RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15602
(72 letters)
>gnl|CDD|237987 cd00020, ARM, Armadillo/beta-catenin-like repeats. An approximately
40 amino acid long tandemly repeated sequence motif
first identified in the Drosophila segment polarity gene
armadillo; these repeats were also found in the
mammalian armadillo homolog beta-catenin, the junctional
plaque protein plakoglobin, the adenomatous polyposis
coli (APC) tumor suppressor protein, and a number of
other proteins. ARM has been implicated in mediating
protein-protein interactions, but no common features
among the target proteins recognized by the ARM repeats
have been identified; related to the HEAT domain; three
consecutive copies of the repeat are represented by this
alignment model.
Length = 120
Score = 28.8 bits (65), Expect = 0.11
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 4 DRVVCAAATALRNLAIDQRNKELIDAFEANLI--LIELNLSPP 44
+ VV AA ALRNLA + +LI EA + L+ L S
Sbjct: 63 EEVVKAALWALRNLAAGPEDNKLI-VLEAGGVPKLVNLLDSSN 104
>gnl|CDD|214547 smart00185, ARM, Armadillo/beta-catenin-like repeats. Approx. 40
amino acid repeat. Tandem repeats form superhelix of
helices that is proposed to mediate interaction of
beta-catenin with its ligands. Involved in transducing
the Wingless/Wnt signal. In plakoglobin arm repeats
bind alpha-catenin and N-cadherin.
Length = 41
Score = 23.5 bits (52), Expect = 4.2
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 4 DRVVCAAATALRNLA 18
+ VV AA AL NL+
Sbjct: 26 EEVVKEAAWALSNLS 40
>gnl|CDD|143432 cd07114, ALDH_DhaS, Uncharacterized Candidatus pelagibacter
aldehyde dehydrogenase, DhaS-like. Uncharacterized
aldehyde dehydrogenase from Candidatus pelagibacter
(DhaS) and other related sequences are present in this
CD.
Length = 457
Score = 24.4 bits (54), Expect = 5.2
Identities = 18/48 (37%), Positives = 21/48 (43%), Gaps = 11/48 (22%)
Query: 2 EVDRVVCAAATAL-----RNLAIDQRNKELI---DAFEAN---LILIE 38
+VDR V AA A R L +R K L D EAN L +E
Sbjct: 20 DVDRAVAAARAAFEGGAWRKLTPTERGKLLRRLADLIEANAEELAELE 67
>gnl|CDD|178251 PLN02645, PLN02645, phosphoglycolate phosphatase.
Length = 311
Score = 24.3 bits (53), Expect = 6.1
Identities = 10/28 (35%), Positives = 12/28 (42%)
Query: 5 RVVCAAATALRNLAIDQRNKELIDAFEA 32
V AA A L + ELID+ E
Sbjct: 3 NVTPAAMAAAAQLLTLENADELIDSVET 30
>gnl|CDD|232998 TIGR00499, lysS_bact, lysyl-tRNA synthetase, eukaryotic and
non-spirochete bacterial. This model represents the
lysyl-tRNA synthetases that are class II amino-acyl tRNA
synthetases. It includes all eukaryotic and most
bacterial examples of the enzyme, but not archaeal or
spirochete forms [Protein synthesis, tRNA
aminoacylation].
Length = 496
Score = 24.3 bits (53), Expect = 6.1
Identities = 6/33 (18%), Positives = 16/33 (48%)
Query: 24 KELIDAFEANLILIELNLSPPAGKYAMRDLVQK 56
+EL+ + +E++ P + M + ++K
Sbjct: 291 QELLGTTKITYGELEIDFKKPFKRITMVEAIKK 323
>gnl|CDD|218395 pfam05037, DUF669, Protein of unknown function (DUF669). Members
of this family are found in various phage proteins.
Length = 142
Score = 24.2 bits (53), Expect = 6.2
Identities = 9/24 (37%), Positives = 11/24 (45%)
Query: 33 NLILIELNLSPPAGKYAMRDLVQK 56
I + N+S GKYAM L
Sbjct: 57 RKIFDDNNVSKETGKYAMGRLNTI 80
>gnl|CDD|222512 pfam14048, MBD_C, C-terminal domain of methyl-CpG binding protein
2 and 3. CpG-methylation is a frequently occurring
epigenetic modification of vertebrate genomes resulting
in transcriptional repression. This domain was found at
the C-terminus of the methyl-CpG-binding domain (MBD)
containing proteins MBD2 and MBD3, the latter was shown
to not bind directly to methyl-CpG DNA but rather
interact with components of the NuRD/Mi2 complex, an
abundant deacetylase complex. The domain is subject to
structure determination by the Joint Center of
Structural Genomics.
Length = 96
Score = 23.8 bits (52), Expect = 7.0
Identities = 7/30 (23%), Positives = 14/30 (46%)
Query: 37 IELNLSPPAGKYAMRDLVQKLPSGNAQHDQ 66
+ + +P G+ + D ++K P DQ
Sbjct: 36 LHTSSAPITGQTSSSDALEKNPGVGLNTDQ 65
>gnl|CDD|177543 PHA03146, PHA03146, helicase-primase primase subunit; Provisional.
Length = 1075
Score = 24.1 bits (52), Expect = 8.0
Identities = 20/76 (26%), Positives = 35/76 (46%), Gaps = 17/76 (22%)
Query: 11 ATALRNLAIDQRNKELIDAFEANLILIEL------NLSPPAGKY---------AMRD--L 53
+ L ++ + +++E ++AF A+++L E+ + AG+Y A D L
Sbjct: 942 ESLLSSVNVSIKSREAVEAFVADVVLAEVVPHLAAHFPQAAGEYQGAGAHTVVAKPDWIL 1001
Query: 54 VQKLPSGNAQHDQGTS 69
Q SG A QG S
Sbjct: 1002 AQLNRSGAAYRSQGFS 1017
>gnl|CDD|237357 PRK13348, PRK13348, chromosome replication initiation inhibitor
protein; Provisional.
Length = 294
Score = 24.2 bits (53), Expect = 8.5
Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 11/56 (19%)
Query: 18 AIDQRNKELIDAFEANLILIELNLSP-PAGK------YAMR----DLVQKLPSGNA 62
A+ QR K L ++ L++ P PAG+ + DL+ LP+
Sbjct: 32 AVSQRIKALEESLGQPLLVRGRPCRPTPAGQRLLRHLRQVALLEADLLSTLPAERG 87
>gnl|CDD|240521 cd13394, Syo1_like, Fungal symportin 1 (syo1) and similar proteins.
This family of eukaryotic proteins includes
Saccharomyces cerevisiae Ydl063c and Chaetomium
thermophilum Syo1, which mediate the co-import of two
ribosomal proteins, Rpl5 and Rpl11 (which both interact
with 5S rRNA) into the nucleus. Import precedes their
association with rRNA and subsequent ribosome assembly
in the nucleolus. The primary structure of syo1 is a
mixture of Armadillo- (ARM, N-terminal part of syo1) and
HEAT-repeats (C-terminal part of syo1).
Length = 597
Score = 24.2 bits (53), Expect = 8.7
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 2 EVDRVVCAAATALRNLAIDQ 21
VV A ALRNLAI++
Sbjct: 91 SNTEVVVEAFGALRNLAIEE 110
>gnl|CDD|221360 pfam11988, Dsl1_N, Retrograde transport protein Dsl1 N terminal.
Dsl1 is a peripheral membrane protein required for
transport between the Golgi and the endoplasmic
reticulum. It is localised to the ER membrane, and in
vitro it specifically binds to coatomer, the major
component of the protein coat of COPI vesicles. It is
comprised primarily of alpha helical bundles. It
complexes with another subunit of the Dsl1p complex
called Tip20 which forms heterodimers by pairing the N
termini of each protein. A central disorganised region
between the N and C termini of Dsl1 contains binding
sites for coatomer. The C terminus of Dsl1 contains a
binding site to the Sec39 subunit of the Dsl1p complex.
Length = 353
Score = 23.9 bits (52), Expect = 9.3
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 26 LIDAFEANLILIELNLSPPAGKYAMRDLVQKLPSGNAQHDQG 67
LI F+AN L+EL Y++++L +KL S ++ Q
Sbjct: 59 LIKEFKANFELLELE----NCYYSLQNLRKKLKSVDSSLKQS 96
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
0.316 0.131 0.361
Gapped
Lambda K H
0.267 0.0877 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,604,538
Number of extensions: 274287
Number of successful extensions: 263
Number of sequences better than 10.0: 1
Number of HSP's gapped: 263
Number of HSP's successfully gapped: 15
Length of query: 72
Length of database: 10,937,602
Length adjustment: 42
Effective length of query: 30
Effective length of database: 9,074,734
Effective search space: 272242020
Effective search space used: 272242020
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 (21.6 bits)
S2: 53 (23.9 bits)