RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5044
(219 letters)
>gnl|CDD|190521 pfam03096, Ndr, Ndr family. This family consists of proteins from
different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3.
Their similarity was previously noted. The precise
molecular and cellular function of members of this
family is still unknown. Yet, they are known to be
involved in cellular differentiation events. The Ndr1
group was the first to be discovered. Their expression
is repressed by the proto-oncogenes N-myc and c-myc, and
in line with this observation, Ndr1 protein expression
is down-regulated in neoplastic cells, and is
reactivated when differentiation is induced by chemicals
such as retinoic acid. Ndr2 and Ndr3 expression is not
under the control of N-myc or c-myc. Ndr1 expression is
also activated by several chemicals: tunicamycin and
homocysteine induce Ndr1 in human umbilical endothelial
cells; nickel induces Ndr1 in several cell types.
Members of this family are found in wide variety of
multicellular eukaryotes, including an Ndr1 type protein
in Helianthus annuus (sunflower), known as Sf21.
Interestingly, the highest scoring matches in the noise
are all alpha/beta hydrolases pfam00561, suggesting that
this family may have an enzymatic function (Bateman A
pers. obs.).
Length = 284
Score = 128 bits (323), Expect = 3e-36
Identities = 55/134 (41%), Positives = 73/134 (54%), Gaps = 19/134 (14%)
Query: 79 ENFSVYHVNAPGQEEGAQPLADDVTQHPLALLMIIRHYGMDICYDTDHTNISNFQAFFNF 138
HV G +G +P +T H L L +H S FQ FN
Sbjct: 6 TPCGSVHVTVYGDPKGKKPPI--LTYHDLGL---------------NHK--SCFQGLFNS 46
Query: 139 SDMRSLLENFSVYHVNAPGQEEGAQPLADDYIYPTMDELSNQLLFVLSYFGLHSVIGLGV 198
M+ +L+NF +YHV+APGQE+GA Y YP++D+L++ + VL +F L SVIG+GV
Sbjct: 47 ESMQEILQNFCIYHVDAPGQEDGAASFPGGYPYPSLDDLADMIPVVLDHFRLKSVIGMGV 106
Query: 199 GAGGNILARFALSH 212
GAG ILARFAL H
Sbjct: 107 GAGAYILARFALKH 120
Score = 103 bits (259), Expect = 8e-27
Identities = 39/76 (51%), Positives = 49/76 (64%), Gaps = 2/76 (2%)
Query: 28 EVYVETDRGSILVAVAGNR--GKPAILTYHDLGLNYISNFQAFFNFSDMRSLLENFSVYH 85
E +ET GS+ V V G+ KP ILTYHDLGLN+ S FQ FN M+ +L+NF +YH
Sbjct: 1 EHIIETPCGSVHVTVYGDPKGKKPPILTYHDLGLNHKSCFQGLFNSESMQEILQNFCIYH 60
Query: 86 VNAPGQEEGAQPLADD 101
V+APGQE+GA
Sbjct: 61 VDAPGQEDGAASFPGG 76
>gnl|CDD|217522 pfam03379, CcmB, CcmB protein. CcmB is the product of one of a
cluster of Ccm genes that are necessary for cytochrome c
biosynthesis in eubacteria. Expression of these proteins
is induced when the organisms are grown under anaerobic
conditions with nitrate or nitrite as the final electron
acceptor. CcmB is required for the export of haem to the
periplasm.
Length = 215
Score = 32.2 bits (74), Expect = 0.14
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 175 DELSNQLLFVLSYFGLHSVIGLGVGAGGNILARFALSHLWYCSL 218
L N LLF L ++ LG+G +LAR A +W +L
Sbjct: 17 GGLINPLLFFLIVV---TLFPLGIGPEPALLARIAPGIIWVAAL 57
>gnl|CDD|215347 PLN02644, PLN02644, acetyl-CoA C-acetyltransferase.
Length = 394
Score = 30.8 bits (70), Expect = 0.50
Identities = 24/87 (27%), Positives = 37/87 (42%), Gaps = 16/87 (18%)
Query: 40 VAVAGNRGKPAILTYHDLGLNYISNFQAFFNFSDMRSLLENF-----SVYHVNAPGQEEG 94
V V G RG+P+++ D GL F+ + +R L +F SV NA +G
Sbjct: 201 VEVPGGRGRPSVIVDKDEGLGK-------FDPAKLRKLRPSFKEDGGSVTAGNASSISDG 253
Query: 95 AQPL----ADDVTQHPLALLMIIRHYG 117
A L + + L ++ IR Y
Sbjct: 254 AAALVLVSGEKALELGLQVIAKIRGYA 280
>gnl|CDD|240016 cd04658, Piwi_piwi-like_Euk, Piwi_piwi-like_Euk: PIWI domain,
Piwi-like subfamily found in eukaryotes. This domain is
found in Piwi and closely related proteins, where it is
believed to perform a crucial role in germline cells,
via RNA silencing. RNA silencing refers to a group of
related gene-silencing mechanisms mediated by short RNA
molecules, including siRNAs, miRNAs, and
heterochromatin-related guide RNAs. The mechanism in
Piwi is believed to be similar to that in Argonaute, the
central component of the RNA-induced silencing complex
(RISC). The PIWI domain is the C-terminal portion of
Argonaute and consists of two subdomains, one of which
provides the 5' anchoring of the guide RNA and the
other, the catalytic site for slicing.
Length = 448
Score = 30.3 bits (69), Expect = 0.77
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 5/51 (9%)
Query: 110 LMIIRHYGMDICYDTDHTNISNFQAFFNFSDMRSLLENFSVYHVNAPGQEE 160
MI+ G+D+ +DT S F S +S+ + FS Y GQEE
Sbjct: 229 TMIV---GIDVYHDTITKKKS-VVGF-VASLNKSITKWFSKYISQVRGQEE 274
>gnl|CDD|240723 cd12277, RRM3_MEI2_EAR1_like, RNA recognition motif 3 in Mei2-like
proteins and terminal EAR1-like proteins. This
subfamily corresponds to the RRM3 of Mei2-like proteins
from plant and fungi, terminal EAR1-like proteins from
plant, and other eukaryotic homologs. Mei2-like proteins
represent an ancient eukaryotic RNA-binding proteins
family whose corresponding Mei2-like genes appear to
have arisen early in eukaryote evolution, been lost from
some lineages such as Saccharomyces cerevisiae and
metazoans, and diversified in the plant lineage. The
plant Mei2-like genes may function in cell fate
specification during development, rather than as
stimulators of meiosis. In the fission yeast
Schizosaccharomyces pombe, the Mei2 protein is an
essential component of the switch from mitotic to
meiotic growth. S. pombe Mei2 stimulates meiosis in the
nucleus upon binding a specific non-coding RNA. The
terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are
mainly found in land plants. They may play a role in the
regulation of leaf initiation. All members in this
family are putative RNA-binding proteins carrying three
RNA recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains). In
addition to the RRMs, the terminal EAR1-like proteins
also contain TEL characteristic motifs that allow
sequence and putative functional discrimination between
them and Mei2-like proteins. .
Length = 86
Score = 28.3 bits (64), Expect = 0.92
Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 6/53 (11%)
Query: 106 PLALLMIIRHYGMDICYD-----TDHTNISNF-QAFFNFSDMRSLLENFSVYH 152
LL ++ +G YD D N N AF NF + + + ++
Sbjct: 12 QEMLLQLLDEHGKGGAYDFLYLPIDFKNKCNVGYAFINFVNPEYAEKFYKAFN 64
>gnl|CDD|237586 PRK14016, PRK14016, cyanophycin synthetase; Provisional.
Length = 727
Score = 29.0 bits (66), Expect = 2.3
Identities = 18/52 (34%), Positives = 21/52 (40%), Gaps = 16/52 (30%)
Query: 22 TDPTVEEVYVETDRGSIL----------VAVAGNRGKPAILTYHDLGLNYIS 63
+P VE +ET RG IL V V N I H LGL I+
Sbjct: 540 MNPDVEAAVLETARGGILREGLAYDRCDVGVVTN-----IGEDH-LGLGGIN 585
>gnl|CDD|204102 pfam08942, DUF1919, Domain of unknown function (DUF1919). This
domain has no known function. It is found in various
hypothetical and putative bacterial proteins.
Length = 198
Score = 28.0 bits (63), Expect = 2.7
Identities = 19/68 (27%), Positives = 30/68 (44%), Gaps = 7/68 (10%)
Query: 52 LTYHDLGLNYISNFQAFFNFS-DMRSLLENFSVYHVNAPGQEEGAQPLADDVTQHPLALL 110
L YHDLGL + S F + D LEN Y E+ + ++ +Q+P+ L
Sbjct: 36 LIYHDLGLQFRSPFINLYIEPADYIKFLENLDYY------LEQELTFINEEKSQYPVGKL 89
Query: 111 MIIRHYGM 118
I + +
Sbjct: 90 GDIEIHFL 97
>gnl|CDD|217460 pfam03259, Robl_LC7, Roadblock/LC7 domain. This family includes
proteins that are about 100 amino acids long and have
been shown to be related. Members of this family of
proteins are associated with both flagellar outer arm
dynein and Drosophila and rat brain cytoplasmic dynein.
It is proposed that roadblock/LC7 family members may
modulate specific dynein functions. This family also
includes Golgi-associated MP1 adapter protein and MglB
from Myxococcus xanthus, a protein involved in gliding
motility. However the family also includes members from
non-motile bacteria such as Streptomyces coelicolor,
suggesting that the protein may play a structural or
regulatory role.
Length = 91
Score = 26.8 bits (60), Expect = 3.0
Identities = 8/41 (19%), Positives = 18/41 (43%), Gaps = 2/41 (4%)
Query: 15 LTRSLART--DPTVEEVYVETDRGSILVAVAGNRGKPAILT 53
++LAR + ++ +E +G + + AG +L
Sbjct: 51 AAKALARDLGGGELRQLLIEGKKGELYLTPAGEGALLVVLA 91
>gnl|CDD|215645 PLN03246, PLN03246, 26S proteasome regulatory subunit; Provisional.
Length = 303
Score = 27.4 bits (61), Expect = 5.8
Identities = 9/20 (45%), Positives = 11/20 (55%)
Query: 97 PLADDVTQHPLALLMIIRHY 116
+ V HPL LL I+ HY
Sbjct: 3 RGIEKVVVHPLVLLSIVDHY 22
>gnl|CDD|179863 PRK04542, PRK04542, elongation factor P; Provisional.
Length = 189
Score = 27.2 bits (61), Expect = 6.0
Identities = 19/46 (41%), Positives = 21/46 (45%), Gaps = 9/46 (19%)
Query: 24 PTVEEVYVETDRGSILVAVAGNRGKPAILTYHDLGLN-----YISN 64
TV+ VET SI A A R KPA L+ GL YIS
Sbjct: 130 QTVDLEIVETAP-SIKGASASARTKPATLS---TGLVIQVPEYIST 171
>gnl|CDD|201306 pfam00561, Abhydrolase_1, alpha/beta hydrolase fold. This
catalytic domain is found in a very wide range of
enzymes.
Length = 226
Score = 27.1 bits (60), Expect = 7.3
Identities = 15/50 (30%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 163 QPLADDYIYPTMDELSNQLLFVLSYFGLHSVIGLGVGAGGNILARFALSH 212
P D Y D+L+ L +L GL V +G GG I +A +
Sbjct: 15 SPPKDFADY-RFDDLAEDLEALLDALGLDKVNLVGHSMGGLIALAYAAKY 63
>gnl|CDD|232901 TIGR00275, TIGR00275, flavoprotein, HI0933 family. The model when
searched with a partial length search brings in proteins
with a dinucleotide-binding motif (Rossman fold) over
the initial 40 residues of the model, including
oxidoreductases and dehydrogenases. Partially
characterized members include an FAD-binding protein
from Bacillus cereus and flavoprotein HI0933 from
Haemophilus influenzae [Unknown function, Enzymes of
unknown specificity].
Length = 400
Score = 27.2 bits (61), Expect = 7.9
Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 12/74 (16%)
Query: 69 FNFSDMRSLLENFSV-YHVNAPGQ----EEGAQPLADDVTQHPLALLMIIRHYGMDICYD 123
F+ D+ E+ + V G+ + A + D ALL ++ G++I +
Sbjct: 73 FSNKDLIDFFESLGLELKVEEDGRVFPCSDSAADVLD-------ALLNELKELGVEILTN 125
Query: 124 TDHTNISNFQAFFN 137
+ +I F
Sbjct: 126 SKVKSIKKDDGGFG 139
>gnl|CDD|234335 TIGR03732, lanti_perm_MutE, lantibiotic protection ABC transporter
permease subunit, MutE/EpiE family. Model TIGR03731
represents the family of all lantibiotics related to
gallidermin, including epidermin, mutatin, and nisin.
This protein family is largely restricted to
gallidermin-family lantibiotic cassettes, but also
include orphan transporter cassettes in species that
lack candidate lantibiotic precursor and synthetase
genes. In most species, this subunit is paralogous to an
adjacent gene, modeled separately.
Length = 241
Score = 26.5 bits (59), Expect = 9.6
Identities = 8/34 (23%), Positives = 13/34 (38%)
Query: 182 LFVLSYFGLHSVIGLGVGAGGNILARFALSHLWY 215
LF+ FG+ I + + G A W+
Sbjct: 144 LFLARKFGMFVSILVNLVLGLIFGIVLATKSFWW 177
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 0.139 0.414
Gapped
Lambda K H
0.267 0.0792 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,479,631
Number of extensions: 1095816
Number of successful extensions: 980
Number of sequences better than 10.0: 1
Number of HSP's gapped: 980
Number of HSP's successfully gapped: 22
Length of query: 219
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 126
Effective length of database: 6,812,680
Effective search space: 858397680
Effective search space used: 858397680
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: 57 (25.6 bits)