RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15193
(106 letters)
>gnl|CDD|240751 cd12305, RRM_NELFE, RNA recognition motif in negative elongation
factor E (NELF-E) and similar proteins. This subfamily
corresponds to the RRM of NELF-E, also termed
RNA-binding protein RD. NELF-E is the RNA-binding
subunit of cellular negative transcription elongation
factor NELF (negative elongation factor) involved in
transcriptional regulation of HIV-1 by binding to the
stem of the viral transactivation-response element
(TAR) RNA which is synthesized by cellular RNA
polymerase II at the viral long terminal repeat. NELF
is a heterotetrameric protein consisting of NELF A, B,
C or the splice variant D, and E. NELF-E contains an
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain). It
plays a role in the control of HIV transcription by
binding to TAR RNA. In addition, NELF-E is associated
with the NELF-B subunit, probably via a leucine zipper
motif. .
Length = 75
Score = 33.8 bits (78), Expect = 0.002
Identities = 14/17 (82%), Positives = 16/17 (94%)
Query: 29 NGTHVQGVKLKVSLARR 45
NGT VQGV+LKVSLAR+
Sbjct: 59 NGTTVQGVQLKVSLARK 75
>gnl|CDD|215629 PLN03200, PLN03200, cellulose synthase-interactive protein;
Provisional.
Length = 2102
Score = 30.1 bits (68), Expect = 0.19
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 5/50 (10%)
Query: 12 EEEITLQ-----AKYQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDAA 56
E+E+T AK ++ RK G+H Q + L VSL R A +N AA
Sbjct: 31 EKELTTARLLELAKTREEARKAIGSHSQAMPLLVSLLRSGTLGAKVNAAA 80
>gnl|CDD|131112 TIGR02057, PAPS_reductase, phosphoadenosine phosphosulfate
reductase, thioredoxin dependent. Requiring thioredoxin
as an electron donor, phosphoadenosine phosphosulfate
reductase catalyzes the reduction of
3'-phosphoadenylylsulfate (PAPS) to sulfite and
phospho-adenosine-phosphate (PAP). Found in
enterobacteria, cyanobacteria, and yeast, PAPS reductase
is related to a group of plant (TIGR00424) and bacterial
(TIGR02055) enzymes preferring 5'-adenylylsulfate (APS)
over PAPS as a substrate for reduction to sulfite
[Central intermediary metabolism, Sulfur metabolism].
Length = 226
Score = 25.9 bits (57), Expect = 3.9
Identities = 10/61 (16%), Positives = 20/61 (32%)
Query: 7 PSNHTEEEITLQAKYQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDAASSTTWSAIAC 66
P +E+ A + +R +++ LKV P+ D + +
Sbjct: 120 PMQRALKELNASAWFTGRRRDQGSARANLPVIEIDEQNGILKVNPLIDWTFEQVYQYLDA 179
Query: 67 H 67
H
Sbjct: 180 H 180
>gnl|CDD|241093 cd12649, RRM1_SXL, RNA recognition motif 1 in Drosophila
sex-lethal (SXL) and similar proteins. This subfamily
corresponds to the RRM1 of SXL which governs sexual
differentiation and X chromosome dosage compensation in
Drosophila melanogaster. It induces female-specific
alternative splicing of the transformer (tra) pre-mRNA
by binding to the tra uridine-rich polypyrimidine tract
at the non-sex-specific 3' splice site during the
sex-determination process. SXL binds also to its own
pre-mRNA and promotes female-specific alternative
splicing. SXL contains an N-terminal Gly/Asn-rich
domain that may be responsible for the protein-protein
interaction, and tandem RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), that show high preference
to bind single-stranded, uridine-rich target RNA
transcripts. .
Length = 81
Score = 24.7 bits (54), Expect = 6.0
Identities = 9/23 (39%), Positives = 15/23 (65%)
Query: 22 QKLKRKVNGTHVQGVKLKVSLAR 44
Q+ R +NG +Q ++KV+ AR
Sbjct: 56 QRAIRTLNGLQLQNKRIKVAYAR 78
>gnl|CDD|221268 pfam11853, DUF3373, Protein of unknown function (DUF3373). This
family of proteins are functionally uncharacterized.
This protein is found in bacteria. Proteins in this
family are typically between 472 to 574 amino acids in
length.
Length = 485
Score = 25.6 bits (56), Expect = 6.4
Identities = 12/59 (20%), Positives = 23/59 (38%), Gaps = 9/59 (15%)
Query: 6 FPSNHTEEEITLQAKYQKLKRKVNGTHVQGVKLKVSLARRQLKVAPINDAASST--TWS 62
P+ +I L K + LK+++ +LK L Q +V ++ T+
Sbjct: 18 LPAAAAAADIDLLQKIEALKKELA-------ELKAQLKDLQKRVDKTEKKSAGDRLTFG 69
>gnl|CDD|216627 pfam01650, Peptidase_C13, Peptidase C13 family. Members of this
family are asparaginyl peptidases. The blood fluke
parasite Schistosoma mansoni has at least five Clan CA
cysteine peptidases in its digestive tract including
cathepsins B (2 isoforms), C, F and L. All have been
recombinantly expressed as active enzymes, albeit in
various stages of activation. In addition, a Clan CD
peptidase, termed asparaginyl endopeptidase or
'legumain' has been identified. This has formerly been
characterized as a 'haemoglobinase', but this term is
probably incorrect. Two cDNAs have been described for
Schistosoma mansoni legumain; one encodes an active
enzyme whereas the active site cysteine residue encoded
by the second cDNA is substituted by an asparagine
residue. Both forms have been recombinantly expressed.
Length = 258
Score = 24.9 bits (55), Expect = 8.9
Identities = 7/25 (28%), Positives = 15/25 (60%)
Query: 10 HTEEEITLQAKYQKLKRKVNGTHVQ 34
H + TL+ +++ +K + G+HV
Sbjct: 216 HDLSKETLEQQFELVKNRTTGSHVM 240
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
0.314 0.129 0.374
Gapped
Lambda K H
0.267 0.0623 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,269,126
Number of extensions: 414571
Number of successful extensions: 258
Number of sequences better than 10.0: 1
Number of HSP's gapped: 258
Number of HSP's successfully gapped: 15
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (24.4 bits)