKEAAQMLRGLG 183
>gnl|CDD|226982 COG4635, HemG, Flavodoxin [Energy production and conversion /
Coenzyme metabolism].
Length = 175
Score = 27.4 bits (61), Expect = 1.9
Identities = 16/59 (27%), Positives = 21/59 (35%), Gaps = 3/59 (5%)
Query: 28 FRGKLVEAEDNMNCAMADVTVTFRDGKVKPMANIYIRGSKIRFLILPDMLKNAPMFKGK 86
F K EA A V +T R K P N Y+R ++ P + F G
Sbjct: 69 FVKKHAEALSTKPSAFFSVNLTARKEKRTPETNSYVRKFLMKSPWQPVAIAV---FGGA 124
>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 = 26.6 bits (58), Expect = 3.5
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 105 QAARGRGRGGPPQRGGRGGWGGPSRG 130
+ RG GR GP +R GR GP G
Sbjct: 53 EWRRGGGRSGPGERSGRPVGKGPRDG 78
>gnl|CDD|235307 PRK04537, PRK04537, ATP-dependent RNA helicase RhlB; Provisional.
Length = 572
Score = 26.8 bits (59), Expect = 4.5
Identities = 11/26 (42%), Positives = 11/26 (42%), Gaps = 1/26 (3%)
Query: 108 RGRGRGGPPQRGGRG-GWGGPSRGGR 132
RG GR GP G GG R G
Sbjct: 432 RGGGRSGPGGGSRSGSVGGGGRRDGA 457
>gnl|CDD|226818 COG4383, COG4383, Mu-like prophage protein gp29 [Function unknown].
Length = 517
Score = 26.0 bits (57), Expect = 7.4
Identities = 18/65 (27%), Positives = 24/65 (36%), Gaps = 16/65 (24%)
Query: 64 RGSKIRFLILPDMLKN--------------APMFKGKQGNKAGAAGRGKSGILRAQAARG 109
R +R L+ P + KN P+ GK AGA K+ +LRA G
Sbjct: 199 RNGLVRTLVWPYIFKNYSVRDFAEFLEIYGLPIRLGKYP--AGATKEEKNTLLRAVMEIG 256
Query: 110 RGRGG 114
G
Sbjct: 257 HNAAG 261
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 25.8 bits (58), Expect = 8.7
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|238601 cd01196, INT_VanD, VanD integrase, IntD, and related integrases,
DNA breaking-rejoining enzymes, integrase/recombinases,
N- and C-terminal domains. This CD includes various
bacterial integrases including those similar to IntD, a
putative integrase-like protein, a component of the vanD
glycopeptide resistance cluster in Enterococcus faecium
BM4339. Members of this CD are predominantly bacterial
in origin.
Length = 263
Score = 25.6 bits (56), Expect = 8.9
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 59 ANIYIRGSKIRFLILPDMLKN 79
A+IY +G KIR L +P L+
Sbjct: 139 ADIYSKGGKIRRLYIPKNLRV 159
>gnl|CDD|227244 COG4907, COG4907, Predicted membrane protein [Function unknown].
Length = 595
Score = 25.7 bits (56), Expect = 9.4
Identities = 13/36 (36%), Positives = 16/36 (44%)
Query: 96 RGKSGILRAQAARGRGRGGPPQRGGRGGWGGPSRGG 131
R + + RA +A R GG G GG S GG
Sbjct: 555 RSFNNLNRAYSAIASSRRSSSSGGGGGFSGGGSGGG 590
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
0.319 0.141 0.429
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: 6,885,528
Number of extensions: 614407
Number of successful extensions: 837
Number of sequences better than 10.0: 1
Number of HSP's gapped: 743
Number of HSP's successfully gapped: 76
Length of query: 132
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 46
Effective length of database: 7,123,158
Effective search space: 327665268
Effective search space used: 327665268
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 (21.7 bits)
S2: 53 (24.0 bits)