RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12376
(89 letters)
>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
proteins that cover a wide variety of functions
including adaptor/regulatory modules in signal
transduction, pre-mRNA processing and cytoskeleton
assembly; typically contains a GH dipeptide 11-24
residues from its N-terminus and the WD dipeptide at its
C-terminus and is 40 residues long, hence the name WD40;
between GH and WD lies a conserved core; serves as a
stable propeller-like platform to which proteins can
bind either stably or reversibly; forms a propeller-like
structure with several blades where each blade is
composed of a four-stranded anti-parallel b-sheet;
instances with few detectable copies are hypothesized to
form larger structures by dimerization; each WD40
sequence repeat forms the first three strands of one
blade and the last strand in the next blade; the last
C-terminal WD40 repeat completes the blade structure of
the first WD40 repeat to create the closed ring
propeller-structure; residues on the top and bottom
surface of the propeller are proposed to coordinate
interactions with other proteins and/or small ligands; 7
copies of the repeat are present in this alignment.
Length = 289
Score = 28.5 bits (64), Expect = 0.38
Identities = 20/75 (26%), Positives = 35/75 (46%), Gaps = 7/75 (9%)
Query: 16 GQVLAIGTARGNLTVYNHMTSKRVPVLGKHTNTIV-------GQVLAIGTARGNLTVYNH 68
G+ L ++ G + +++ T K + L H N + G +LA G+ G + V++
Sbjct: 189 GEKLLSSSSDGTIKLWDLSTGKCLGTLRGHENGVNSVAFSPDGYLLASGSEDGTIRVWDL 248
Query: 69 MTSKRVPVLGKHTKS 83
T + V L HT S
Sbjct: 249 RTGECVQTLSGHTNS 263
>gnl|CDD|226607 COG4122, COG4122, Predicted O-methyltransferase [General function
prediction only].
Length = 219
Score = 27.3 bits (61), Expect = 0.89
Identities = 8/19 (42%), Positives = 11/19 (57%)
Query: 8 FLLQTSQVGQVLAIGTARG 26
L + S ++L IGTA G
Sbjct: 53 LLARLSGPKRILEIGTAIG 71
>gnl|CDD|188564 TIGR04049, AIR_rel_sll0787, AIR synthase-related protein, sll0787
family. Members of this family include sll0787 from
Synechocystis sp. PCC 6803 and resemble the C-terminal
region of MSMEG_0567 from Mycobacterium smegmatis, where
the N-terminal is a GNAT family N-acetyltransferase. The
conserved cluster is found broadly (Cyanobacteria,
Proteobacteria, Actinobacteria) in about 8 percent of
genomes and appears to be biosynthetic. The product is
unkown [Unknown function, Enzymes of unknown
specificity].
Length = 316
Score = 25.8 bits (57), Expect = 3.2
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 4/33 (12%)
Query: 39 VPVLGKHTNT-IVGQVLAI---GTARGNLTVYN 67
VP++G HTN L++ G AR L+ ++
Sbjct: 125 VPIVGGHTNIRSPYGQLSVAILGRARRLLSSFD 157
>gnl|CDD|239758 cd04091, mtEFG1_II_like, mtEFG1_C: C-terminus of mitochondrial
Elongation factor G1 (mtEFG1)-like proteins found in
eukaryotes. Eukaryotic cells harbor 2 protein
synthesis systems: one localized in the cytoplasm, the
other in the mitochondria. Most factors regulating
mitochondrial protein synthesis are encoded by nuclear
genes, translated in the cytoplasm, and then
transported to the mitochondria. The eukaryotic system
of elongation factor (EF) components is more complex
than that in prokaryotes, with both cytoplasmic and
mitochondrial elongation factors and multiple isoforms
being expressed in certain species. Eukaryotic EF-2
operates in the cytosolic protein synthesis machinery
of eukaryotes, EF-Gs in protein synthesis in bacteria.
Eukaryotic mtEFG1 proteins show significant homology to
bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired
mitochondrial protein synthesis, respiratory defects
and a tendency to lose mitochondrial DNA. There are two
forms of mtEFG present in mammals (designated mtEFG1s
and mtEFG2s) mtEFG2s are not present in this group.
Length = 81
Score = 24.9 bits (55), Expect = 3.3
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 6 YIFLLQTSQVGQVLAI----GTARGNLTVYNHMTSKRVPV 41
F L+ + GQ+ + G + T+YN T K+V V
Sbjct: 4 LAFKLEEGRFGQLTYMRIYQGKLKKGDTIYNVRTGKKVRV 43
>gnl|CDD|226205 COG3680, COG3680, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 259
Score = 25.7 bits (56), Expect = 3.5
Identities = 8/32 (25%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 3 LRYYIFLLQTSQVGQVLAIGTARGNLTVYNHM 34
L +Y++ L + ++ +G GN V+ H
Sbjct: 14 LGFYVYCLTDPRKDKIFYVGKGCGN-RVFEHE 44
>gnl|CDD|165451 PHA03180, PHA03180, helicase-primase primase subunit; Provisional.
Length = 1071
Score = 24.8 bits (54), Expect = 7.3
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 2/29 (6%)
Query: 30 VYNHMTSKRVPVLGK--HTNTIVGQVLAI 56
VY H S R+P GK I G++L
Sbjct: 836 VYGHGRSLRLPFFGKIDEEGLISGRLLPF 864
>gnl|CDD|227281 COG4945, COG4945, Membrane-anchored protein predicted to be
involved in regulation of amylopullulanase [Carbohydrate
transport and metabolism].
Length = 570
Score = 24.5 bits (53), Expect = 8.6
Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 27 NLTVYN-HMTSKRVPVLGKHTNTIVGQV 53
+TV N HM+ +PV+G +I+ V
Sbjct: 364 LVTVSNGHMSISMIPVMGSSPGSIIAAV 391
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
0.318 0.131 0.371
Gapped
Lambda K H
0.267 0.0744 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,126,692
Number of extensions: 315074
Number of successful extensions: 252
Number of sequences better than 10.0: 1
Number of HSP's gapped: 251
Number of HSP's successfully gapped: 9
Length of query: 89
Length of database: 10,937,602
Length adjustment: 57
Effective length of query: 32
Effective length of database: 8,409,424
Effective search space: 269101568
Effective search space used: 269101568
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.2 bits)