RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11109
(93 letters)
>gnl|CDD|218120 pfam04511, DER1, Der1-like family. The endoplasmic reticulum (ER)
of the yeast Saccharomyces cerevisiae contains of
proteolytic system able to selectively degrade misfolded
lumenal secretory proteins. For examination of the
components involved in this degradation process, mutants
were isolated. They could be divided into four
complementation groups. The mutations led to
stabilisation of two different substrates for this
process. The mutant classes were called 'der' for
'degradation in the ER'. DER1 was cloned by
complementation of the der1-2 mutation. The DER1 gene
codes for a novel, hydrophobic protein, that is
localised to the ER. Deletion of DER1 abolished
degradation of the substrate proteins. The function of
the Der1 protein seems to be specifically required for
the degradation process associated with the ER.
Interestingly this family seems distantly related to the
Rhomboid family of membrane peptidases. Suggesting that
this family may also mediate degradation of misfolded
proteins (Bateman A pers. obs.).
Length = 192
Score = 67.7 bits (166), Expect = 1e-15
Identities = 35/53 (66%), Positives = 40/53 (75%), Gaps = 1/53 (1%)
Query: 3 APYLPWVLLGVSILLGN-PIWVDLLGIAVGHMYYFIEDVFPNLRGGFRLLQTP 54
A YLPWVLLG S LLGN VDL+GI VGH+YYF +DV+P L GG LL+TP
Sbjct: 139 ASYLPWVLLGFSFLLGNRSSLVDLMGILVGHLYYFFKDVYPRLPGGKDLLKTP 191
>gnl|CDD|227611 COG5291, COG5291, Predicted membrane protein [Function unknown].
Length = 313
Score = 43.1 bits (101), Expect = 3e-06
Identities = 26/64 (40%), Positives = 39/64 (60%), Gaps = 3/64 (4%)
Query: 3 APYLPWVLLGVSILLGNPIWV-DLLGIAVGHMYYFIEDVFPNLRGGFRLLQTPRILKVLF 61
YLP++LLG S L I + D+LG VGH++++ D++P G +L TP +K LF
Sbjct: 158 GKYLPFILLGFSFLSRRGISIDDVLGFVVGHLFHYFGDIYP--MIGRDILSTPCWVKKLF 215
Query: 62 DPHP 65
+ HP
Sbjct: 216 NEHP 219
>gnl|CDD|221012 pfam11169, DUF2956, Protein of unknown function (DUF2956). This
family of proteins with unknown function appears to be
restricted to Gammaproteobacteria.
Length = 103
Score = 28.4 bits (64), Expect = 0.27
Identities = 10/35 (28%), Positives = 12/35 (34%), Gaps = 13/35 (37%)
Query: 2 NAPYLPWVLLGVSILLGNPIWVDLLGIAVGHMYYF 36
+ LPW LL +S W G Y F
Sbjct: 81 QSNKLPWGLLALS-------W---AGFIA---YIF 102
>gnl|CDD|218219 pfam04707, PRELI, PRELI-like family. This family includes a
conserved region found in the PRELI protein and yeast
YLR168C gene MSF1 product. The function of this protein
is unknown, though it is thought to be involved in
intra-mitochondrial protein sorting. This region is also
found in a number of other eukaryotic proteins.
Length = 157
Score = 27.3 bits (61), Expect = 0.88
Identities = 16/62 (25%), Positives = 25/62 (40%), Gaps = 16/62 (25%)
Query: 20 PIWV-DLLGIAVGHMYYFIEDVFPNLRGGFRLLQT-------PRILKV----LFDPHPED 67
P W+ L+G+A Y +E + + R L L V + PHPE+
Sbjct: 48 PRWLKKLIGVA--DTVYVLEVSVVDPKK--RTLTLETRNLTFSSRLSVDERCTYTPHPEN 103
Query: 68 PD 69
P+
Sbjct: 104 PN 105
>gnl|CDD|215558 PLN03073, PLN03073, ABC transporter F family; Provisional.
Length = 718
Score = 27.5 bits (61), Expect = 1.0
Identities = 10/17 (58%), Positives = 11/17 (64%), Gaps = 3/17 (17%)
Query: 67 DPDYS---PLPEDRPGG 80
DPDY P P+DRPG
Sbjct: 490 DPDYKFEFPTPDDRPGP 506
>gnl|CDD|233392 TIGR01391, dnaG, DNA primase, catalytic core. Members of this
family are DNA primase, a ubiquitous bacteria protein.
Most members of this family contain nearly two hundred
additional residues C-terminal to the region represented
here, but conservation between species is poor and the
C-terminal region was not included in the seed
alignment. This protein contains a CHC2 zinc finger
(pfam01807) and a Toprim domain (pfam01751) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 415
Score = 27.2 bits (61), Expect = 1.1
Identities = 10/26 (38%), Positives = 13/26 (50%)
Query: 44 LRGGFRLLQTPRILKVLFDPHPEDPD 69
LR LL +KV+ P +DPD
Sbjct: 318 LRAIELLLPLGINVKVIKLPGGKDPD 343
>gnl|CDD|99851 cd06148, Egl_like_exo, DEDDy 3'-5' exonuclease domain of
Drosophila Egalitarian (Egl) and similar proteins. The
Egalitarian (Egl) protein subfamily is composed of
Drosophila Egl and similar proteins. Egl is a component
of an mRNA-binding complex which is required for oocyte
specification. Egl contains a DEDDy-type DnaQ-like
3'-5' exonuclease domain possessing three conserved
sequence motifs termed ExoI, ExoII and ExoIII, with a
specific YX(3)D pattern at ExoIII. The motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. The conservation
of this subfamily throughout eukaryotes suggests that
its members may be part of ancient RNA processing
complexes that are likely to participate in the
regulated processing of specific mRNAs. Some members of
this subfamily do not have a completely conserved
YX(3)D pattern at the ExoIII motif.
Length = 197
Score = 26.9 bits (60), Expect = 1.5
Identities = 11/43 (25%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 25 LLGIAVGHMYYFIEDVFPN----LRGGFR-LLQTPRILKVLFD 62
L+ IA ++ D+ G + +L++ +ILKV+ D
Sbjct: 30 LVQIATRTGQIYLFDILKLGSIVFINGLKDILESKKILKVIHD 72
>gnl|CDD|176652 cd06140, DNA_polA_I_Bacillus_like_exo, inactive DEDDy 3'-5'
exonuclease domain of Bacillus stearothermophilus DNA
polymerase I and similar family-A DNA polymerases.
Bacillus stearothermophilus-like Polymerase I (Pol I),
a subgroup of the family-A DNA polymerases, contains an
inactive DnaQ-like 3'-5' exonuclease domain in the same
polypeptide chain as the polymerase region. The
exonuclease-like domain of these proteins possess the
same fold as the Klenow fragment (KF) of Escherichia
coli Pol I, but does not contain the four critical
metal-binding residues necessary for activity. The
function of this domain is unknown. It might act as a
spacer between the polymerase and the 5'-3' exonuclease
domains. Some members of this subgroup, such as those
from Bacillus sphaericus and Thermus aquaticus, are
thermostable DNA polymerases.
Length = 178
Score = 25.7 bits (57), Expect = 4.1
Identities = 16/56 (28%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 11 LGVSILLGNPIWVDLLGIAVGHM--YYFI--EDVFPNLRGGFRLLQTPRILKVLFD 62
L V +L N D++G+A+ + Y+I E +L L+ +I KV D
Sbjct: 8 LYVELLGENYHTADIIGLALANGGGAYYIPLELALLDLAALKEWLEDEKIPKVGHD 63
>gnl|CDD|99838 cd06135, Orn, DEDDh 3'-5' exonuclease domain of oligoribonuclease
and similar proteins. Oligoribonuclease (Orn) is a
DEDDh-type DnaQ-like 3'-5' exoribonuclease that is
responsible for degrading small oligoribonucleotides to
mononucleotides. It contains three conserved sequence
motifs termed ExoI, ExoII and ExoIII, with a specific
Hx(4)D conserved pattern at ExoIII. These motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. Orn is essential
for Escherichia coli survival. The human homolog, also
called Sfn (small fragment nuclease), is able to
hydrolyze short single-stranded RNA and DNA oligomers.
It plays a role in cellular nucleotide recycling.
Length = 173
Score = 25.2 bits (56), Expect = 4.9
Identities = 11/39 (28%), Positives = 17/39 (43%), Gaps = 6/39 (15%)
Query: 8 WVLLGVSILLGNPIWVDLLGIA------VGHMYYFIEDV 40
+V G S L GN + D + +++Y I DV
Sbjct: 89 YVPKGKSPLAGNSVHQDRRFLDKYMPELEEYLHYRILDV 127
>gnl|CDD|234492 TIGR04188, methyltr_grsp, methyltransferase, ATP-grasp peptide
maturase system. Members of this protein family are
predicted SAM-dependent methyltransferases that
regularly occur in the context of a putative peptide
modification ATP-grasp enzyme (TIGR04187, related to
enzymes of microviridin maturation) and a putative
ribosomal peptide modification target (TIGR04186).
Length = 363
Score = 25.4 bits (56), Expect = 5.0
Identities = 11/42 (26%), Positives = 17/42 (40%)
Query: 42 PNLRGGFRLLQTPRILKVLFDPHPEDPDYSPLPEDRPGGFDW 83
P R + L F+P P+ + P+ DRP +W
Sbjct: 14 PAWREAVEAVPRHLFLPGFFEPLPDGRGWRPVTADRPDPDEW 55
>gnl|CDD|233153 TIGR00857, pyrC_multi, dihydroorotase, multifunctional complex
type. In contrast to the homodimeric type of
dihydroorotase found in E. coli, this class tends to
appear in a large, multifunctional complex with
aspartate transcarbamoylase. Homologous domains appear
in multifunctional proteins of higher eukaryotes. In
some species, including Pseudomonas putida and P.
aeruginosa, this protein is inactive but is required as
a non-catalytic subunit of aspartate transcarbamoylase
(ATCase). In these species, a second, active
dihydroorotase is also present. The seed for this model
does not include any example of the dihydroorotase
domain of eukaryotic multidomain pyrimidine synthesis
proteins. All proteins described by This model should
represent active and inactive dihydroorotase per se and
functionally equivalent domains of multifunctional
proteins from higher eukaryotes, but exclude related
proteins such as allantoinase [Purines, pyrimidines,
nucleosides, and nucleotides, Pyrimidine ribonucleotide
biosynthesis].
Length = 411
Score = 24.7 bits (54), Expect = 9.2
Identities = 16/57 (28%), Positives = 20/57 (35%), Gaps = 4/57 (7%)
Query: 29 AVGHMYYFIEDVFP--NLRGGFRLLQTPRILKVLFDPHPEDPDYSPLPEDRPGGFDW 83
AVG M F +D ++ R L+ I V H EDPD G
Sbjct: 131 AVGRM--FTDDGSEVQDILSMRRALEYAAIAGVPIALHAEDPDLIYGGVMHEGPSAA 185
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
0.324 0.152 0.522
Gapped
Lambda K H
0.267 0.0820 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,466,895
Number of extensions: 490284
Number of successful extensions: 484
Number of sequences better than 10.0: 1
Number of HSP's gapped: 482
Number of HSP's successfully gapped: 32
Length of query: 93
Length of database: 10,937,602
Length adjustment: 60
Effective length of query: 33
Effective length of database: 8,276,362
Effective search space: 273119946
Effective search space used: 273119946
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.0 bits)