RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5397
(112 letters)
>gnl|CDD|216878 pfam02109, DAD, DAD family. Members of this family are thought to
be integral membrane proteins. Some members of this
family have been shown to cause apoptosis if mutated,
these proteins are known as DAD for defender against
death. The family also includes the epsilon subunit of
the oligosaccharyltransferase that is involved in
N-linked glycosylation.
Length = 113
Score = 171 bits (435), Expect = 5e-57
Identities = 73/109 (66%), Positives = 88/109 (80%)
Query: 4 FQAVLGKIHHEYVNNTPKKLKIIDAYLFYILLTGAFQFLYCCLVGTFPFNSFLSGFISCV 63
FQ V Y + TP++LK+IDA+L +++LTG QFLYC LVGTFPFNSFLSGFISCV
Sbjct: 5 FQDVFSSFWDAYTSKTPQRLKLIDAFLLFLVLTGIIQFLYCLLVGTFPFNSFLSGFISCV 64
Query: 64 SSFVLGVCLRLQVNPQNQKDFVGISPERGFADFIFAHVILHLVVMNFIG 112
FVL VCLR+Q+NPQN+ +F GISPER FADFIFA ++LHLVV+NFIG
Sbjct: 65 GQFVLTVCLRIQLNPQNKSEFPGISPERAFADFIFASLVLHLVVVNFIG 113
>gnl|CDD|238343 cd00620, Methyltransferase_Sun, N-terminal RNA binding domain of
the methyltransferase Sun. The rRNA-specific
5-methylcytidine transferase Sun, also known as RrmB or
Fmu shares the RNA-binding non-catalytic domain with
the transcription termination factor NusB. The precise
biological role of this domain in Sun is unknown,
although it is likely to be involved in
sequence-specific RNA binding. The C-terminal
methyltransferase domain of Sun has been shown to
catalyze formation of m5C at position 967 of 16S rRNA
in Escherichia coli.
Length = 126
Score = 28.5 bits (64), Expect = 0.44
Identities = 7/23 (30%), Positives = 10/23 (43%)
Query: 21 KKLKIIDAYLFYILLTGAFQFLY 43
K D + +L G +Q LY
Sbjct: 65 KPDVGKDPDVRNLLRLGLYQLLY 87
>gnl|CDD|224776 COG1863, MnhE, Multisubunit Na+/H+ antiporter, MnhE subunit
[Inorganic ion transport and metabolism].
Length = 158
Score = 26.9 bits (60), Expect = 2.1
Identities = 12/47 (25%), Positives = 21/47 (44%), Gaps = 2/47 (4%)
Query: 30 LFYILLTGAFQFLYCCLVGTFPFNSFLSGFISCVSSFVLGVCLRLQV 76
+ ++LL + L G+F + + GFI V + VL + R
Sbjct: 2 MPFLLLNILLALFWLLLTGSFSPANLILGFI--VGAIVLLLLRRFLP 46
>gnl|CDD|222785 PHA00368, PHA00368, internal virion protein D.
Length = 1315
Score = 27.1 bits (60), Expect = 2.2
Identities = 7/16 (43%), Positives = 11/16 (68%)
Query: 76 VNPQNQKDFVGISPER 91
+NP+ K+F + PER
Sbjct: 484 LNPKTLKEFAEVDPER 499
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 26.7 bits (60), Expect = 2.6
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 21 KKLKIIDAYLFYILLTGAFQFLY 43
KK K +D ++ +L +Q LY
Sbjct: 67 KKRKKLDPWVRNLLRMSLYQLLY 89
>gnl|CDD|173870 cd08505, PBP2_NikA_DppA_OppA_like_18, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 528
Score = 26.1 bits (58), Expect = 4.4
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 23 LKIIDAYLFYILLTGAF-QFLY 43
++ +D Y I LTG + QFLY
Sbjct: 111 VEAVDRYTLRIRLTGPYPQFLY 132
>gnl|CDD|130665 TIGR01604, PYST-C2, Plasmodium yoelii subtelomeric domain
PYST-C2. This model represents a domain of a
paralogous family of Plasmodium yoelii genes
preferentially located in the subtelomeric regions of
the chromosomes. There are no obvious homologs to these
genes in any other organism. The genes found by this
model often are associated with an N-terminal domain
yoelii-specific domain such as PYST-C1 (TIGR01601).
Length = 150
Score = 25.7 bits (56), Expect = 4.8
Identities = 11/48 (22%), Positives = 16/48 (33%), Gaps = 6/48 (12%)
Query: 8 LGKIHHEYVNNTPKKLKIIDAYLFYILLTGAFQFLYCCLVGTFPFNSF 55
G +H EY K L+I Y+ L F+ P +
Sbjct: 27 NGNVHDEYELKDQKHLEI------YLNLNEKFEHRSSNENSLEPDYTL 68
>gnl|CDD|216253 pfam01029, NusB, NusB family. The NusB protein is involved in
the regulation of rRNA biosynthesis by transcriptional
antitermination.
Length = 126
Score = 25.6 bits (57), Expect = 4.9
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 21 KKLKIIDAYLFYILLTGAFQFLYC 44
L+ +D IL G ++ LY
Sbjct: 66 WPLERLDPVDRAILRLGLYELLYL 89
>gnl|CDD|237159 PRK12651, PRK12651, putative monovalent cation/H+ antiporter
subunit E; Reviewed.
Length = 158
Score = 25.2 bits (56), Expect = 7.9
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 31 FYILLTGAFQFLYCCLVGTFPFNSFLSGFISCV 63
F +LL L+ L G+F +F+ GFI +
Sbjct: 3 FQLLLNIILAVLWLFLTGSFSLGNFIIGFILGL 35
>gnl|CDD|150281 pfam09553, RE_Eco47II, Eco47II restriction endonuclease. This
family includes the Eco47II (which recognises GGNCC, but
the cleavage site unknown) restriction endonuclease.
Length = 214
Score = 25.1 bits (55), Expect = 8.3
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 21 KKLKIIDAYLFYILLTG---AFQFLY 43
+++ I FY L+TG AF+ L
Sbjct: 176 PRIRRISGDQFYELVTGIEDAFKQLC 201
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
0.334 0.149 0.470
Gapped
Lambda K H
0.267 0.0757 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,939,395
Number of extensions: 516262
Number of successful extensions: 802
Number of sequences better than 10.0: 1
Number of HSP's gapped: 801
Number of HSP's successfully gapped: 45
Length of query: 112
Length of database: 10,937,602
Length adjustment: 76
Effective length of query: 36
Effective length of database: 7,566,698
Effective search space: 272401128
Effective search space used: 272401128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.5 bits)
S2: 53 (24.1 bits)