RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy17485
(237 letters)
>gnl|CDD|99725 cd06404, PB1_aPKC, PB1 domain is an essential modular domain of
the atypical protein kinase C (aPKC) which in complex
with Par6 and Par3 proteins is crucial for
establishment of apical-basal polarity of animal cells.
PB1 domain is a modular domain mediating specific
protein-protein interaction which play roles in many
critical cell processes. A canonical PB1-PB1
interaction, which involves heterodimerization of two
PB1 domains, is required for the formation of
macromolecular signaling complexes ensuring specificity
and fidelity during cellular signaling. The interaction
between two PB1 domain depends on the type of PB1.
There are three types of PB1 domains: type I which
contains an OPCA motif, acidic aminoacid cluster, type
II which contains a basic cluster, and type I/II which
contains both an OPCA motif and a basic cluster.
Interactions of PB1 domains with other protein domains
have been described as noncanonical PB1-interactions.
The PB1 domain module is conserved in amoebas, fungi,
animals, and plants. The aPKC protein contains a type
I/II PB1 domain.
Length = 83
Score = 29.2 bits (66), Expect = 0.48
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 7/47 (14%)
Query: 30 NFALLQLVGVKVSKREGD----SSLMQLKEEFRTYESLRREHDAQIV 72
F Q +K EGD SS M+L+E FR YE + D+++
Sbjct: 34 RFHNDQPFTLKWIDEEGDPCTISSQMELEEAFRLYELNK---DSELN 77
>gnl|CDD|232986 TIGR00464, gltX_bact, glutamyl-tRNA synthetase, bacterial family.
The glutamyl-tRNA synthetases of the eukaryotic cytosol
and of the Archaea are more similar to glutaminyl-tRNA
synthetases than to bacterial glutamyl-tRNA synthetases.
This model models just the bacterial and mitochondrial
forms of the enzyme. In many species, the charging of
tRNA(gln) proceeds first through misacylation with Glu
and then transamidation. For this reason, glutamyl-tRNA
synthetases may act on both tRNA(gln) and tRNA(glu).
This model is highly specific. Proteins with positive
scores below the trusted cutoff may be fragments rather
than full-length sequences [Protein synthesis, tRNA
aminoacylation].
Length = 470
Score = 30.8 bits (70), Expect = 0.65
Identities = 17/34 (50%), Positives = 24/34 (70%), Gaps = 5/34 (14%)
Query: 27 IPVNFALLQLV----GVKVSKREGDSSLMQLKEE 56
IPV FA L ++ G K+SKR+G +S+MQ KE+
Sbjct: 225 IPV-FAHLPMILGEDGKKLSKRDGATSIMQFKEQ 257
>gnl|CDD|173905 cd00808, GluRS_core, catalytic core domain of discriminating
glutamyl-tRNA synthetase. Discriminating Glutamyl-tRNA
synthetase (GluRS) catalytic core domain . The
discriminating form of GluRS is only found in bacteria
and cellular organelles. GluRS is a monomer that
attaches Glu to the appropriate tRNA. Like other class
I tRNA synthetases, GluRS aminoacylates the 2'-OH of the
nucleotide at the 3' end of the tRNA. The core domain is
based on the Rossman fold and is responsible for the
ATP-dependent formation of the enzyme bound
aminoacyl-adenylate. It contains the characteristic
class I HIGH and KMSKS motifs, which are involved in ATP
binding.
Length = 239
Score = 29.5 bits (67), Expect = 1.3
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 5/34 (14%)
Query: 27 IPVNFALLQLV----GVKVSKREGDSSLMQLKEE 56
P FA L L+ G K+SKR+GD+S+ +EE
Sbjct: 146 PPK-FAHLPLILNPDGKKLSKRKGDTSISDYREE 178
>gnl|CDD|223087 COG0008, GlnS, Glutamyl- and glutaminyl-tRNA synthetases
[Translation, ribosomal structure and biogenesis].
Length = 472
Score = 29.6 bits (67), Expect = 1.6
Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 6/34 (17%)
Query: 38 GVKVSKREGDSSLMQLKEE------FRTYESLRR 65
G K+SKR+G S+ + + E +L
Sbjct: 248 GKKLSKRKGAVSIGEYRVEGWLPPALPNLLALLG 281
>gnl|CDD|185288 PRK15390, PRK15390, fumarate hydratase FumA; Provisional.
Length = 548
Score = 28.9 bits (64), Expect = 3.0
Identities = 20/67 (29%), Positives = 35/67 (52%), Gaps = 7/67 (10%)
Query: 53 LKEEFRTYESLRREHDAQIVEIATEAGLRIAPDQWSSLL---YGDAS---RKSHMQSIID 106
LK++ Y L EH + E + L++AP+ + L + DAS R +H Q + D
Sbjct: 14 LKKDDTEYYLLTSEH-VSVSEFEGQEILKVAPEALTLLARQAFHDASFMLRPAHQQQVAD 72
Query: 107 KLQNPQS 113
L++P++
Sbjct: 73 ILRDPEA 79
>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
Snu114p subfamily. Snu114p is one of several proteins
that make up the U5 small nuclear ribonucleoprotein
(snRNP) particle. U5 is a component of the spliceosome,
which catalyzes the splicing of pre-mRNA to remove
introns. Snu114p is homologous to EF-2, but typically
contains an additional N-terminal domain not found in
Ef-2. This protein is part of the GTP translation factor
family and the Ras superfamily, characterized by five
G-box motifs.
Length = 213
Score = 28.0 bits (63), Expect = 3.3
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 3/42 (7%)
Query: 65 REHDAQIVEIATEAGLRIAPDQWSSLLYGDASRKSHMQSIID 106
R D + E ++ P SL+ D+ KS++ +IID
Sbjct: 39 RYTDTRKDEQERGISIKSNP---ISLVLEDSKGKSYLINIID 77
>gnl|CDD|224490 COG1574, COG1574, Predicted metal-dependent hydrolase with the
TIM-barrel fold [General function prediction only].
Length = 535
Score = 28.5 bits (64), Expect = 3.6
Identities = 20/72 (27%), Positives = 25/72 (34%), Gaps = 13/72 (18%)
Query: 22 LDLDSIPVNFALLQLVGVKVSKREGDSSL----MQLKEEFRTYESLR------REHDAQI 71
LDL LLQ GVK+ D SL L + E ++
Sbjct: 270 LDLLRQTGAKGLLQGGGVKLF---ADGSLGERTALLAAPYADGPGPSGELLLTEEELEEL 326
Query: 72 VEIATEAGLRIA 83
V A E GL +A
Sbjct: 327 VRAADERGLPVA 338
>gnl|CDD|114076 pfam05332, DUF743, Protein of unknown function (DUF743). This
family consists of several uncharacterized Calicivirus
proteins of unknown function.
Length = 105
Score = 27.1 bits (60), Expect = 3.8
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 54 KEEFRTYESLRREHDAQIVEIATEAGLRIAPDQWSSLLYGDASRKSHMQS 103
KE+F T LR + Q V+ AG R+ P + +Y D + +++ S
Sbjct: 49 KEQFETNLELRVQGPIQRVQALRAAGFRVNPYSNGNQIYYDEALNANLHS 98
>gnl|CDD|216650 pfam01696, Adeno_E1B_55K, Adenovirus EB1 55K protein / large
t-antigen. This family consists of adenovirus E1B 55K
protein or large t-antigen. E1B 55K binds p53 the tumour
suppressor protein converting it from a transcriptional
activator which responds to damaged DNA in to an
unregulated repressor of genes with a p53 binding site.
This protects the virus against p53 induced host
antiviral responses and prevents apoptosis as induced by
the adenovirus E1A protein. The E1B region of adenovirus
encodes two proteins E1B 55K the large t-antigen as
found in this family and E1B 19K pfam01691 the small
t-antigen which is not found in this family; both of
these proteins inhibit E1A induced apoptosis. This
family shows distant similarities to the pectate lyase
superfamily.
Length = 387
Score = 28.0 bits (63), Expect = 4.3
Identities = 7/14 (50%), Positives = 7/14 (50%)
Query: 223 LWAAVRARGCQFLG 236
WA V RGC F
Sbjct: 165 SWAGVEVRGCSFYA 178
>gnl|CDD|129562 TIGR00470, sepS, O-phosphoserine--tRNA ligase. This family of
archaeal proteins resembles known phenylalanyl-tRNA
synthetase alpha chains. Recently, it was shown to act
in a proposed pathway of tRNA(Cys) indirect
aminoacylation, resulting in Cys biosynthesis from
O-phosphoserine, in certain archaea. It charges
tRNA(Cys) with O-phosphoserine. The pscS gene product
converts the phosphoserine to Cys [Amino acid
biosynthesis, Serine family, Protein synthesis, tRNA
aminoacylation].
Length = 533
Score = 27.9 bits (62), Expect = 4.7
Identities = 19/90 (21%), Positives = 34/90 (37%), Gaps = 19/90 (21%)
Query: 41 VSKREGDSSLMQLKEEFRTYESLRREHD------AQIVEIATEAGLRIAPDQWSSL---- 90
+ D +L+E F Y+ + D A+ + ++ E GL++ +
Sbjct: 118 LGIDIDDEKKERLREVFHLYKKGAIDGDDLVFEIAKALNVSNEMGLKVLETVFPEFKDLK 177
Query: 91 -LYGDASRKSHM--------QSIIDKLQNP 111
+ +SHM SIIDK + P
Sbjct: 178 PESTTLTLRSHMTSGWFITLSSIIDKRKLP 207
>gnl|CDD|182099 PRK09831, PRK09831, putative acyltransferase; Provisional.
Length = 147
Score = 26.8 bits (59), Expect = 7.4
Identities = 12/24 (50%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 204 RAVTELNLQHQNPQQLSANLWAAV 227
RAVT QH +PQQ++A WA +
Sbjct: 20 RAVTMTASQHYSPQQIAA--WAQI 41
>gnl|CDD|218460 pfam05138, PaaA_PaaC, Phenylacetic acid catabolic protein. This
family includes proteins such as PaaA and PaaC that are
part of a catabolic pathway of phenylacetic acid. These
proteins may form part of a dioxygenase complex.
Length = 248
Score = 27.1 bits (61), Expect = 8.8
Identities = 10/52 (19%), Positives = 22/52 (42%), Gaps = 6/52 (11%)
Query: 61 ESLRREHDAQIVEIATEAGLRIAPDQWSSLLYGDASRKSH---MQSIIDKLQ 109
+ LR+ +V + EAGL + + L + H + ++ ++Q
Sbjct: 189 DELRQAWLDTVVPVLEEAGLTLPDEPA---LRWGGRQGRHTEHLGYLLAEMQ 237
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
0.317 0.130 0.378
Gapped
Lambda K H
0.267 0.0694 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,600,295
Number of extensions: 1043699
Number of successful extensions: 975
Number of sequences better than 10.0: 1
Number of HSP's gapped: 975
Number of HSP's successfully gapped: 19
Length of query: 237
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 143
Effective length of database: 6,768,326
Effective search space: 967870618
Effective search space used: 967870618
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: 57 (25.8 bits)