RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy874
(191 letters)
>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer
and more complex than their prokaryotic counterparts
and unlike prokaryote, RNase H are essential in higher
eukaryote. Ribonuclease H (RNase H) is classified into
two families, type 1 (prokaryotic RNase HI, eukaryotic
RNase H1 and viral RNase H) and type 2 (prokaryotic
RNase HII and HIII, and eukaryotic RNase H2). RNase H
is an endonuclease that cleaves the RNA strand of an
RNA/DNA hybrid in a sequence non-specific manner. RNase
H is involved in DNA replication, repair and
transcription. One of the important functions of RNase
H is to remove Okazaki fragments during DNA
replication. RNase H is widely present in various
organisms, including bacteria, archaea and eukaryote
and most prokaryotic and eukaryotic genomes contain
multiple RNase H genes. Despite the lack of amino acid
sequence homology, Type 1 and type 2 RNase H share a
main-chain fold and steric configurations of the four
acidic active-site (DEDD) residues and have the same
catalytic mechanism and functions in cells. Eukaryotic
RNase H is longer and more complex than in prokaryotes.
Almost all eukaryotic RNase HI have highly conserved
regions at the N-terminal called hybrid binding domain
(HBD). It is speculated that the HBD contributes to
binding the RNA/DNA hybrid. Prokaryotes and some
single-cell eukaryotes do not require RNase H for
viability, but RNase H is essential in higher
eukaryotes. RNase H knockout mice lack mitochondrial
DNA replication and die as embryos.
Length = 150
Score = 94.6 bits (236), Expect = 4e-25
Identities = 33/63 (52%), Positives = 42/63 (66%), Gaps = 1/63 (1%)
Query: 8 VVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRV-TNNNAEIQGAIHALKQAKS 66
VV+TDGAC NG+ GA AGYGVYFG +P NV+ ++ G TN AE++ IHAL+ K
Sbjct: 1 VVYTDGACRGNGRSGARAGYGVYFGPGHPRNVSERLPGPPQTNQRAELRAVIHALRLIKE 60
Query: 67 ANE 69
E
Sbjct: 61 VGE 63
>gnl|CDD|215695 pfam00075, RNase_H, RNase H. RNase H digests the RNA strand of an
RNA/DNA hybrid. Important enzyme in retroviral
replication cycle, and often found as a domain
associated with reverse transcriptases. Structure is a
mixed alpha+beta fold with three a/b/a layers.
Length = 126
Score = 53.0 bits (128), Expect = 2e-09
Identities = 27/114 (23%), Positives = 40/114 (35%), Gaps = 22/114 (19%)
Query: 4 DNHVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQ 63
V V+TDG+C N G AGY G+ K TN AE+ I AL+
Sbjct: 1 PEAVTVYTDGSCNGNPGPGG-AGYVTDGGKQ-----RSKPLPGTTNQRAELLALIEALEA 54
Query: 64 AKSANEKVKLK-----------RSYNDTHAQKKVRNVSSVAMRIAQKVD-YISH 105
+KV + + K ++N + + +K YI
Sbjct: 55 LSG--QKVNIYTDSQYVIGGITNGWPTKSESKPIKNE--IWELLQKKHKVYIQW 104
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination,
and repair].
Length = 154
Score = 51.6 bits (124), Expect = 1e-08
Identities = 22/60 (36%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
V +FTDGAC N G G+G + GR TNN AE++ I AL+ K
Sbjct: 3 KVEIFTDGACLGNPGPG---GWGAVLRYGDGEKELSGGEGRTTNNRAELRALIEALEALK 59
>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA
strand of an RNA/DNA hybrid in a sequence non-specific
manner. Ribonuclease H (RNase H) enzymes are divided
into two major families, Type 1 and Type 2, based on
amino acid sequence similarities and biochemical
properties. RNase H is an endonuclease that cleaves the
RNA strand of an RNA/DNA hybrid in a sequence
non-specific manner in the presence of divalent
cations. RNase H is widely present in various
organisms, including bacteria, archaea and eukaryotes.
Most prokaryotic and eukaryotic genomes contain
multiple RNase H genes. Despite the lack of amino acid
sequence homology, Type 1 and type 2 RNase H share a
main-chain fold and steric configurations of the four
acidic active-site residues and have the same catalytic
mechanism and functions in cells. RNase H is involved
in DNA replication, repair and transcription. One of
the important functions of RNase H is to remove Okazaki
fragments during DNA replication. RNase H inhibitors
have been explored as an anti-HIV drug target because
RNase H inactivation inhibits reverse transcription.
Length = 123
Score = 45.4 bits (108), Expect = 1e-06
Identities = 19/63 (30%), Positives = 27/63 (42%), Gaps = 5/63 (7%)
Query: 10 FTDGACPRNGKVGASAGYGVYFGENN-PLNVAGKVTGRV-TNNNAEIQGAIHALKQAKSA 67
TDG+C N AG G ++ AG ++ TNN AE+ + AL+ A
Sbjct: 1 NTDGSCKGNPG---PAGAGGVLRDHEGAWLFAGSLSIPAATNNEAELLALLEALELALDL 57
Query: 68 NEK 70
K
Sbjct: 58 GLK 60
>gnl|CDD|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly
in prokaryotes. Ribonuclease H (RNase H) is classified
into two evolutionarily unrelated families, type 1
(prokaryotic RNase HI, eukaryotic RNase H1 and viral
RNase H) and type 2 (prokaryotic RNase HII and HIII,
and eukaryotic RNase H2). RNase H is an endonuclease
that cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is involved in
DNA replication, repair and transcription. RNase H is
widely present in various organisms, including
bacteria, archaea and eukaryotes and most prokaryotic
and eukaryotic genomes contain multiple RNase H genes.
Despite the lack of amino acid sequence homology, Type
1 and type 2 RNase H share a main-chain fold and steric
configurations of the four acidic active-site (DEDD),
residues and have the same catalytic mechanism and
functions in cells. One of the important functions of
RNase H is to remove Okazaki fragments during DNA
replication. Prokaryotic RNase H varies greatly in
domain structures and substrate specificities.
Prokaryotes and some single-cell eukaryotes do not
require RNase H for viability.
Length = 139
Score = 37.9 bits (89), Expect = 6e-04
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 6/68 (8%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVY-FGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
+ ++TDGAC N G G+ ++ ++G G TNN E+ I AL+ K
Sbjct: 2 ITIYTDGACLGNPGPG---GWAAILRYGDHEKELSGGEAGT-TNNRMELTAVIEALEALK 57
Query: 66 SANEKVKL 73
V L
Sbjct: 58 -EPCPVLL 64
>gnl|CDD|187703 cd09279, RNase_HI_archaeal_like, RNAse HI family that includes
Archaeal RNase HI. Ribonuclease H (RNase H) is
classified into two evolutionarily unrelated families,
type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and
viral RNase H) and type 2 (prokaryotic RNase HII and
HIII, and eukaryotic RNase H2). RNase H is an
endonuclease that cleaves the RNA strand of an RNA/DNA
hybrid in a sequence non-specific manner. RNase H is
involved in DNA replication, repair and transcription.
RNase H is widely present in various organisms,
including bacteria, archaea and eukaryotes and most
prokaryotic and eukaryotic genomes contain multiple
RNase H genes. Despite the lack of amino acid sequence
homology, Type 1 and type 2 RNase H share a main-chain
fold and steric configurations of the four acidic
active-site (DEDD) residues and have the same catalytic
mechanism and functions in cells. One of the important
functions of RNase H is to remove Okazaki fragments
during DNA replication. Most archaeal genomes contain
only type 2 RNase H (RNase HII); however, a few contain
RNase HI as well. Although archaeal RNase HI sequences
conserve the DEDD active-site motif, they lack other
common features important for catalytic function, such
as the basic protrusion region. Archaeal RNase HI
homologs are more closely related to retroviral RNase
HI than bacterial and eukaryotic type I RNase H in
enzymatic properties.
Length = 128
Score = 37.1 bits (87), Expect = 0.001
Identities = 17/64 (26%), Positives = 25/64 (39%), Gaps = 1/64 (1%)
Query: 7 VVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKS 66
++ DGA N A AG + + L + + TNN AE + I L+ A
Sbjct: 1 WTLYFDGASRGNPG-PAGAGIVIKSPDGEVLEQSIPLGFPATNNEAEYEALIAGLELALE 59
Query: 67 ANEK 70
K
Sbjct: 60 LGIK 63
>gnl|CDD|222037 pfam13307, Helicase_C_2, Helicase C-terminal domain. This domain
is the second of two tandem AAA domains found in a wide
variety of helicase enzymes.
Length = 165
Score = 36.4 bits (85), Expect = 0.003
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 3/34 (8%)
Query: 107 VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPF 140
VI VG+PFPS D V+ +R Y D ++ F
Sbjct: 83 VIIVGLPFPSPDDPLVEARREYLD---KQGKDGF 113
Score = 33.7 bits (78), Expect = 0.027
Identities = 11/38 (28%), Positives = 15/38 (39%)
Query: 137 GIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSVAMRIA 174
G+PFPS D V+ +R Y D + R
Sbjct: 87 GLPFPSPDDPLVEARREYLDKQGKDGFREYYLPQAIRK 124
>gnl|CDD|214694 smart00491, HELICc2, helicase superfamily c-terminal domain.
Length = 142
Score = 35.7 bits (83), Expect = 0.004
Identities = 17/92 (18%), Positives = 36/92 (39%), Gaps = 5/92 (5%)
Query: 58 IHALKQAKSANEKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDYISHD----VISVGIP 113
+ K + E +L Y+ + ++ ++++ +D+ D VI VGIP
Sbjct: 21 KPVFIEGKDSGETEELLEKYSAACEARGALLLAVARGKVSEGIDF-PDDLGRAVIIVGIP 79
Query: 114 FPSIQDENVKLKRSYNDTHAQKKGIPFPSIQD 145
FP+ ++ + Y D + + D
Sbjct: 80 FPNPDSPILRARLEYLDEKGGIRPFDEVYLFD 111
Score = 27.6 bits (62), Expect = 2.7
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 137 GIPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSV--AMR-IAQ 175
GIPFP+ ++ + Y D + + + AMR +AQ
Sbjct: 77 GIPFPNPDSPILRARLEYLDEKGGIRPFDEVYLFDAMRALAQ 118
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 34.8 bits (81), Expect = 0.010
Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 9/61 (14%)
Query: 5 NHVVVFTDGACPRNGKVGASAGYGV---YFGENNPLNVAGKVTGRVTNNNAEIQGAIHAL 61
V ++TDGAC N G G+G Y G L+ +T TNN E+ AI AL
Sbjct: 2 KQVEIYTDGACLGNPGPG---GWGAILRYKGHEKELSGGEALT---TNNRMELMAAIEAL 55
Query: 62 K 62
+
Sbjct: 56 E 56
>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse
transcriptases. Ribonuclease H (RNase H) is classified
into two families, type 1 (prokaryotic RNase HI,
eukaryotic RNase H1 and viral RNase H) and type 2
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2). Ribonuclease HI (RNase HI) is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is widely present
in various organisms, including bacteria, archaea and
eukaryotes. RNase HI has also been observed as an
adjunct domain to the reverse transcriptase gene in
retroviruses, long-term repeat (LTR)-bearing
retrotransposons and non-LTR retrotransposons. RNase HI
in LTR retrotransposons perform degradation of the
original RNA template, generation of a polypurine tract
(the primer for plus-strand DNA synthesis), and final
removal of RNA primers from newly synthesized minus and
plus strands. The catalytic residues for RNase H
enzymatic activity, three aspartatic acids and one
glutamatic acid residue (DEDD), are unvaried across all
RNase H domains. The position of the RNase domain of
non-LTR and LTR transposons is at the carboxyl terminal
of the reverse transcriptase (RT) domain and their RNase
domains group together, indicating a common evolutionary
origin. Many non-LTR transposons have lost the RNase
domain because their activity is at the nucleus and
cellular RNase may suffice; however LTR retotransposons
always encode their own RNase domain because it requires
RNase activity in RNA-protein particles in the
cytoplasm. RNase H inhibitors have been explored as an
anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 128
Score = 33.8 bits (78), Expect = 0.019
Identities = 20/111 (18%), Positives = 49/111 (44%), Gaps = 13/111 (11%)
Query: 8 VVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSA 67
V++TDG+ K+ G G ++ + K+ + +AE+ + AL+ A
Sbjct: 1 VIYTDGS-----KLEGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLA--L 53
Query: 68 NEKVKLKRSYNDTHAQ------KKVRNVSSVAMRIAQKVDYISHDVISVGI 112
E + ++ + +Q + R+ S + +RI + + +++ + V +
Sbjct: 54 REGRRARKITIFSDSQAALKALRSPRSSSPLVLRIRKAIRELANHGVKVRL 104
>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA
replication, recombination, and repair].
Length = 654
Score = 34.4 bits (79), Expect = 0.032
Identities = 11/34 (32%), Positives = 18/34 (52%), Gaps = 3/34 (8%)
Query: 107 VISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPF 140
V+ VG+PFP+ D +K + + + G PF
Sbjct: 552 VVIVGLPFPNPDDPLLKARLEFL---KRLGGDPF 582
Score = 27.5 bits (61), Expect = 5.2
Identities = 6/25 (24%), Positives = 11/25 (44%)
Query: 137 GIPFPSIQDEKVKLKRSYNDTHAQK 161
G+PFP+ D +K + +
Sbjct: 556 GLPFPNPDDPLLKARLEFLKRLGGD 580
>gnl|CDD|132840 cd07201, cPLA2_Grp-IVB-IVD-IVE-IVF, Group IVB, IVD, IVE, and IVF
cytosolic phospholipase A2; catalytic domain;
Ca-dependent. Group IVB, IVD, IVE, and IVF cPLA2
consists of two domains: the regulatory C2 domain and
alpha/beta hydrolase PLA2 domain. Group IVB, IVD, IVE,
and IVF cPLA2 are also referred to as cPLA2-beta,
-delta, -epsilon, and -zeta respectively. cPLA2-beta is
approximately 30% identical to cPLA2-alpha and it shows
low enzymatic activity compared to cPLA2alpha.
cPLA2-beta hydrolyzes palmitic acid from
1-[14C]palmitoyl-2-arachidonoyl-PC and arachidonic acid
from 1-palmitoyl-2[14C]arachidonoyl-PC, but not from
1-O-alkyl-2[3H]arachidonoyl-PC. cPLA2-delta, -epsilon,
and -zeta are approximately 45-50% identical to
cPLA2-beta and 31-37% identical to cPLA2-alpha. It's
possible that cPLA2-beta, -delta, -epsilon, and -zeta
may have arisen by gene duplication from an ancestral
gene. The catalytic domain of cytosolic phospholipase A2
(PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond
of phospholipids to release arachidonic acid. At the
active site, cPLA2 contains a serine nucleophile through
which the catalytic mechanism is initiated. The active
site is partially covered by a solvent-accessible
flexible lid. cPLA2 displays interfacial activation as
it exists in both "closed lid" and "open lid" forms.
Movement of the cPLA2 lid possibly exposes a greater
hydrophobic surface and the active site. cPLA2 belongs
to the alpha-beta hydrolase family which is identified
by a characteristic nucleophile elbow with a consensus
sequence of Sm-X-Nu-Sm (Sm = small residue, X = any
residue and Nu = nucleophile). Calcium is required for
cPLA2 to bind with membranes or phospholipids. The
calcium-dependent phospholipid binding domain resides in
the N-terminal region of cPLA2; it is homologous to the
C2 domain superfamily which is not included in this
hierarchy. It includes PLA2G4B, PLA2G4D, PLA2G4E, and
PLA2G4F from humans.
Length = 541
Score = 32.3 bits (74), Expect = 0.13
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 12/64 (18%)
Query: 94 MRIAQKVDYISHDVISVGIPFPSIQDENVKLKRSYNDTHAQKKGIPFPSIQ---DEKVKL 150
+R +KVD I S+G F E +K Y ++GIPFP I+ +++ L
Sbjct: 390 LRPERKVDVILSLNYSLGSQF-----EPLKQASEY----CSEQGIPFPKIELSPEDQENL 440
Query: 151 KRSY 154
K Y
Sbjct: 441 KECY 444
>gnl|CDD|238634 cd01309, Met_dep_hydrolase_C, Metallo-dependent hydrolases,
subgroup C is part of the superfamily of
metallo-dependent hydrolases, a large group of proteins
that show conservation in their 3-dimensional fold (TIM
barrel) and in details of their active site. The vast
majority of the members have a conserved metal binding
site, involving four histidines and one aspartic acid
residue. In the common reaction mechanism, the metal ion
(or ions) deprotonate a water molecule for a
nucleophilic attack on the substrate. The function of
this subgroup is unknown.
Length = 359
Score = 30.0 bits (68), Expect = 0.82
Identities = 18/75 (24%), Positives = 26/75 (34%), Gaps = 1/75 (1%)
Query: 6 HVVVFTDGACPRNGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAK 65
VV+ TDG + + A AG + GEN P V G A +A+
Sbjct: 101 GVVIKTDGGTIEDMFIKAPAGLKMALGEN-PKRVYGGKGKEPATRMGVAALLRDAFIKAQ 159
Query: 66 SANEKVKLKRSYNDT 80
K L ++
Sbjct: 160 EYGRKYDLGKNAKKD 174
>gnl|CDD|180903 PRK07238, PRK07238, bifunctional RNase H/acid phosphatase;
Provisional.
Length = 372
Score = 29.6 bits (67), Expect = 1.0
Identities = 23/61 (37%), Positives = 28/61 (45%), Gaps = 6/61 (9%)
Query: 7 VVVFTDGACPRNGKVGASAGYG-VYFGENN--PLNVAGKVTGRVTNNNAEIQGAIHALKQ 63
VVV DG N AGYG V + + L + GR TNN AE +G I L+
Sbjct: 3 VVVEADGGSRGNPGP---AGYGAVVWDADRGEVLAERAEAIGRATNNVAEYRGLIAGLEA 59
Query: 64 A 64
A
Sbjct: 60 A 60
>gnl|CDD|217900 pfam04109, APG9, Autophagy protein Apg9. In yeast, 15 Apg proteins
coordinate the formation of autophagosomes. Autophagy is
a bulk degradation process induced by starvation in
eukaryotic cells. Apg9 plays a direct role in the
formation of the cytoplasm to vacuole targeting and
autophagic vesicles, possibly serving as a marker for a
specialised compartment essential for these
vesicle-mediated alternative targeting pathways.
Length = 365
Score = 29.1 bits (66), Expect = 1.4
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 4/54 (7%)
Query: 69 EKVKLKRSYNDTHAQKKVRNVSSVAMRIAQKVDY----ISHDVISVGIPFPSIQ 118
E++ + N A KK + +A RI +K +Y I+ D++ + +P P +
Sbjct: 14 ERIMELQDSNALTAHKKRLDAHDIANRIMRKENYLIALINKDILDLTLPLPFLG 67
>gnl|CDD|235880 PRK06860, PRK06860, lipid A biosynthesis lauroyl acyltransferase;
Provisional.
Length = 309
Score = 28.7 bits (65), Expect = 1.8
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 5/43 (11%)
Query: 26 GYGVYFGENNPLNVAGKVTGRVTNNNA-----EIQGAIHALKQ 63
G GVY +NPL + GR+ +N + +++G I ALK+
Sbjct: 151 GIGVYRPNDNPLYDWLQTWGRLRSNKSMLDRKDLKGMIKALKK 193
>gnl|CDD|233436 TIGR01490, HAD-SF-IB-hyp1, HAD-superfamily subfamily IB hydrolase,
TIGR01490. This hypothetical equivalog is a member of
the IB subfamily (TIGR01488) of the haloacid
dehalogenase (HAD) superfamily of aspartate-nucleophile
hydrolases. The sequences modelled by This model are all
bacterial. The IB subfamily includes the enzyme
phosphoserine phosphatase (TIGR00338). Due to this
relationship, several of these sequences have been
annotated as "phosphoserine phosphatase related
proteins," or "Phosphoserine phosphatase-family
enzymes." There is presently no evidence that any of the
enzymes in This model possess PSPase activity.
OMNI|NTL01ML1250 is annotated as a "possible
transferase," however this is due to the C-terminal
domain found on this sequence which is homologous to a
group of glycerol-phosphate acyltransferases (between
trusted and noise to TIGR00530). A subset of these
sequences including OMNI|CC1962, the Caulobacter
crescentus CicA protein cluster together and may
represent a separate equivalog [Unknown function,
Enzymes of unknown specificity].
Length = 202
Score = 28.1 bits (63), Expect = 2.1
Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 41 GKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSY 77
G TG + NN + +G +HAL + A E++ LK SY
Sbjct: 140 GIYTGNIDGNNCKGEGKVHALAE-LLAEEQIDLKDSY 175
>gnl|CDD|132765 cd07303, Porin3, Eukaryotic porin family that forms channels in the
mitochondrial outer membrane. The porin family 3
contains two sub-families that play vital roles in the
mitochondrial outer membrane, a translocase for unfolded
pre-proteins (Tom40) and the voltage-dependent anion
channel (VDAC) that regulates the flux of mostly anionic
metabolites through the outer mitochondrial membrane.
Length = 274
Score = 28.0 bits (62), Expect = 3.3
Identities = 22/97 (22%), Positives = 34/97 (35%), Gaps = 5/97 (5%)
Query: 18 NGKVGASAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALKQAKSANEKVKLKRSY 77
G + G V F PL + G + A Q + + +N V K Y
Sbjct: 112 TGYKRINLGCDVDFDIAGPL-IRGALVLGYEGWLAGYQMVFETVSRVTQSNFAVGYKTDY 170
Query: 78 NDTHAQKKVRNVSSVAMRIAQKVDYISHDVISVGIPF 114
N+ A V + + I KV+ D + VG+
Sbjct: 171 NEFQAHTNVNDGTEFGGSIYHKVN----DKLEVGVNL 203
>gnl|CDD|218788 pfam05872, DUF853, Bacterial protein of unknown function (DUF853).
This family consists of several bacterial proteins of
unknown function. BMEI1370 is thought to be an ATPase.
Length = 504
Score = 27.8 bits (62), Expect = 3.7
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 24 SAGYGVYFGENNPLNVAGKVTGRVTNNNAEIQGAIHALK 62
S G GVYF NPL++ V ++ N +Q HAL+
Sbjct: 290 SKGVGVYFVTQNPLDLPDTVLAQLGN---RVQ---HALR 322
>gnl|CDD|188492 TIGR03977, rSAM_pair_HxsC, His-Xaa-Ser system radical SAM maturase
HxsC. This model describes the downstream member, HxsC,
of a pair of uncharacterized radical SAM proteins,
regularly found in the context of a small protein with
four or more repeats of the tripeptide His-Xaa-Ser
(HXS). This enzyme appears to be part of a peptide
modification system.
Length = 292
Score = 27.6 bits (62), Expect = 4.3
Identities = 8/41 (19%), Positives = 21/41 (51%), Gaps = 4/41 (9%)
Query: 96 IAQKVDYISHDVISVGIPF----PSIQDENVKLKRSYNDTH 132
A+++ + H+ ++ GIP + D V+ + ++ +T
Sbjct: 116 FAKQLAALCHERLTFGIPLYAAIAELHDYIVQARGAFEETI 156
>gnl|CDD|106159 PRK13190, PRK13190, putative peroxiredoxin; Provisional.
Length = 202
Score = 27.1 bits (60), Expect = 4.4
Identities = 15/42 (35%), Positives = 20/42 (47%), Gaps = 2/42 (4%)
Query: 88 NVSSVAMRIAQKVDYISHDVISVGIPFPSIQDENVKLKRSYN 129
+V S+ IA D + IPFP I D + +L R YN
Sbjct: 68 SVDSIYSHIAWLRDIEER--FGIKIPFPVIADIDKELAREYN 107
Score = 26.4 bits (58), Expect = 8.2
Identities = 14/31 (45%), Positives = 17/31 (54%), Gaps = 2/31 (6%)
Query: 138 IPFPSIQDEKVKLKRSYN--DTHAQKKVRNV 166
IPFP I D +L R YN D ++ VR V
Sbjct: 90 IPFPVIADIDKELAREYNLIDENSGATVRGV 120
>gnl|CDD|233778 TIGR02207, lipid_A_htrB, lipid A biosynthesis lauroyl (or
palmitoleoyl) acyltransferase. This model represents a
narrow clade of acyltransferases, nearly all of which
transfer a lauroyl group to KDO2-lipid IV-A, a lipid A
precursor; these proteins are termed lipid A
biosynthesis lauroyl acyltransferase, HtrB. An exception
is a closely related paralog of E. coli HtrB, LpxP,
which acts in cold shock conditions by transferring a
palmitoleoyl rather than lauroyl group to the lipid A
precursor. Members of this family are homologous to the
family of acyltransferases responsible for the next step
in lipid A biosynthesis [Cell envelope, Biosynthesis and
degradation of surface polysaccharides and
lipopolysaccharides].
Length = 303
Score = 27.3 bits (61), Expect = 5.4
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 5/43 (11%)
Query: 26 GYGVYFGENNPLNVAGKVTGRVTNNNA-----EIQGAIHALKQ 63
G GVY NNPL + GR+ +N A +++G I ALK
Sbjct: 145 GIGVYRPHNNPLFDWIQTRGRLRSNKAMIDRKDLRGMIKALKN 187
>gnl|CDD|216223 pfam00974, Rhabdo_glycop, Rhabdovirus spike glycoprotein.
Frequently abbreviated to G protein. The glycoprotein
spike is made up of a trimer of G proteins. Channel
formed by glycoprotein spike is thought to function in a
similar manner to Influenza virus M2 protein channel,
thus allowing a signal to pass across the viral membrane
to signal for viral uncoating.
Length = 501
Score = 26.6 bits (59), Expect = 8.8
Identities = 10/32 (31%), Positives = 12/32 (37%), Gaps = 2/32 (6%)
Query: 138 IPFPSIQDEKVKLKRSYNDTHAQKKVRNVSSV 169
+P PSI+D L N K V V
Sbjct: 415 VPHPSIKDAYNTLDFFDNHIGVSKN--PVDLV 444
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
0.314 0.130 0.366
Gapped
Lambda K H
0.267 0.0745 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,364,042
Number of extensions: 832007
Number of successful extensions: 575
Number of sequences better than 10.0: 1
Number of HSP's gapped: 567
Number of HSP's successfully gapped: 39
Length of query: 191
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 100
Effective length of database: 6,901,388
Effective search space: 690138800
Effective search space used: 690138800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (25.3 bits)