RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16584
(202 letters)
>gnl|CDD|220378 pfam09749, HVSL, Uncharacterized conserved protein. This entry is
of proteins of approximately 300 residues conserved from
plants to humans. It contains two conserved motifs, HxSL
and FHVSL. The function is unknown.
Length = 238
Score = 153 bits (389), Expect = 6e-47
Identities = 78/221 (35%), Positives = 120/221 (54%), Gaps = 21/221 (9%)
Query: 1 MDNPNEHGGRIRSFPHQRNSWATLVYIP-------------LQTNLARLYAMLKEELNSV 47
D+P HGGR+RSFPH +WAT VY+ L + L + L+ + +
Sbjct: 19 RDDPALHGGRVRSFPHVEGNWATHVYLEWRPSSAELELLDKLISQLNEDHTKLEATFDPL 78
Query: 48 GISVEVIPEP-HLSLSKTLVIPYHWIDTLVETLGNNLRHLN--RLTIKFNSIEIFCNEEK 104
IS +P P H+SLS+T+V+ H ID V++L LR R ++F+ ++++ NEEK
Sbjct: 79 LISDLGVPLPLHISLSRTVVLRTHQIDPFVDSLRQALRSAGIRRFKVQFSGLKVYSNEEK 138
Query: 105 TRSFIALGAN-SCKTSLTSIVQAVDKSAQEFKLPTYY-EEPNFHASIAWCLQDKTATLKP 162
TR+F+ L + S K +L ++ A++++ +EF LP Y ++P+FH SIAWCL D + LK
Sbjct: 139 TRTFLVLEVSESSKNALNRLLDAINEALREFGLPPLYDDDPSFHVSIAWCLGDPSEELKE 198
Query: 163 LLTKLD--NIFTQFKLTSDESFHVVTHIHMKTGNKFYSFPL 201
+ +L D F V + K GNK +S PL
Sbjct: 199 KSLSELQEILDALEELIFDLQFP-VNEVKCKIGNKVFSIPL 238
>gnl|CDD|212527 cd10003, HDAC6-dom2, Histone deacetylase 6, domain 2. Histone
deacetylase 6 is a class IIb Zn-dependent enzyme that
catalyzes hydrolysis of N(6)-acetyl-lysine residue of a
histone to yield a deacetylated histone (EC 3.5.1.98).
Histone acetylation/deacetylation process is important
for mediation of transcriptional regulation of many
genes. HDACs usually act via association with DNA
binding proteins to target specific chromatin regions.
HDAC6 is the only histone deacetylase with internal
duplication of two catalytic domains which appear to
function independently of each other, and also has a
C-terminal ubiquitin-binding domain. It is located in
the cytoplasm and associates with microtubule motor
complex, functioning as the tubulin deacetylase and
regulating microtubule-dependent cell motility. Known
interaction partners of HDAC6 are alpha tubulin and
ubiquitin-like modifier FAT10 (also known as Ubiquitin D
or UBD).
Length = 350
Score = 29.2 bits (66), Expect = 1.4
Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 1/44 (2%)
Query: 70 HWIDTLVETLGNNLRHLNRLTIKFNSIEIFCNEEKTRSFIALGA 113
+D + R LNRL +++SI + + +A G
Sbjct: 59 EHLDEMKSLEKMKPRELNRLGKEYDSI-YIHPDSYQCALLAAGC 101
>gnl|CDD|173877 cd08512, PBP2_NikA_DppA_OppA_like_7, 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 = 476
Score = 29.1 bits (66), Expect = 1.6
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 23 TLVYIPLQTNLARLYAMLKEELNSVGISVEVIPEP 57
TL Y + +L+ L +GI VE+ P P
Sbjct: 337 TLSYNSGNEPREDIAQLLQASLAQIGIKVEIEPVP 371
>gnl|CDD|227860 COG5573, COG5573, Predicted nucleic-acid-binding protein,
contains PIN domain [General function prediction only].
Length = 142
Score = 27.5 bits (61), Expect = 3.4
Identities = 12/46 (26%), Positives = 18/46 (39%), Gaps = 2/46 (4%)
Query: 49 ISVEVIPEPHLSLSKTLVIPYHWIDTLVETLGNNLR--HLNRLTIK 92
+SV+V+ E L + I TL+E R HL +
Sbjct: 42 VSVQVLNETCYVLKRKYGASEQLIQTLIEAFRRQCRIVHLTHEEVV 87
>gnl|CDD|132160 TIGR03116, cas_csf3, CRISPR type AFERR-associated protein Csf3.
Members of this family show up near CRISPR repeats in
Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp.
EbN1, and Rhodoferax ferrireducens DSM 15236. In the
latter two species, the CRISPR/cas locus is found on a
plasmid. This family is one of several characteristic of
a type of CRISPR-associated (cas) gene cluster we
designate Aferr after A. ferrooxidans, where it is both
chromosomal and the only type of cas gene cluster found.
The gene is designated csf3 (CRISPR/cas Subtype as in A.
ferrooxidans protein 3), as it lies third closest to the
repeats [Mobile and extrachromosomal element functions,
Other].
Length = 214
Score = 27.6 bits (61), Expect = 4.1
Identities = 23/93 (24%), Positives = 38/93 (40%), Gaps = 7/93 (7%)
Query: 79 LGNNLRHLNRLTIKFNSIEIFCNEEKTRSFI-ALGANSCKTSLTSIVQAVDKSAQEFKLP 137
L R+ T+ F F ++ R A G + +T + K+ Q
Sbjct: 76 LPYPKRYETAKTLPFTDPSRFIGDDLDRGLWQARGKVNPETFRIDTNRGQQKNYQM---- 131
Query: 138 TYYEEPNFHASIAWCLQDKTATLKPLLTKLDNI 170
YY N AWC+ D+ A L+ LL+++ +I
Sbjct: 132 -YYTTENAQELAAWCIGDEEA-LEFLLSQITHI 162
>gnl|CDD|187838 cd09707, Csf3_U, CRISPR/Cas system-associated RAMP superfamily
protein Csf3. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
RAMP superfamily protein.
Length = 214
Score = 27.2 bits (60), Expect = 4.7
Identities = 23/93 (24%), Positives = 38/93 (40%), Gaps = 7/93 (7%)
Query: 79 LGNNLRHLNRLTIKFNSIEIFCNEEKTRSFI-ALGANSCKTSLTSIVQAVDKSAQEFKLP 137
L R+ T+ F F ++ R A G + +T + K+ Q
Sbjct: 76 LPYPKRYETAKTLPFTDPSRFIGDDLDRGLWQARGKVNPETFRIDTNRGQQKNYQM---- 131
Query: 138 TYYEEPNFHASIAWCLQDKTATLKPLLTKLDNI 170
YY N AWC+ D+ A L+ LL+++ +I
Sbjct: 132 -YYTTENAQELAAWCIGDEEA-LEFLLSQITHI 162
>gnl|CDD|197503 smart00076, IFabd, Interferon alpha, beta and delta. Interferons
produce antiviral and antiproliferative responses in
cells. They are classified into five groups, all of
them related but gamma-interferon.
Length = 117
Score = 26.5 bits (59), Expect = 6.0
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 68 PYHWIDTLVETLGNNL-RHLNRL 89
W +TL+E+L N L + LN L
Sbjct: 40 SAAWNETLLESLLNELHQQLNHL 62
>gnl|CDD|234234 TIGR03502, lipase_Pla1_cef, extracellular lipase, Pla-1/cef family.
Members of this protein family are bacterial
lipoproteins largely from the Gammaproteobacteria.
Characterized members are expressed extracellularly and
have esterase activity. Members include the lipase Pla-1
from Aeromonas hydrophila (AF092033) and CHO cell
elongation factor (cef) from Vibrio hollisae.
Length = 792
Score = 27.5 bits (61), Expect = 6.2
Identities = 13/50 (26%), Positives = 19/50 (38%), Gaps = 6/50 (12%)
Query: 118 TSLTSIVQAVDKSAQEFKLPTYYEEPNFHASIAWCLQDKTATLKPLLTKL 167
+L + A + +LP Y E P+ AW Q + P L K
Sbjct: 304 AALAEVASAANVYKGTVRLPYYLETPS-----AWNPQP-FNSAMPSLAKR 347
>gnl|CDD|178166 PLN02551, PLN02551, aspartokinase.
Length = 521
Score = 27.0 bits (60), Expect = 7.7
Identities = 27/105 (25%), Positives = 45/105 (42%), Gaps = 23/105 (21%)
Query: 33 LARLYAMLKEELNSVGISVEVIPEPHLSLSKTLVIPYHW--------IDTLVETLGN--N 82
LA++++ E+L GISV+V+ +S+S TL W +D LVE L
Sbjct: 383 LAKVFSTF-EDL---GISVDVVATSEVSISLTLDPSKLWSRELIQQELDHLVEELEKIAV 438
Query: 83 LRHLNRLTIKFNSIEIFCNEEKT-----RSFIALGANSCKTSLTS 122
+ L +I I + N +++ + F L N + S
Sbjct: 439 VNLLQGRSI----ISLIGNVQRSSLILEKVFRVLRTNGVNVQMIS 479
>gnl|CDD|238047 cd00095, IFab, Interferon alpha, beta. Includes also interferon
omega and tau. Different from interferon gamma family.
Type I interferons(alpha, beta) belong to the larger
helical cytokine superfamily, which includes growth
hormones, interleukins, several colony-stimulating
factors and several other regulatory molecules. All
function as regulators of cellular activty by
interacting with cell-surface receptors and activating
various signalling pathways. Interferons produce
antiviral and antiproliferative responses in cells.
Receptor specificity determines function of the various
members of the family.
Length = 152
Score = 26.1 bits (58), Expect = 9.4
Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 1/23 (4%)
Query: 68 PYHWIDTLVETLGNNL-RHLNRL 89
W +TL+E+L N L + LN L
Sbjct: 72 SAAWNETLLESLLNELHQQLNHL 94
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
0.320 0.133 0.400
Gapped
Lambda K H
0.267 0.0729 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,833,104
Number of extensions: 857330
Number of successful extensions: 771
Number of sequences better than 10.0: 1
Number of HSP's gapped: 766
Number of HSP's successfully gapped: 16
Length of query: 202
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 110
Effective length of database: 6,857,034
Effective search space: 754273740
Effective search space used: 754273740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.3 bits)