RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5326
(157 letters)
>gnl|CDD|133004 cd02510, pp-GalNAc-T, pp-GalNAc-T initiates the formation of
mucin-type O-linked glycans. UDP-GalNAc: polypeptide
alpha-N-acetylgalactosaminyltransferases (pp-GalNAc-T)
initiate the formation of mucin-type, O-linked glycans
by catalyzing the transfer of
alpha-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to
hydroxyl groups of Ser or Thr residues of core proteins
to form the Tn antigen (GalNAc-a-1-O-Ser/Thr). These
enzymes are type II membrane proteins with a GT-A type
catalytic domain and a lectin domain located on the
lumen side of the Golgi apparatus. In human, there are
15 isozymes of pp-GalNAc-Ts, representing the largest of
all glycosyltransferase families. Each isozyme has
unique but partially redundant substrate specificity for
glycosylation sites on acceptor proteins.
Length = 299
Score = 32.2 bits (74), Expect = 0.078
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 95 PTIGGFSWSGHYTWIPIPDFDTRIMNNPTDPVP 127
GGF WS H+ W+P+P+ + R +PT P+
Sbjct: 136 DARGGFDWSLHFKWLPLPEEERR-RESPTAPIR 167
>gnl|CDD|222834 PHA01755, PHA01755, hypothetical protein.
Length = 562
Score = 29.6 bits (66), Expect = 0.67
Identities = 13/43 (30%), Positives = 20/43 (46%)
Query: 106 YTWIPIPDFDTRIMNNPTDPVPPDFKNLEHPPIKCITFTPTPL 148
+ IPI + I N+ DP P F+ L + I +P+ L
Sbjct: 218 FYVIPITAYTITITNSQPDPTPSPFQQLLILNLSNIISSPSQL 260
>gnl|CDD|227903 COG5616, COG5616, Predicted integral membrane protein [Function
unknown].
Length = 152
Score = 27.7 bits (62), Expect = 1.7
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 48 GLTNDIITKIMKIEAFNKVLSDHISYTRKIPDARFPE 84
GLT DIIT + + V++ + S+T K E
Sbjct: 47 GLTEDIITDLSRFREL-FVIARNSSFTYKGKAVDVRE 82
>gnl|CDD|132910 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryotic RNA polymerase
(RNAP) I and RNAP III. The eukaryotic AC40 subunit of
RNA polymerase (RNAP) I and RNAP III is involved in the
assembly of RNAP subunits. RNAP is a large multi-subunit
complex responsible for the synthesis of RNA. It is the
principal enzyme of the transcription process, and is a
final target in many regulatory pathways that control
gene expression in all living cells. At least three
distinct RNAP complexes are found in eukaryotic nuclei:
RNAP I, RNAP II, and RNAP III. RNAP I is responsible for
the synthesis of ribosomal RNA precursor, while RNAP III
functions in the synthesis of 5S and tRNA. The AC40
subunit is the equivalent of the RPB3 subunit of RNAP
II. The RPB3 subunit is similar to the bacterial RNAP
alpha subunit in that it contains two subdomains: one
subdomain is similar the eukaryotic Rpb11/AC19/archaeal
L subunit which is involved in dimerization; and the
other is an inserted beta sheet subdomain. The RPB3
subunit heterodimerizes with the RPB11 subunit, and
together with RPB10 and RPB12, anchors the two largest
subunits, RPB1 and RPB2, and stabilizes their
association. The homology of AC40 to RPB3 suggests a
similar function. The AC40 subunit is likely to
associate with the RPB11 counterpart, AC19, to form a
heterodimer, which stabilizes the association of the two
largest subunits of RNAP I and RNAP III.
Length = 291
Score = 27.9 bits (63), Expect = 2.5
Identities = 12/27 (44%), Positives = 15/27 (55%)
Query: 103 SGHYTWIPIPDFDTRIMNNPTDPVPPD 129
SG W+PI + R +NP PV PD
Sbjct: 122 SGDLKWVPIGSQEKRFADNPIRPVHPD 148
>gnl|CDD|219404 pfam07415, Herpes_LMP2, Gammaherpesvirus latent membrane protein
(LMP2) protein. This family consists of several
Gammaherpesvirus latent membrane protein (LMP2)
proteins. Epstein-Barr virus is a human Gammaherpesvirus
that infects and establishes latency in B lymphocytes in
vivo. The latent membrane protein 2 (LMP2) gene is
expressed in latently infected B cells and encodes two
protein isoforms, LMP2A and LMP2B, that are identical
except for an additional N-terminal 119 aa cytoplasmic
domain which is present in the LMP2A isoform. LMP2A is
thought to play a key role in either the establishment
or the maintenance of latency and/or the reactivation of
productive infection from the latent state. The
significance of LMP2B and its role in pathogenesis
remain unclear.
Length = 489
Score = 27.5 bits (61), Expect = 3.8
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 120 NNPTDPVPPDFKNLEHPP 137
+ P PVP D+ H P
Sbjct: 40 DRPGPPVPEDYDAPSHRP 57
>gnl|CDD|204057 pfam08767, CRM1_C, CRM1 C terminal. CRM1 (also known as
Exportin1) mediates the nuclear export of proteins
bearing a leucine-rich nuclear export signal (NES).
CRM1 forms a complex with the NES containing protein
and the small GTPase Ran. This region forms an alpha
helical structure formed by six helical hairpin motifs
that are structurally similar to the HEAT repeat, but
share little sequence similarity to the HEAT repeat.
Length = 279
Score = 27.2 bits (61), Expect = 4.1
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 8/43 (18%)
Query: 42 RAGTLPGLTNDIITKIMKIEAFNKVLSDHISYTRKIPDARFPE 84
+A L + N+++ ++ + VL D Y R +PDAR PE
Sbjct: 57 KAEDLEEVGNNLVPPLL-----DAVLGD---YQRNVPDAREPE 91
>gnl|CDD|220556 pfam10082, DUF2320, Uncharacterized protein conserved in bacteria
(DUF2320). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 380
Score = 27.3 bits (61), Expect = 4.2
Identities = 8/24 (33%), Positives = 10/24 (41%), Gaps = 1/24 (4%)
Query: 90 YDED-LPTIGGFSWSGHYTWIPIP 112
+D+ L I G SW W P
Sbjct: 247 FDDPRLEDISGLSWDASLVWSPTR 270
>gnl|CDD|221843 pfam12903, DUF3830, Protein of unknown function (DUF3830). This is
a family of bacterial and archaeal proteins, the
structure for one of whose members has been
characterized. PDB:3kop probably adopts a new hexameric
form compared to previous structures. The putative
active is near the domain interface. 3kop is most
closely related, structurally to PDB:1zx8, where the
potential active site is located near residues E51 and
Y53 (conserved in 1zx8). Beyond the two residues above,
the other residues are not conserved. Also the shape of
the active site differs from that of 1zx8. PDB:1zx8
belongs to family DUF369. pfam04126, which is part of
the cyclophilin-like clan.
Length = 147
Score = 26.6 bits (59), Expect = 4.4
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 3/31 (9%)
Query: 102 WSGHYTWIPIPDFDTRIM--NNPT-DPVPPD 129
++G+ + +P F + NPT P+P D
Sbjct: 41 YAGNEIYTLLPSFAAQEPPAENPTVTPIPGD 71
>gnl|CDD|234894 PRK01059, PRK01059, ATP:guanido phosphotransferase; Provisional.
Length = 346
Score = 26.7 bits (60), Expect = 5.4
Identities = 13/39 (33%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 49 LTNDIITKIMKIEA--FNKVLSDHISYTRKIPDARFPEC 85
L ND ++ MK + + VLS I R + D FP
Sbjct: 3 LPNDALSNWMKGDGPDSDIVLSSRIRLARNLKDIPFPNK 41
>gnl|CDD|221385 pfam12028, DUF3515, Protein of unknown function (DUF3515). This
family of proteins is functionally uncharacterized. This
protein is found in bacteria. Proteins in this family
are typically between 166 to 214 amino acids in length.
This protein has a conserved RCG sequence motif.
Length = 158
Score = 26.2 bits (58), Expect = 5.8
Identities = 11/25 (44%), Positives = 12/25 (48%), Gaps = 3/25 (12%)
Query: 78 PDARFPECHELKYDEDLP-TIGGFS 101
PDA P C L LP T+GG
Sbjct: 33 PDADSPACAAL--VAALPDTLGGLR 55
>gnl|CDD|173864 cd08499, PBP2_Ylib_like, The substrate-binding component of an
uncharacterized ABC-type peptide import system Ylib
contains the type 2 periplasmic binding fold. This
family represents the periplasmic substrate-binding
component of an uncharacterized ATP-binding cassette
(ABC)-type peptide transport system YliB. Although the
ligand specificity of Ylib protein is not known, it
shares significant sequence similarity to the ABC-type
dipeptide and oligopeptide binding proteins. 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 = 474
Score = 26.4 bits (59), Expect = 8.2
Identities = 11/19 (57%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 22 YEGLIKEDED-KIIPGLGE 39
YEGL+ D+D KI+P L E
Sbjct: 31 YEGLVGFDKDMKIVPVLAE 49
>gnl|CDD|226624 COG4143, TbpA, ABC-type thiamine transport system, periplasmic
component [Coenzyme metabolism].
Length = 336
Score = 26.2 bits (58), Expect = 8.2
Identities = 7/25 (28%), Positives = 11/25 (44%), Gaps = 1/25 (4%)
Query: 121 NPTDPVPPDFKNLEHPPIKCITFTP 145
P+P F L P K ++ +P
Sbjct: 293 VKNVPLPAVFDALVKPA-KTVSLSP 316
>gnl|CDD|218792 pfam05880, Fiji_64_capsid, Fijivirus 64 kDa capsid protein. This
family consists of several Fijivirus 64 kDa capsid
proteins.
Length = 559
Score = 26.3 bits (58), Expect = 8.9
Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 3/49 (6%)
Query: 4 VYFKIPDNKLSTQDLHARYEGLIKEDEDKIIPGLGENGRAGTLPGLTND 52
VY P + + L +R LIK D ++ TL T D
Sbjct: 500 VYKTDPSSVIMNSVLISRANNLIKSDRKRLRKK---TQADNTLTANTLD 545
>gnl|CDD|173859 cd08494, PBP2_NikA_DppA_OppA_like_6, 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 = 448
Score = 26.1 bits (58), Expect = 9.1
Identities = 11/19 (57%), Positives = 14/19 (73%), Gaps = 1/19 (5%)
Query: 22 YEGLIKEDED-KIIPGLGE 39
YE L++ DED K+ PGL E
Sbjct: 32 YETLVRRDEDGKVQPGLAE 50
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
0.320 0.142 0.451
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,646,625
Number of extensions: 811086
Number of successful extensions: 655
Number of sequences better than 10.0: 1
Number of HSP's gapped: 655
Number of HSP's successfully gapped: 17
Length of query: 157
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 68
Effective length of database: 6,990,096
Effective search space: 475326528
Effective search space used: 475326528
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: 55 (25.0 bits)