RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11419
(244 letters)
>gnl|CDD|211388 cd11302, O-FucT-1, GDP-fucose protein O-fucosyltransferase 1. The
protein O-fucosyltransferase 1 (Ofut1 or O-FucT-1) adds
O-fucose to EGF (epidermal growth factor-like) repeats.
The O-fucsosylation of the Notch receptor signaling
protein is dependent on this enzyme, which requires
GDP-fucose as a substrate. O-fucose residues added to
the target of O-FucT-1 may be further elongated by other
glycosyltransferases. On top of O-fucosylation, O-FucT-1
may have other functions such as the regulation of the
Notch receptor exit from the ER. Six highly conserved
cysteines are present in O-FucT-1, which is a soluble ER
protein, as well as a DXD-like motif (ERD), conserved in
mammals, Drosophila, and C. elegans. Both features are
characteristic of several glycosyltransferase families.
The membrane-bound pre-protein is released by
proteolysis and, as for most glycosyltransferases, is
strongly activated by manganese. O-FucT-1 is similar to
family 1 glycosyltransferases (GT1).
Length = 347
Score = 360 bits (926), Expect = e-126
Identities = 127/240 (52%), Positives = 154/240 (64%), Gaps = 36/240 (15%)
Query: 1 RFGNQADNFLGALALAKGINRTLVLPPWVEYRYGEPKSIQVPFDTYFQVEPLQEYHRVMT 60
RFGNQAD+FLG+LA AK +NRTLVLPPW+EYR+G P S+Q+PFD YF+VEPLQEYHRV+T
Sbjct: 14 RFGNQADHFLGSLAFAKALNRTLVLPPWIEYRHGPPPSVQIPFDDYFKVEPLQEYHRVIT 73
Query: 61 MEKFMQDIAPHIWPPHKRIAFCYMARGSTNESSCNAKEGNPFGPFWDTYGIDFVGSEFYG 120
ME FM+++AP IWPP KR +CY R S + C KEGNPFGPFWD +G+DF GSE YG
Sbjct: 74 MEDFMEELAPTIWPPGKRKGYCYSPRASPDSKDCPMKEGNPFGPFWDHFGVDFDGSELYG 133
Query: 121 PLHYDVHHSDIAEHWKMRYPSDDWPVSGYCRTMGRTPSLAAIQTLNPLGKKSLSNFQCFP 180
PL YD + D+ E W R+P + P
Sbjct: 134 PLSYDTFYPDVREAWNERFPPSEH-----------------------------------P 158
Query: 181 VIAFTGAPGSFPVQDENRVLQKYLVWTEKIANQAKTFIKNKLPAGAYIGIHLRNGIDWPR 240
V+AFTGAP SFPV ENR L KYL W+++I +A FI LP ++GIHLRNGIDW
Sbjct: 159 VLAFTGAPASFPVLPENRPLHKYLEWSDEIVKEADEFINENLP-RPFVGIHLRNGIDWKN 217
>gnl|CDD|220652 pfam10250, O-FucT, GDP-fucose protein O-fucosyltransferase. This
is a family of conserved proteins representing the
enzyme responsible for adding O-fucose to EGF (epidermal
growth factor-like) repeats. Six highly conserved
cysteines are present in O-FucT-1 as well as a DXD-like
motif (ERD), conserved in mammals, Drosophila, and C.
elegans. Both features are characteristic of several
glycosyltransferase families. The enzyme is a
membrane-bound protein released by proteolysis and, as
for most glycosyltransferases, is strongly activated by
manganese.
Length = 315
Score = 139 bits (352), Expect = 7e-40
Identities = 58/245 (23%), Positives = 85/245 (34%), Gaps = 82/245 (33%)
Query: 1 RFGNQADNFLGALALAKGINRTLVLPPWVE-YRYGEPKSIQVPFDTYFQVEPLQEYH-RV 58
F Q D A+A+A+ +N TLVLPPW E Y + +P F +F VE Y RV
Sbjct: 9 GFNQQRDVICDAVAVARLLNATLVLPPWDELYHWKDPSK----FSDFFDVEHFISYLSRV 64
Query: 59 MTMEKFMQDIAPHIWPPHKRIAFCYMARGSTNESSCNAKEGNPFGPFWDTYGIDFVGSEF 118
+ + KF+ P P KR+ +DT+ +DF
Sbjct: 65 VEIVKFL----PKELPSAKRLQ-------------------------YDTFKVDFRVCVQ 95
Query: 119 YGPLHYDVHHSDIAEHWKMRYPSDDWPVSGYCRTMGRTPSLAAIQTLNPLGKKSLSNFQC 178
P +Y ++++ PL KK
Sbjct: 96 SSPSYY-------------------------------------LESVLPLLKKH------ 112
Query: 179 FPVIAFTGAPGSFPVQDENRVLQK--YLVWTEKIANQAKTFIKNKL-PAGAYIGIHLRNG 235
VIA TGAP LQ+ L ++ +I + L G ++ +HLR
Sbjct: 113 -KVIALTGAPARLANNYLPPDLQRLHALRFSPEIEELGNKLVSRLLAKGGPFLAVHLRRE 171
Query: 236 IDWPR 240
ID
Sbjct: 172 IDMFS 176
>gnl|CDD|211383 cd11296, O-FucT_like, GDP-fucose protein O-fucosyltransferase and
related proteins. O-fucosyltransferase-like proteins
are GDP-fucose dependent enzymes with similarities to
the family 1 glycosyltransferases (GT1). They are
soluble ER proteins that may be proteolytically cleaved
from a membrane-associated preprotein, and are involved
in the O-fucosylation of protein substrates, the core
fucosylation of growth factor receptors, and other
processes.
Length = 206
Score = 37.4 bits (87), Expect = 0.003
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 197 NRVLQKYLVWTEKIANQAKTFIKN--KLPAGAYIGIHLRNGIDW 238
R++ K+L ++ +I A F++ LP G Y+ +HLR G
Sbjct: 42 IRLVGKHLRFSPEIRKLADRFVRKLLGLPGGPYLAVHLRRGDFE 85
Score = 35.5 bits (82), Expect = 0.012
Identities = 15/26 (57%), Positives = 17/26 (65%)
Query: 2 FGNQADNFLGALALAKGINRTLVLPP 27
F NQ + FL AL LA + RTLVLP
Sbjct: 11 FNNQRNEFLNALLLAILLGRTLVLPL 36
>gnl|CDD|211384 cd11298, O-FucT-2, GDP-fucose protein O-fucosyltransferase 2.
O-FucT-2 adds O-fucose to thrombospondin type 1 repeats
(TSRs), and appears conserved in bilateria. The
O-fucosylation of TSRs appears to play a role in
regulating secretion of metalloproteases of the ADAMTS
superfamily. O-fucosyltransferase-like proteins are
GDP-fucose dependent enzymes with similarities to the
family 1 glycosyltransferases (GT1). They are soluble
ER proteins that may be proteolytically cleaved from a
membrane-associated preprotein, and are involved in the
O-fucosylation of protein substrates, the core
fucosylation of growth factor receptors, and other
processes.
Length = 374
Score = 32.2 bits (74), Expect = 0.22
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 3/53 (5%)
Query: 23 LVLPPW---VEYRYGEPKSIQVPFDTYFQVEPLQEYHRVMTMEKFMQDIAPHI 72
LVLPPW ++ + K ++P+ +F +E L Y V+ E+F+++ P
Sbjct: 40 LVLPPWGRLYHWKSRDIKQSRLPWSLFFDLESLNRYIPVIEYEEFLKETGPVS 92
>gnl|CDD|132588 TIGR03549, TIGR03549, YcaO domain protein. This family consists of
remarkably well-conserved proteins from gamma and beta
Proteobacteria, heavily skewed towards organisms of
marine environments. Its gene neighborhood is not
conserved. This family has an OsmC-like N-terminal
domain. It shares a YcaO domain, frequently associated
with ATP-dependent cyclodehydration for peptide
modification. The function is unknown. Fifteen of the
first sixteen members of this family are from
selenouridine-positive genomes, but this correlation may
not be meaningful.
Length = 718
Score = 30.2 bits (68), Expect = 1.3
Identities = 24/85 (28%), Positives = 39/85 (45%), Gaps = 19/85 (22%)
Query: 66 QDIAPHIWPPHKRIAFCYM----ARGSTNESS-CNAKEGNPFGPFWDTYGID-FVGSEFY 119
++I P++W H R A M +G+T ES+ C+A G F + + F +F+
Sbjct: 182 RNIVPNVWSLHIRDAASPMCFTNGKGATKESALCSA-----LGEFIERLNCNFFYNDQFF 236
Query: 120 GPLHYDVHHSDIAEHWKMRYPSDDW 144
G DIA + YP++ W
Sbjct: 237 G--------EDIANSAFVHYPNEKW 253
>gnl|CDD|150430 pfam09755, DUF2046, Uncharacterized conserved protein H4 (DUF2046).
This is the conserved N-terminal 350 residues of a
family of proteins of unknown function possibly
containing a coiled-coil domain.
Length = 308
Score = 29.2 bits (65), Expect = 2.0
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 193 VQDENRVLQKYLVWTEKIANQAKTFIKNKL 222
+Q+ENR L++ V + A Q + FI N L
Sbjct: 53 LQEENRALRQASVSIQAKAEQEEEFISNTL 82
>gnl|CDD|132160 TIGR03116, cas_csf3, CRISPR type AFERR-associated protein Csf3.
Members of this family show up near CRISPR repeats in
Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp.
EbN1, and Rhodoferax ferrireducens DSM 15236. In the
latter two species, the CRISPR/cas locus is found on a
plasmid. This family is one of several characteristic of
a type of CRISPR-associated (cas) gene cluster we
designate Aferr after A. ferrooxidans, where it is both
chromosomal and the only type of cas gene cluster found.
The gene is designated csf3 (CRISPR/cas Subtype as in A.
ferrooxidans protein 3), as it lies third closest to the
repeats [Mobile and extrachromosomal element functions,
Other].
Length = 214
Score = 28.4 bits (63), Expect = 2.6
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 132 AEHWKMRYPSDDWPVSGYCRTMGRT 156
A+ WK R+ D P + Y MGR
Sbjct: 185 ADRWKKRWLPKDMPGADYAPIMGRL 209
>gnl|CDD|187838 cd09707, Csf3_U, CRISPR/Cas system-associated RAMP superfamily
protein Csf3. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily protein.
Length = 214
Score = 28.4 bits (63), Expect = 2.6
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 132 AEHWKMRYPSDDWPVSGYCRTMGRT 156
A+ WK R+ D P + Y MGR
Sbjct: 185 ADRWKKRWLPKDMPGADYAPIMGRL 209
>gnl|CDD|240791 cd12345, RRM2_SECp43_like, RNA recognition motif 2 in tRNA
selenocysteine-associated protein 1 (SECp43) and similar
proteins. This subfamily corresponds to the RRM2 in
tRNA selenocysteine-associated protein 1 (SECp43), yeast
negative growth regulatory protein NGR1 (RBP1), yeast
protein NAM8, and similar proteins. SECp43 is an
RNA-binding protein associated specifically with
eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play
an adaptor role in the mechanism of selenocysteine
insertion. SECp43 is located primarily in the nucleus
and contains two N-terminal RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), and a C-terminal
polar/acidic region. Yeast proteins, NGR1 and NAM8, show
high sequence similarity with SECp43. NGR1 is a putative
glucose-repressible protein that binds both RNA and
single-stranded DNA (ssDNA). It may function in
regulating cell growth in early log phase, possibly
through its participation in RNA metabolism. NGR1
contains three RRMs, two of which are followed by a
glutamine-rich stretch that may be involved in
transcriptional activity. In addition, NGR1 has an
asparagine-rich region near the C-terminus which also
harbors a methionine-rich region. NAM8 is a putative
RNA-binding protein that acts as a suppressor of
mitochondrial splicing deficiencies when overexpressed
in yeast. It may be a non-essential component of the
mitochondrial splicing machinery. NAM8 also contains
three RRMs. .
Length = 80
Score = 26.9 bits (60), Expect = 2.9
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 116 SEFYGPLHYDVHHSDIAEHWKMRYPS 141
S F G L DV + E ++ RYPS
Sbjct: 3 SIFVGDLAPDVTDYMLQETFRARYPS 28
>gnl|CDD|197317 cd09083, EEP-1, Exonuclease-Endonuclease-Phosphatase domain;
uncharacterized family 1. This family of
uncharacterized proteins belongs to a superfamily that
includes the catalytic domain
(exonuclease/endonuclease/phosphatase, EEP, domain) of a
diverse set of proteins including the ExoIII family of
apurinic/apyrimidinic (AP) endonucleases, inositol
polyphosphate 5-phosphatases (INPP5), neutral
sphingomyelinases (nSMases), deadenylases (such as the
vertebrate circadian-clock regulated nocturnin),
bacterial cytolethal distending toxin B (CdtB),
deoxyribonuclease 1 (DNase1), the endonuclease domain of
the non-LTR retrotransposon LINE-1, and related domains.
These diverse enzymes share a common catalytic mechanism
of cleaving phosphodiester bonds. Their substrates range
from nucleic acids to phospholipids and perhaps,
proteins.
Length = 252
Score = 27.6 bits (62), Expect = 6.6
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 5/46 (10%)
Query: 102 FGPFWDTYGIDFV-GSEFYGPLHYDVHHSDIAEHWKMRYPSDDWPV 146
F ID++ S L Y++ + + + RYPSD +PV
Sbjct: 207 FKGPPGGSRIDYIFVSPGVKVLSYEI----LTDRYDGRYPSDHFPV 248
>gnl|CDD|236100 PRK07798, PRK07798, acyl-CoA synthetase; Validated.
Length = 533
Score = 27.2 bits (61), Expect = 9.7
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 214 AKTFIKNKLPAGAYIGIHLRNGIDWP 239
A I L G ++GI+ RN I++
Sbjct: 42 AHYLIAQGLGPGDHVGIYARNRIEYV 67
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
0.322 0.140 0.462
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,837,036
Number of extensions: 1189274
Number of successful extensions: 873
Number of sequences better than 10.0: 1
Number of HSP's gapped: 866
Number of HSP's successfully gapped: 17
Length of query: 244
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 150
Effective length of database: 6,768,326
Effective search space: 1015248900
Effective search space used: 1015248900
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 (21.9 bits)
S2: 58 (26.1 bits)