RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10181
(198 letters)
>gnl|CDD|206020 pfam13849, Y_phosphatase_m, Myotubularin Y_phosphatase-like. This
short region is highly conserved and seems to be common
to many myotubularin proteins with protein tyrosine
pyrophosphate activity. As the family has a number of
highly conserved residues such as histidine, cysteine,
glutamine and aspartate, it is possible that this
represents a catalytic core of the active enzymatic part
of the proteins.
Length = 55
Score = 111 bits (279), Expect = 2e-32
Identities = 38/55 (69%), Positives = 45/55 (81%)
Query: 117 SSVMLCLEDGWDITCQLSSLAQLCLDPYYRTLEGFRVLVEKEWIAFGHRFSHRSN 171
SSV++ DGWD T QLSSLAQL LDPYYRT+EGF+VL+EKEW++FGH FS R
Sbjct: 1 SSVLVHCSDGWDRTSQLSSLAQLLLDPYYRTIEGFQVLIEKEWLSFGHPFSDRCG 55
>gnl|CDD|153293 cd07609, BAR_SIP3_fungi, The Bin/Amphiphysin/Rvs (BAR) domain of
fungal Snf1p-interacting protein 3. BAR domains are
dimerization, lipid binding and curvature sensing
modules found in many different proteins with diverse
functions including organelle biogenesis, membrane
trafficking or remodeling, and cell division and
migration. This group is composed of mostly
uncharacterized fungal proteins with similarity to
Saccharomyces cerevisiae Snf1p-interacting protein 3
(SIP3). These proteins contain an N-terminal BAR domain
followed by a Pleckstrin Homology (PH) domain. SIP3
interacts with SNF1 protein kinase and activates
transcription when anchored to DNA. It may function in
the SNF1 pathway. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 214
Score = 29.9 bits (68), Expect = 0.64
Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 50 LKQIESSQWLQQIQNIMQLSGAVVDLLYLPKRLSTFLKQIESSQWLQQIQNIMQLSGAVV 109
L+++ +S +L + + +SG V+D Y P L F ++ W + + ++
Sbjct: 34 LERVINS-FLSHLLPPLLVSGGVIDQDYTPLALKRFGDGLKDF-WGGVLSALKGNDSLIL 91
Query: 110 DLLD 113
D L
Sbjct: 92 DPLR 95
>gnl|CDD|218459 pfam05137, PilN, Fimbrial assembly protein (PilN).
Length = 78
Score = 28.3 bits (64), Expect = 0.79
Identities = 10/55 (18%), Positives = 23/55 (41%), Gaps = 10/55 (18%)
Query: 45 PDQTFLKQIESSQWLQQIQNIMQLSGAVVDLLYLPKRLSTFLKQIESSQWLQQIQ 99
PD +L + +Q N + +SG R++ ++ +E S + ++
Sbjct: 11 PDGVWLTSL------KQDGNTLTISGVAESN----ARVAALMRNLEQSPLFEDVE 55
>gnl|CDD|219814 pfam08385, DHC_N1, Dynein heavy chain, N-terminal region 1.
Dynein heavy chains interact with other heavy chains to
form dimers, and with intermediate chain-light chain
complexes to form a basal cargo binding unit. The
region featured in this family includes the sequences
implicated in mediating these interactions. It is
thought to be flexible and not to adopt a rigid
conformation.
Length = 577
Score = 29.9 bits (68), Expect = 0.85
Identities = 10/26 (38%), Positives = 18/26 (69%), Gaps = 2/26 (7%)
Query: 46 DQTFLKQIESS--QWLQQIQNIMQLS 69
D FL +ES +W++QIQ++++L
Sbjct: 1 DSDFLNSLESIVNKWIKQIQSVLKLD 26
>gnl|CDD|163426 TIGR03714, secA2, accessory Sec system translocase SecA2. Members
of this protein family are homologous to SecA and part
of the accessory Sec system. This system, including both
five core proteins for export and a variable number of
proteins for glycosylation, operates in certain
Gram-positive pathogens for the maturation and delivery
of serine-rich glycoproteins such as the cell surface
glycoprotein GspB in Streptococcus gordonii [Protein
fate, Protein and peptide secretion and trafficking].
Length = 762
Score = 29.6 bits (67), Expect = 1.1
Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 41 TNAEPDQTFLKQIESSQWLQQIQNIMQLSGAVVDLLYLPKRLSTFLKQIESSQWLQQIQN 100
N E + FLK+I + ++ + ++ D RLS LK I+ + W++Q+
Sbjct: 672 KNKEAIKDFLKEIADKELSEK-KKVLNNDYLFNDFE----RLS-ILKAIDEN-WIEQVDY 724
Query: 101 IMQLSGAV 108
+ QL V
Sbjct: 725 LQQLKTVV 732
>gnl|CDD|200466 cd11327, AmyAc_Glg_debranch_2, Alpha amylase catalytic domain found
in glycogen debranching enzymes. Debranching enzymes
facilitate the breakdown of glycogen through
glucosyltransferase and glucosidase activity. These
activities are performed by a single enzyme in mammals,
yeast, and some bacteria, but by two distinct enzymes in
Escherichia coli and other bacteria. Debranching enzymes
perform two activities, 4-alpha-D-glucanotransferase (EC
2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33).
4-alpha-D-glucanotransferase catalyzes the
endohydrolysis of 1,6-alpha-D-glucoside linkages at
points of branching in chains of 1,4-linked
alpha-D-glucose residues. Amylo-alpha-1,6-glucosidase
catalyzes the endohydrolysis of 1,6-alpha-D-glucoside
linkages at points of branching in chains of 1,4-linked
alpha-D-glucose residues. The catalytic triad (DED),
which is highly conserved in other debranching enzymes,
is not present in this group. The Alpha-amylase family
comprises the largest family of glycoside hydrolases
(GH), with the majority of enzymes acting on starch,
glycogen, and related oligo- and polysaccharides. These
proteins catalyze the transformation of alpha-1,4 and
alpha-1,6 glucosidic linkages with retention of the
anomeric center. The protein is described as having 3
domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a
loop between the beta 3 strand and alpha 3 helix of A; C
is the C-terminal extension characterized by a Greek
key. The majority of the enzymes have an active site
cleft found between domains A and B where a triad of
catalytic residues (Asp, Glu and Asp) performs
catalysis. Other members of this family have lost the
catalytic activity as in the case of the human 4F2hc, or
only have 2 residues that serve as the catalytic
nucleophile and the acid/base, such as Thermus A4
beta-galactosidase with 2 Glu residues (GH42) and human
alpha-galactosidase with 2 Asp residues (GH31). The
family members are quite extensive and include: alpha
amylase, maltosyltransferase, cyclodextrin
glycotransferase, maltogenic amylase, neopullulanase,
isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase,
4-alpha-glucotransferase, oligo-1,6-glucosidase,
amylosucrase, sucrose phosphorylase, and amylomaltase.
Length = 478
Score = 29.1 bits (66), Expect = 1.7
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 7/63 (11%)
Query: 9 ILKTDYIP----VEY--ADIRHTKAAFKKLMRACIPSRTNAEPDQTFLKQIESSQWLQQI 62
ILK + +P E+ D+ FK+ +++ P D + L I + L I
Sbjct: 180 ILKEEVLPPLKLWEFYVLDVEKAVEQFKEALKSGKPKLPKKGSDVS-LADILKKEELLII 238
Query: 63 QNI 65
Q+
Sbjct: 239 QDP 241
>gnl|CDD|240722 cd12276, RRM2_MEI2_EAR1_like, RNA recognition motif 2 in
Mei2-like proteins and terminal EAR1-like proteins.
This subfamily corresponds to the RRM2 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 = 71
Score = 26.0 bits (58), Expect = 4.2
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 17 VEYADIRHTKAAFKKLMRA 35
VE+ DIR +AA L
Sbjct: 43 VEFYDIRAAEAALDALNGR 61
>gnl|CDD|239160 cd02759, MopB_Acetylene-hydratase, The MopB_Acetylene-hydratase CD
contains acetylene hydratase (Ahy) and other related
proteins. The acetylene hydratase of Pelobacter
acetylenicus is a tungsten iron-sulfur protein involved
in the fermentation of acetylene to ethanol and acetate.
Members of this CD belong to the molybdopterin_binding
(MopB) superfamily of proteins.
Length = 477
Score = 27.3 bits (61), Expect = 5.7
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 93 QW---LQQIQNIMQLSGAVVDL------LDVQGSSVM 120
QW + Q +N Q S A+ L LDV G +++
Sbjct: 289 QWGLAIDQQKNGTQTSRAIAILRAITGNLDVPGGNLL 325
>gnl|CDD|227439 COG5108, RPO41, Mitochondrial DNA-directed RNA polymerase
[Transcription].
Length = 1117
Score = 27.3 bits (60), Expect = 6.1
Identities = 8/26 (30%), Positives = 13/26 (50%)
Query: 172 LNVHSPASGFTPTFLQFLDAVHQLIS 197
++ SG P F+ LDA H ++
Sbjct: 983 VDKRKQGSGIPPNFIHSLDAAHMQLT 1008
>gnl|CDD|217890 pfam04097, Nic96, Nup93/Nic96. Nup93/Nic96 is a component of the
nuclear pore complex. It is required for the correct
assembly of the nuclear pore complex. In Saccharomyces
cerevisiae, Nic96 has been shown to be involved in the
distribution and cellular concentration of the GTPase
Gsp1. The structure of Nic96 has revealed a mostly alpha
helical structure.
Length = 607
Score = 26.9 bits (60), Expect = 7.6
Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 17/81 (20%)
Query: 7 DSILKTDYIPVEYADIRHTKAAFKKL---MRACIPS--------------RTNAEPDQTF 49
D+I K +P++ + +R F L + IP R +
Sbjct: 520 DAIEKLPLLPLDPSSVRRCAEEFSNLPDEVAKVIPDLLLATMTCLSNLYKRLKTSIYGSS 579
Query: 50 LKQIESSQWLQQIQNIMQLSG 70
+ + + +Q + +M +G
Sbjct: 580 GRTDQLNSLRKQAKALMNYAG 600
>gnl|CDD|198426 cd10028, UDG_F2_MUG, G:T/U mismatch specific DNA glcosylase (MUG).
G:T/U mismatch specific DNA glycosylases (MUG) are
classified as Family 2 of Uracil DNA glycosylase
enzymes. MUG catalyzes the removal of thymine or uracil
bases mispaired with guanine through the hydrolysis of
their N-glycosidic bond, generating abasic sites in DNA
to initiate the base excision repair pathway. G:U and
G:T mismatched base pairs arise in DNA either by
mis-incorporation during DNA replication or by
hydrolytic deamination of cytosine and 5-methyl
cytosine, respectively. MUGs are dsDNA specific base
excision repair enzymes. They explicitly recognize the
widowed guanine on the complementary strand rather than
the extrahelical scissile pyrimidine. This allows a
broader specificity so that some MUGs can excise uracil,
thymine or 3, N(4)-ethenocytosine from mismatches with
guanine. MUGs are found in Eubacteria and Eukarya, where
they appear to have complementary functions of Family 1
UDGs. MUG is an essential enzyme for maintaining the
integrity of genetic information.
Length = 162
Score = 26.3 bits (59), Expect = 8.0
Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 5/31 (16%)
Query: 163 GHRFSHRSNL---NVHSPASGFTPTFLQFLD 190
GH ++H N +H +G TP L +
Sbjct: 26 GHHYAHPGNRFWKLLH--EAGLTPRLLAPEE 54
>gnl|CDD|215422 PLN02788, PLN02788, phenylalanine-tRNA synthetase.
Length = 402
Score = 26.7 bits (59), Expect = 9.2
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 143 PYYRTLEGFRVLVEKEWIAFG 163
P + +EG RV +EW A G
Sbjct: 168 PVFHQMEGVRVFSPEEWEASG 188
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
0.323 0.135 0.406
Gapped
Lambda K H
0.267 0.0830 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,011,088
Number of extensions: 888339
Number of successful extensions: 766
Number of sequences better than 10.0: 1
Number of HSP's gapped: 762
Number of HSP's successfully gapped: 25
Length of query: 198
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 106
Effective length of database: 6,857,034
Effective search space: 726845604
Effective search space used: 726845604
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 56 (25.2 bits)