RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16651
(153 letters)
>gnl|CDD|216043 pfam00651, BTB, BTB/POZ domain. The BTB (for BR-C, ttk and bab) or
POZ (for Pox virus and Zinc finger) domain is present
near the N-terminus of a fraction of zinc finger
(pfam00096) proteins and in proteins that contain the
pfam01344 motif such as Kelch and a family of pox virus
proteins. The BTB/POZ domain mediates homomeric
dimerisation and in some instances heteromeric
dimerisation. The structure of the dimerised PLZF
BTB/POZ domain has been solved and consists of a tightly
intertwined homodimer. The central scaffolding of the
protein is made up of a cluster of alpha-helices flanked
by short beta-sheets at both the top and bottom of the
molecule. POZ domains from several zinc finger proteins
have been shown to mediate transcriptional repression
and to interact with components of histone deacetylase
co-repressor complexes including N-CoR and SMRT. The POZ
or BTB domain is also known as BR-C/Ttk or ZiN.
Length = 101
Score = 67.3 bits (165), Expect = 1e-15
Identities = 32/116 (27%), Positives = 51/116 (43%), Gaps = 34/116 (29%)
Query: 23 FSSLLRSETMCDVTLATEGKHILAHKIVLSACSSYFQVAYHINICELFIFVLVILKRQLQ 82
+ L + +CDVTL K AHK VL+ACS YF+
Sbjct: 1 LNELRENGELCDVTLVVGDKEFHAHKAVLAACSPYFK----------------------- 37
Query: 83 YTSLCLTAWMLFSINPCKHPIVILKDVQFKDLKTLIDFIYFGEVNVSQEHLPSLLK 138
LF+ N + L+DV +D + L++FIY G++ +++E++ LL
Sbjct: 38 ---------ALFTGNKEVE--ITLEDVSPEDFEALLEFIYTGKLEITEENVDDLLA 82
>gnl|CDD|197585 smart00225, BTB, Broad-Complex, Tramtrack and Bric a brac. Domain
in Broad-Complex, Tramtrack and Bric a brac. Also known
as POZ (poxvirus and zinc finger) domain. Known to be a
protein-protein interaction motif found at the N-termini
of several C2H2-type transcription factors as well as
Shaw-type potassium channels. Known structure reveals a
tightly intertwined dimer formed via interactions
between N-terminal strand and helix structures. However
in a subset of BTB/POZ domains, these two secondary
structures appear to be missing. Be aware SMART predicts
BTB/POZ domains without the beta1- and alpha1-secondary
structures.
Length = 97
Score = 57.7 bits (140), Expect = 7e-12
Identities = 29/107 (27%), Positives = 46/107 (42%), Gaps = 34/107 (31%)
Query: 34 DVTLATEGKHILAHKIVLSACSSYFQVAYHINICELFIFVLVILKRQLQYTSLCLTAWML 93
DVTL GK AHK VL+A S YF+ L
Sbjct: 1 DVTLVVGGKKFHAHKAVLAAHSPYFK--------------------------------AL 28
Query: 94 FSINPC--KHPIVILKDVQFKDLKTLIDFIYFGEVNVSQEHLPSLLK 138
FS + + L DV +D + L++F+Y G++++ +E++ LL+
Sbjct: 29 FSSDFKESDKSEIYLDDVSPEDFRALLNFLYTGKLDLPEENVEELLE 75
>gnl|CDD|165086 PHA02713, PHA02713, hypothetical protein; Provisional.
Length = 557
Score = 36.1 bits (83), Expect = 0.004
Identities = 17/49 (34%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 15 HQPNFIAVFSSLLRSETMCDVTLAT-EGKHILAHKIVLSACSSYFQVAY 62
H ++ S+LL + +CDV + +G+ I AHK +L+A S YF+ +
Sbjct: 8 HNRRVVSNISNLLDDDILCDVIITIGDGEEIKAHKTILAAGSKYFRTLF 56
>gnl|CDD|222983 PHA03098, PHA03098, kelch-like protein; Provisional.
Length = 534
Score = 31.7 bits (72), Expect = 0.15
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 7/52 (13%)
Query: 23 FSSLLRSETMCDVTLATEGKHILAHKIVLSACSSYFQVA-------YHINIC 67
+S L+ + + G I HKI+LS+ S YF+ IN+
Sbjct: 2 YSFELQKFCDESIIIVNGGGIIKVHKIILSSSSEYFKKMFKNNFKENEINLN 53
>gnl|CDD|214592 smart00268, ACTIN, Actin. ACTIN subfamily of
ACTIN/mreB/sugarkinase/Hsp70 superfamily.
Length = 373
Score = 29.5 bits (67), Expect = 0.71
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 4/54 (7%)
Query: 92 MLFSINPCKHPIVILKDVQFKDLKTLIDFIYFGEVNVSQEHLPSLLKPRVRFPP 145
L P ++ IV D D++ + D+ +F E+ V E P LL P
Sbjct: 59 GLELKYPIENGIVENWD----DMEKIWDYTFFNELRVEPEEHPVLLTEPPMNPK 108
>gnl|CDD|187643 cd08939, KDSR-like_SDR_c, 3-ketodihydrosphingosine reductase (KDSR)
and related proteins, classical (c) SDR. These proteins
include members identified as KDSR, ribitol type
dehydrogenase, and others. The group shows strong
conservation of the active site tetrad and glycine rich
NAD-binding motif of the classical SDRs. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold (alpha/beta folding pattern with a central
beta-sheet), an NAD(P)(H)-binding region, and a
structurally diverse C-terminal region. Classical SDRs
are typically about 250 residues long, while extended
SDRs are approximately 350 residues. Sequence identity
between different SDR enzymes are typically in the
15-30% range, but the enzymes share the Rossmann fold
NAD-binding motif and characteristic NAD-binding and
catalytic sequence patterns. These enzymes catalyze a
wide range of activities including the metabolism of
steroids, cofactors, carbohydrates, lipids, aromatic
compounds, and amino acids, and act in redox sensing.
Classical SDRs have an TGXXX[AG]XG cofactor binding
motif and a YXXXK active site motif, with the Tyr
residue of the active site motif serving as a critical
catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase (15-PGDH)
numbering). In addition to the Tyr and Lys, there is
often an upstream Ser (Ser-138, 15-PGDH numbering)
and/or an Asn (Asn-107, 15-PGDH numbering) contributing
to the active site; while substrate binding is in the
C-terminal region, which determines specificity. The
standard reaction mechanism is a 4-pro-S hydride
transfer and proton relay involving the conserved Tyr
and Lys, a water molecule stabilized by Asn, and
nicotinamide. Extended SDRs have additional elements in
the C-terminal region, and typically have a TGXXGXXG
cofactor binding motif. Complex (multidomain) SDRs such
as ketoreductase domains of fatty acid synthase have a
GGXGXXG NAD(P)-binding motif and an altered active site
motif (YXXXN). Fungal type ketoacyl reductases have a
TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs
have lost catalytic activity and/or have an unusual
NAD(P)-binding motif and missing or unusual active site
residues. Reactions catalyzed within the SDR family
include isomerization, decarboxylation, epimerization,
C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 239
Score = 28.0 bits (63), Expect = 2.0
Identities = 10/35 (28%), Positives = 19/35 (54%)
Query: 108 DVQFKDLKTLIDFIYFGEVNVSQEHLPSLLKPRVR 142
D+ ++ + +D YFG +NV+ LP + + R
Sbjct: 100 DLTAEEFERGMDVNYFGSLNVAHAVLPLMKEQRPG 134
>gnl|CDD|200463 cd11324, AmyAc_Amylosucrase, Alpha amylase catalytic domain found
in Amylosucrase. Amylosucrase is a glucosyltransferase
that catalyzes the transfer of a D-glucopyranosyl moiety
from sucrose onto an acceptor molecule. When the
acceptor is another saccharide, only alpha-1,4 linkages
are produced. Unlike most amylopolysaccharide synthases,
it does not require any alpha-D-glucosyl nucleoside
diphosphate substrate. In the presence of glycogen it
catalyzes the transfer of a D-glucose moiety onto a
glycogen branch, but in its absence, it hydrolyzes
sucrose and synthesizes polymers, smaller
maltosaccharides, and sucrose isoforms. The
Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 536
Score = 27.5 bits (62), Expect = 3.4
Identities = 14/29 (48%), Positives = 17/29 (58%), Gaps = 1/29 (3%)
Query: 113 DLKTLIDFI-YFGEVNVSQEHLPSLLKPR 140
DLK L + I Y E+ V+ HL LLKP
Sbjct: 84 DLKGLAEKIPYLKELGVTYLHLMPLLKPP 112
>gnl|CDD|214391 CHL00192, syfB, phenylalanyl-tRNA synthetase beta chain;
Provisional.
Length = 704
Score = 27.0 bits (60), Expect = 4.9
Identities = 14/57 (24%), Positives = 22/57 (38%), Gaps = 5/57 (8%)
Query: 69 LFIFVLVILKRQLQYTSLCLTAWMLFSINPCKH---PIVILKDVQFKDLKTLIDFIY 122
LF L IL+ +Q L ++ +S P +I K + +K LI
Sbjct: 586 LFEINLDILQYSIQ--QNNLISYQPYSSYPKIIRDLSFIIKKSISISKIKELIYQNG 640
>gnl|CDD|107298 cd06303, PBP1_LuxPQ_Quorum_Sensing, Periplasmic binding protein
(LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from
Vibrio harveyi and its close homologs. Periplasmic
binding protein (LuxP) of autoinducer-2 (AI-2) receptor
LuxPQ from Vibrio harveyi and its close homologs from
other bacteria. The members of this group are highly
homologous to a family of periplasmic pentose/hexose
sugar-binding proteins that function as the primary
receptors for chemotaxis and transport of many sugar
based solutes in bacteria and archaea, and that are
members of the type I periplasmic binding protein
superfamily. The Vibrio harveyi AI-2 receptor consists
of two polypeptides, LuxP and LuxQ: LuxP is a
periplasmic binding protein that binds AI-2 by clamping
it between two domains, LuxQ is an integral membrane
protein belonging to the two-component sensor kinase
family. Unlike AI-2 bound to the LsrB receptor in
Salmonella typhimurium, the Vibrio harveyi AI-2
signaling molecule has an unusual furanosyl borate
diester. Hence, many bacteria coordinate their gene
expression according to the local density of their
population by producing species specific AI-2. This
process of quorum sensing allows LuxPQ to control light
production as well as its motility behavior.
Length = 280
Score = 26.9 bits (60), Expect = 4.9
Identities = 7/34 (20%), Positives = 10/34 (29%)
Query: 11 RWNNHQPNFIAVFSSLLRSETMCDVTLATEGKHI 44
W HQP F + + D + H
Sbjct: 99 AWLKHQPLLYVGFDHAAGARLLADYFIKRYPNHA 132
>gnl|CDD|133157 cd05490, Cathepsin_D2, Cathepsin_D2, pepsin family of proteinases.
Cathepsin D is the major aspartic proteinase of the
lysosomal compartment where it functions in protein
catabolism. It is a member of the pepsin family of
proteinases. This enzyme is distinguished from other
members of the pepsin family by two features that are
characteristic of lysosomal hydrolases. First, mature
Cathepsin D is found predominantly in a two-chain form
due to a posttranslational cleavage event. Second, it
contains phosphorylated, N-linked oligosaccharides that
target the enzyme to lysosomes via mannose-6-phosphate
receptors. Cathepsin D preferentially attacks peptide
bonds flanked by bulky hydrophobic amino acids and its
pH optimum is between pH 2.8 and 4.0. Two active site
aspartic acid residues are essential for the catalytic
activity of aspartic proteinases. Like other aspartic
proteinases, Cathepsin D is a bilobed molecule; the two
evolutionary related lobes are mostly made up of
beta-sheets and flank a deep active site cleft. Each of
the two related lobes contributes one active site
aspartic acid residue and contains a single carbohydrate
group. Cathepsin D is an essential enzyme. Mice
deficient for proteinase cathepsin D, generated by gene
targeting, develop normally during the first 2 weeks,
stop thriving in the third week and die in a state of
anorexia in the fourth week. The mice develop atrophy of
ileal mucosa followed by other degradation of intestinal
organs. In these knockout mice, lysosomal proteolysis
was normal. These results suggest that vital functions
of cathepsin D are exerted by limited proteolysis of
proteins regulating cell growth and/or tissue
homeostasis, while its contribution to bulk proteolysis
in lysosomes appears to be non-critical. This family of
aspartate proteases is classified by MEROPS as the
peptidase family A1 (pepsin A, clan AA).
Length = 325
Score = 26.7 bits (59), Expect = 6.5
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 76 ILKRQLQYTSLCLTAWMLFSINPCKHPIVILKDV 109
ILK + T++CL+ +M I P P+ IL DV
Sbjct: 272 ILKVSQRGTTICLSGFMGLDIPPPAGPLWILGDV 305
>gnl|CDD|176530 cd08588, PI-PLCc_At5g67130_like, Catalytic domain of Arabidopsis
thaliana PI-PLC X domain-containing protein At5g67130
and its uncharacterized homologs. This subfamily
corresponds to the catalytic domain present in
Arabidopsis thaliana PI-PLC X domain-containing protein
At5g67130 and its uncharacterized homologs. Members in
this family show high sequence similarity to bacterial
phosphatidylinositol-specific phospholipase C (PI-PLC,
EC 4.6.1.13), which participates in Ca2+-independent PI
metabolism, hydrolyzing the membrane lipid
phosphatidylinositol (PI) to produce phosphorylated
myo-inositol and diacylglycerol (DAG).
Length = 270
Score = 26.5 bits (59), Expect = 6.8
Identities = 6/18 (33%), Positives = 8/18 (44%), Gaps = 1/18 (5%)
Query: 6 QQFCLR-WNNHQPNFIAV 22
C +PNF+AV
Sbjct: 237 LNNCRPAAGGRKPNFVAV 254
>gnl|CDD|225382 COG2826, Tra8, Transposase and inactivated derivatives, IS30 family
[DNA replication, recombination, and repair].
Length = 318
Score = 26.2 bits (58), Expect = 7.4
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 114 LKTLIDFIYFGEVNVSQEHLPSLLKPR 140
+T+ ++Y G+ + HL L R
Sbjct: 107 FETIYRWLYQGKSEALRHHLRYLRHKR 133
>gnl|CDD|133162 cd06098, phytepsin, Phytepsin, a plant homolog of mammalian
lysosomal pepsins. Phytepsin, a plant homolog of
mammalian lysosomal pepsins, resides in grains, roots,
stems, leaves and flowers. Phytepsin may participate in
metabolic turnover and in protein processing events. In
addition, it highly expressed in several plant tissues
undergoing apoptosis. Phytepsin contains an internal
region consisting of about 100 residues not present in
animal or microbial pepsins. This region is thus called
a plant specific insert. The insert is highly similar to
saponins, which are lysosomal sphingolipid-activating
proteins in mammalian cells. The saponin-like domain may
have a role in the vacuolar targeting of phytepsin.
Phytepsin, as its animal counterparts, possesses a
topology typical of all aspartic proteases. They are
bilobal enzymes, each lobe contributing a catalytic Asp
residue, with an extended active site cleft localized
between the two lobes of the molecule. One lobe has
probably evolved from the other through a gene
duplication event in the distant past. This family of
aspartate proteases is classified by MEROPS as the
peptidase family A1 (pepsin A, clan AA).
Length = 317
Score = 25.8 bits (57), Expect = 9.7
Identities = 12/45 (26%), Positives = 21/45 (46%)
Query: 76 ILKRQLQYTSLCLTAWMLFSINPCKHPIVILKDVQFKDLKTLIDF 120
ILK + C++ + + P + P+ IL DV T+ D+
Sbjct: 264 ILKVGEGAAAQCISGFTALDVPPPRGPLWILGDVFMGAYHTVFDY 308
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
0.331 0.142 0.450
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,767,369
Number of extensions: 688600
Number of successful extensions: 587
Number of sequences better than 10.0: 1
Number of HSP's gapped: 584
Number of HSP's successfully gapped: 28
Length of query: 153
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 64
Effective length of database: 6,990,096
Effective search space: 447366144
Effective search space used: 447366144
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: 40 (21.9 bits)
S2: 55 (24.9 bits)