RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8542
(182 letters)
>gnl|CDD|173963 cd07979, TAF9, TATA Binding Protein (TBP) Associated Factor 9
(TAF9) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 9 (TAF9) is one of several TAFs that bind TBP and
are involved in forming the TFIID complex. TFIID is one
of seven General Transcription Factors (GTF) (TFIIA,
TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved
in accurate initiation of transcription by RNA
polymerase II in eukaryotes. TFIID plays an important
role in the recognition of promoter DNA and assembly of
the pre-initiation complex. The TFIID complex is
composed of the TBP and at least 13 TAFs. TAFs from
various species were originally named by their predicted
molecular weight or their electrophoretic mobility in
polyacrylamide gels. A new, unified nomenclature for the
pol II TAFs has been suggested to show the relationship
between TAFs orthologs and paralogs. Human TAF9 has a
paralogue gene (TAF9L) which has a redundant function.
Several hypotheses are proposed for TAF function such as
serving as activator-binding sites, in core-promoter
recognition or a role in essential catalytic activity.
It has been shown that TAF9 interacts directly with
different transcription factors such as p53, herpes
simplex virus activator vp16 and the basal transcription
factor TFIIB. Each TAF, with the help of a specific
activator, is required only for expression of subset of
genes and are not universally involved for transcription
as are GTFs. In yeast and human cells, TAFs have been
found as components of other complexes besides TFIID.
TAF9 is a component of TFIID in multiple organisms as
well as different TBP-free TAF complexes containing the
GCN5-type histone acetyltransferase. Several TAFs
interact via histone-fold (HFD) motifs; HFD is the
interaction motif involved in heterodimerization of the
core histones and their assembly into nucleosome
octamers. The minimal HFD contains three alpha-helices
linked by two loops and is found in core histones, TAFS
and many other transcription factors. TFIID has a
histone octamer-like substructure. TFIID has a histone
octamer-like substructure. TAF9 is a shared subunit of
both, histone acetyltransferase complex (SAGA) and TFIID
complexes. TAF9 domain interacts with TAF6 to form a
novel histone-like heterodimer that is structurally
related to the histone H3 and H4 oligomer.
Length = 117
Score = 106 bits (266), Expect = 4e-30
Identities = 36/77 (46%), Positives = 54/77 (70%)
Query: 63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
RDA+VI + + GI Y+PR + Q+LEF YTT +L+D++VY+ HA K +D +D+KL
Sbjct: 2 RDARVIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKL 61
Query: 123 AITNQLSGSFAKPPPRE 139
AI +++ SF PPPR+
Sbjct: 62 AIQSRVDYSFTSPPPRD 78
>gnl|CDD|111209 pfam02291, TFIID-31kDa, Transcription initiation factor IID, 31kD
subunit. This family represents the N-terminus of the
31kD subunit (42kD in drosophila) of transcription
initiation factor IID (TAFII31). TAFII31 binds to p53,
and is an essential requirement for p53 mediated
transcription activation.
Length = 129
Score = 95.3 bits (237), Expect = 1e-25
Identities = 37/77 (48%), Positives = 57/77 (74%)
Query: 63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKL 122
+DA++I ++ +E GI+ Y+PR V Q+L+F + YT IL+D++VY+ HA+K +D ED++L
Sbjct: 13 KDARLIHSILKELGIQEYEPRVVLQLLDFAHRYTQKILQDAKVYSRHARKANIDAEDVRL 72
Query: 123 AITNQLSGSFAKPPPRE 139
AI +L SF PPPRE
Sbjct: 73 AIAARLDVSFTGPPPRE 89
>gnl|CDD|227425 COG5094, TAF9, Transcription initiation factor TFIID, subunit TAF9
(also component of histone acetyltransferase SAGA)
[Transcription].
Length = 145
Score = 70.0 bits (171), Expect = 1e-15
Identities = 31/80 (38%), Positives = 50/80 (62%), Gaps = 3/80 (3%)
Query: 63 RDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKK---KTVDVED 119
RD ++I + + GI+ Y+P+ Q+LEF + YT +LED+ VYA H + T+ VED
Sbjct: 15 RDVRLIHLILRSLGIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVED 74
Query: 120 IKLAITNQLSGSFAKPPPRE 139
++LA+ ++ F PPP+E
Sbjct: 75 VRLALATKVGRHFVPPPPKE 94
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 45.4 bits (108), Expect = 5e-07
Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 3/51 (5%)
Query: 84 CVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAK 134
+Q+ LE Y I ED+ A HAK+KTV EDIKLA+ + +
Sbjct: 44 ELQEALE---EYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIYGE 91
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 44.1 bits (105), Expect = 1e-06
Identities = 15/45 (33%), Positives = 25/45 (55%)
Query: 83 RCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ 127
+ + E + + ILED+ + A HAK+KT+ DI+LA+
Sbjct: 31 KAPVALQEALEDLLEEILEDAGLLARHAKRKTITPRDIQLAVRLD 75
Score = 27.5 bits (62), Expect = 1.0
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 35 RCVQQMLEFVNNYTTTILEDSRVYANHAR 63
+ + E + + ILED+ + A HA+
Sbjct: 31 KAPVALQEALEDLLEEILEDAGLLARHAK 59
>gnl|CDD|173964 cd07981, TAF12, TATA Binding Protein (TBP) Associated Factor 12
(TAF12) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 12 (TAF12) is one of several TAFs that bind TBP
and are involved in forming the TFIID complex. TFIID is
one of the seven General Transcription Factors (GTFs)
(TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are
involved in accurate initiation of transcription by RNA
polymerase II in eukaryotes. TFIID plays an important
role in the recognition of promoter DNA and assembly of
the pre-initiation complex. TFIID complex is composed of
the TBP and at least 13 TAFs. TAFs are named after their
electrophoretic mobility in polyacrylamide gels in
different species. A new, unified nomenclature has been
suggested for the pol II TAFs to show the relationship
between TAF orthologs and paralogs. Several hypotheses
are proposed for TAFs function such as serving as
activator-binding sites, core-promoter recognition or a
role in essential catalytic activity. These TAFs, with
the help of specific activators, are required only for
expression of a subset of genes and are not universally
involved for transcription as are GTFs. In yeast and
human cells, TAFs have been found as components of other
complexes besides TFIID. Several TAFs interact via
histone-fold (HFD) motifs; the HFD is the interaction
motif involved in heterodimerization of the core
histones and their assembly into nucleosome octamers.
The minimal HFD contains three alpha-helices linked by
two loops and is found in core histones, TAFs and many
other transcription factors. TFIID has a histone
octamer-like substructure. TAF12 domain interacts with
TAF4 and makes a novel histone-like heterodimer that
binds DNA and has a core promoter function of a subset
of genes.
Length = 72
Score = 36.4 bits (85), Expect = 7e-04
Identities = 11/40 (27%), Positives = 24/40 (60%)
Query: 88 MLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ 127
+LE +++ ++ED+ A H K T++V+D++L +
Sbjct: 28 LLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67
>gnl|CDD|238031 cd00076, H4, Histone H4, one of the four histones, along with H2A,
H2B and H3, which forms the eukaryotic nucleosome core;
along with H3, it plays a central role in nucleosome
formation; histones bind to DNA and wrap the genetic
material into "beads on a string" in which DNA (the
string) is wrapped around small blobs of histones (the
beads) at regular intervals; play a role in the
inheritance of specialized chromosome structures and the
control of gene activity; defects in the establishment
of proper chromosome structure by histones may activate
or silence genes aberrantly and thus lead to disease;
the sequence of histone H4 has remained almost invariant
in more than 2 billion years of evolution.
Length = 85
Score = 36.7 bits (85), Expect = 8e-04
Identities = 15/60 (25%), Positives = 28/60 (46%)
Query: 68 IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ 127
I + + G+K ++ + +Y ++ D+ Y HAK+KTV D+ A+ Q
Sbjct: 19 IRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQ 78
Score = 26.7 bits (59), Expect = 2.6
Identities = 12/65 (18%), Positives = 25/65 (38%), Gaps = 4/65 (6%)
Query: 20 IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQV----IVNMFQEA 75
I + + G+K ++ + +Y ++ D+ Y HA+ V +V +
Sbjct: 19 IRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQ 78
Query: 76 GIKNY 80
G Y
Sbjct: 79 GRTLY 83
>gnl|CDD|201453 pfam00808, CBFD_NFYB_HMF, Histone-like transcription factor
(CBF/NF-Y) and archaeal histone. This family includes
archaebacterial histones and histone like transcription
factors from eukaryotes.
Length = 65
Score = 32.2 bits (74), Expect = 0.020
Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 19/63 (30%)
Query: 62 ARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIK 121
++DA+ ++ CV++ +EF I ++ K+KT++ E IK
Sbjct: 22 SQDAKELIA------------ECVEEFIEF-------IASEAAEICKKEKRKTINAEHIK 62
Query: 122 LAI 124
LA+
Sbjct: 63 LAV 65
>gnl|CDD|185397 PTZ00015, PTZ00015, histone H4; Provisional.
Length = 102
Score = 32.4 bits (74), Expect = 0.034
Identities = 10/34 (29%), Positives = 18/34 (52%)
Query: 94 NYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ 127
+ ++ DS Y +A++KTV D+ A+ Q
Sbjct: 62 AFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQ 95
>gnl|CDD|219450 pfam07524, Bromo_TP, Bromodomain associated. This domain is
predicted to bind DNA and is often found associated with
pfam00439 and in transcription factors. It has a
histone-like fold.
Length = 77
Score = 31.9 bits (73), Expect = 0.036
Identities = 10/66 (15%), Positives = 28/66 (42%)
Query: 61 HARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDI 120
H V+ + + AG + + ++ + + +Y + ++ +A HA + + D+
Sbjct: 5 HDLLKVVVAQILETAGFDSAEESALETLTDIAQSYIQELGRQAKRFAEHAGRSEPTLFDV 64
Query: 121 KLAITN 126
L +
Sbjct: 65 VLTLKE 70
Score = 28.8 bits (65), Expect = 0.47
Identities = 11/66 (16%), Positives = 29/66 (43%), Gaps = 4/66 (6%)
Query: 18 QVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQV----IVNMFQ 73
V+ + + AG + + ++ + + +Y + ++ +A HA ++ +V +
Sbjct: 10 VVVAQILETAGFDSAEESALETLTDIAQSYIQELGRQAKRFAEHAGRSEPTLFDVVLTLK 69
Query: 74 EAGIKN 79
E GI
Sbjct: 70 EMGINV 75
>gnl|CDD|223818 COG0747, DdpA, ABC-type dipeptide transport system, periplasmic
component [Amino acid transport and metabolism].
Length = 556
Score = 32.2 bits (73), Expect = 0.12
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 8/56 (14%)
Query: 23 MFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIK 78
+ EAG K+ D F T LE + A++I + GIK
Sbjct: 372 LLDEAGYKDNDG--------FGGGPLTLTLESAGYNPGARAIAELIQAQLAKIGIK 419
>gnl|CDD|173968 cd08050, TAF6, TATA Binding Protein (TBP) Associated Factor 6
(TAF6) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 6 (TAF6) is one of several TAFs that bind TBP and
are involved in forming Transcription Factor IID (TFIID)
complex. TFIID is one of seven General Transcription
Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and
TFIID) that are involved in accurate initiation of
transcription by RNA polymerase II in eukaryotes. TFIID
plays an important role in the recognition of promoter
DNA and assembly of the pre-initiation complex. TFIID
complex is composed of the TBP and at least 13 TAFs.
TAFs are named after their electrophoretic mobility in
polyacrylamide gels in different species. A new, unified
nomenclature has been suggested for the pol II TAFs to
show the relationship between TAF orthologs and
paralogs. Several hypotheses are proposed for TAFs
functions such as serving as activator-binding sites,
core-promoter recognition or a role in essential
catalytic activity. These TAFs, with the help of
specific activators, are required only for expression of
a subset of genes and are not universally involved for
transcription as are GTFs. In yeast and human cells,
TAFs have been found as components of other complexes
besides TFIID. Several TAFs interact via histone-fold
(HFD) motifs; the HFD is the interaction motif involved
in heterodimerization of the core histones and their
assembly into nucleosome octamers. The minimal HFD
contains three alpha-helices linked by two loops and is
found in core histones, TAFs and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF6 is a shared subunit of histone
acetyltransferase complex SAGA and TFIID complexes. TAF6
domain interacts with TAF9 and makes a novel
histone-like heterodimer that is structurally related to
histones H4 and H3. TAF6 may also interact with the
downstream core promoter element (DPE).
Length = 343
Score = 31.1 bits (71), Expect = 0.28
Identities = 11/57 (19%), Positives = 26/57 (45%)
Query: 68 IVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAI 124
I + + GI + Q + E V I++++ + H+K++ + D+ A+
Sbjct: 5 IKLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHAL 61
>gnl|CDD|133319 cd04119, RJL, Rab GTPase family J-like (RabJ-like). RJLs are
found in many protists and as chimeras with C-terminal
DNAJ domains in deuterostome metazoa. They are not
found in plants, fungi, and protostome metazoa,
suggesting a horizontal gene transfer between protists
and deuterostome metazoa. RJLs lack any known membrane
targeting signal and contain a degenerate
phosphate/magnesium-binding 3 (PM3) motif, suggesting
an impaired ability to hydrolyze GTP. GTPase activating
proteins (GAPs) interact with GTP-bound Rab and
accelerate the hydrolysis of GTP to GDP. Guanine
nucleotide exchange factors (GEFs) interact with
GDP-bound Rabs to promote the formation of the
GTP-bound state. Rabs are further regulated by guanine
nucleotide dissociation inhibitors (GDIs), which
facilitate Rab recycling by masking C-terminal lipid
binding and promoting cytosolic localization.
Length = 168
Score = 29.6 bits (67), Expect = 0.56
Identities = 14/38 (36%), Positives = 18/38 (47%)
Query: 43 FVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIKNY 80
FV+ Y TI D V R+ +V VN F +G Y
Sbjct: 25 FVSKYLPTIGIDYGVKKVSVRNKEVRVNFFDLSGHPEY 62
>gnl|CDD|129039 smart00803, TAF, TATA box binding protein associated factor. TAFs
(TATA box binding protein associated factors) are part
of the transcription initiation factor TFIID multimeric
protein complex. TFIID is composed of the TATA box
binding protein (TBP) and a number of TAFs. The TAFs
provide binding sites for many different transcriptional
activators and co-activators that modulate transcription
initiation by Pol II. TAF proteins adopt a histone-like
fold.
Length = 65
Score = 28.0 bits (63), Expect = 0.70
Identities = 12/54 (22%), Positives = 25/54 (46%)
Query: 71 MFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAI 124
+ + GI N + + E V I++++ + H+K+ T+ DI A+
Sbjct: 11 VAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSAL 64
>gnl|CDD|177669 PLN00035, PLN00035, histone H4; Provisional.
Length = 103
Score = 28.6 bits (64), Expect = 0.81
Identities = 10/37 (27%), Positives = 19/37 (51%)
Query: 91 FVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQ 127
+ + ++ D+ Y HA++KTV D+ A+ Q
Sbjct: 58 VLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94
>gnl|CDD|173881 cd08516, PBP2_NikA_DppA_OppA_like_11, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 457
Score = 29.1 bits (66), Expect = 1.2
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 31 NYDPRCVQQMLE---FVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIK 78
YDP + +L + N + TIL S+ Y H AQVI GI
Sbjct: 299 KYDPEKAKALLAEAGYPNGFDFTILVTSQ-YGMHVDTAQVIQAQLAAIGIN 348
>gnl|CDD|204764 pfam11865, DUF3385, Domain of unknown function (DUF3385). This
domain is functionally uncharacterized. This domain is
found in eukaryotes. This presumed domain is typically
between 160 to 172 amino acids in length. This domain is
found associated with pfam00454, pfam02260, pfam02985,
pfam02259 and pfam08771.
Length = 160
Score = 28.4 bits (64), Expect = 1.3
Identities = 10/29 (34%), Positives = 18/29 (62%)
Query: 51 ILEDSRVYANHARDAQVIVNMFQEAGIKN 79
IL+D + ++H Q I+N+F+ G+K
Sbjct: 94 ILKDPSLSSHHTAVVQAIMNIFKSLGLKC 122
>gnl|CDD|128846 smart00576, BTP, Bromodomain transcription factors and PHD domain
containing proteins. subdomain of archael histone-like
transcription factors.
Length = 77
Score = 27.3 bits (61), Expect = 1.4
Identities = 11/67 (16%), Positives = 29/67 (43%)
Query: 61 HARDAQVIVNMFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDI 120
A + + + AG ++ ++ + + + +Y + + YA A + ++ D+
Sbjct: 5 FALLRIAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDV 64
Query: 121 KLAITNQ 127
LA+ N
Sbjct: 65 VLALENL 71
>gnl|CDD|215692 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac,
Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with
GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025,
pfam00063. As regards Rab GTPases, these are important
regulators of vesicle formation, motility and fusion.
They share a fold in common with all Ras GTPases: this
is a six-stranded beta-sheet surrounded by five
alpha-helices.
Length = 162
Score = 27.9 bits (63), Expect = 2.0
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 5/35 (14%)
Query: 90 EFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAI 124
+F Y TI D + K VD + +KL I
Sbjct: 23 KFPEEYIPTIGVD-----FYTKTIEVDGKTVKLQI 52
>gnl|CDD|185400 PTZ00018, PTZ00018, histone H3; Provisional.
Length = 136
Score = 27.6 bits (61), Expect = 2.8
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 85 VQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLA 123
V + E Y + ED+ + A HAK+ T+ +DI+LA
Sbjct: 90 VLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 128
>gnl|CDD|215949 pfam00496, SBP_bac_5, Bacterial extracellular solute-binding
proteins, family 5 Middle. The borders of this family
are based on the PDBSum definitions of the domain edges
for Salmonella typhimurium oppA.
Length = 362
Score = 27.8 bits (62), Expect = 3.8
Identities = 11/56 (19%), Positives = 17/56 (30%), Gaps = 12/56 (21%)
Query: 23 MFQEAGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIK 78
+ EAG K+ D + T A+ I ++ GIK
Sbjct: 269 LLAEAGYKDGDGD-----GRLLLLLTND-------NPPAKAIAEAIQQQLKKIGIK 312
>gnl|CDD|128694 smart00417, H4, Histone H4.
Length = 74
Score = 26.0 bits (57), Expect = 4.0
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 95 YTTTILEDSRVYANHAKKKTVDVEDIKLA 123
+ ++ D+ Y HA++KTV D+ A
Sbjct: 46 FLENVVRDAVTYTEHARRKTVTAMDVVYA 74
>gnl|CDD|225116 COG2206, COG2206, c-di-GMP phosphodiesterase class II (HD-GYP
domain) [Signal transduction mechanisms].
Length = 344
Score = 27.1 bits (60), Expect = 6.4
Identities = 9/44 (20%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 17 AQVIVNMFQEAGIKNYDPRCVQQMLEFVNNY---TTTILEDSRV 57
+ + + + +G +DP+ V L+ ++ Y + +L + RV
Sbjct: 285 EEALEELRKNSG-GKFDPKVVDAFLKALSKYPIGSLVLLNNGRV 327
Score = 27.1 bits (60), Expect = 6.4
Identities = 9/44 (20%), Positives = 22/44 (50%), Gaps = 4/44 (9%)
Query: 65 AQVIVNMFQEAGIKNYDPRCVQQMLEFVNNY---TTTILEDSRV 105
+ + + + +G +DP+ V L+ ++ Y + +L + RV
Sbjct: 285 EEALEELRKNSG-GKFDPKVVDAFLKALSKYPIGSLVLLNNGRV 327
>gnl|CDD|227505 COG5178, PRP8, U5 snRNP spliceosome subunit [RNA processing and
modification].
Length = 2365
Score = 27.2 bits (60), Expect = 6.6
Identities = 12/66 (18%), Positives = 29/66 (43%)
Query: 75 AGIKNYDPRCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVDVEDIKLAITNQLSGSFAK 134
+G+ R + + +++ + + RV+A +A+K+ + + L S+ +
Sbjct: 1384 SGMTTNGERLIPAAMRYISRWEYEFEDSQRVWAEYARKRQEAGQQNRRLTLEDLEMSWDR 1443
Query: 135 PPPRES 140
PR S
Sbjct: 1444 GIPRIS 1449
>gnl|CDD|128705 smart00428, H3, Histone H3.
Length = 105
Score = 25.5 bits (56), Expect = 9.0
Identities = 12/29 (41%), Positives = 19/29 (65%)
Query: 95 YTTTILEDSRVYANHAKKKTVDVEDIKLA 123
Y + ED+ + A HAK+ T+ +DI+LA
Sbjct: 69 YLVGLFEDTNLLAIHAKRVTIMPKDIQLA 97
>gnl|CDD|173880 cd08515, PBP2_NikA_DppA_OppA_like_10, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 460
Score = 26.4 bits (59), Expect = 9.4
Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 3/51 (5%)
Query: 31 NYDPRCVQQMLE---FVNNYTTTILEDSRVYANHARDAQVIVNMFQEAGIK 78
YDP + +L + + + Y N A+ IV M++ GI
Sbjct: 305 PYDPEKAKALLAEAGYPDGFEIDYYAYRGYYPNDRPVAEAIVGMWKAVGIN 355
>gnl|CDD|222968 PHA03065, PHA03065, Hypothetical protein; Provisional.
Length = 438
Score = 26.5 bits (59), Expect = 9.6
Identities = 25/128 (19%), Positives = 42/128 (32%), Gaps = 30/128 (23%)
Query: 20 IVNMFQEAGIKNYDPRC------VQQMLEFVNNYTTTILEDSRVYANHARDAQVIVNMFQ 73
I N+ + IKNY + V +++F+N Y + D VY A V F
Sbjct: 267 IDNVVRSLAIKNYSLKTTDRTVDVDNIIDFINRYASL---DESVYREVPPCA-CTVQEFI 322
Query: 74 EAGI----KNYDP-------------RCVQQMLEFVNNYTTTILEDSRVYANHAKKKTVD 116
+ + ++ C LE + +E + A+ K V
Sbjct: 323 FSALAEKWADFKDTYLLTGVSLCAQLICA---LEPRKEISVEEVETLLSLIDSARNKKVT 379
Query: 117 VEDIKLAI 124
+ DI
Sbjct: 380 INDIASVA 387
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
0.313 0.126 0.347
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,551,712
Number of extensions: 751206
Number of successful extensions: 570
Number of sequences better than 10.0: 1
Number of HSP's gapped: 569
Number of HSP's successfully gapped: 41
Length of query: 182
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 91
Effective length of database: 6,901,388
Effective search space: 628026308
Effective search space used: 628026308
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 (21.9 bits)
S2: 56 (25.3 bits)