RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5396
(291 letters)
>gnl|CDD|216040 pfam00644, PARP, Poly(ADP-ribose) polymerase catalytic domain.
Poly(ADP-ribose) polymerase catalyzes the covalent
attachment of ADP-ribose units from NAD+ to itself and
to a limited number of other DNA binding proteins, which
decreases their affinity for DNA. Poly(ADP-ribose)
polymerase is a regulatory component induced by DNA
damage. The carboxyl-terminal region is the most highly
conserved region of the protein. Experiments have shown
that a carboxyl 40 kDa fragment is still catalytically
active.
Length = 206
Score = 77.4 bits (191), Expect = 5e-17
Identities = 39/180 (21%), Positives = 62/180 (34%), Gaps = 38/180 (21%)
Query: 130 PDFIFQVQYSPQSSIESNWSKLSLGRKKILHAFHGSRLENFHSILNFGLQQHFNKNSL-- 187
P FI ++ + + R + L +HGSRL NF IL+ GL+ + +
Sbjct: 33 PLFILEIFRVQREGEWDRFQPHKKLRNRRL-LWHGSRLTNFAGILSQGLRIAPPEAPVTG 91
Query: 188 --FGQGIYLSSQLGICLIYSPYSAGWGGSCVGSE-----LSIVSLCSIVD---------D 231
FG+GIY + SA + + LS V+L + +
Sbjct: 92 YMFGKGIYFADDAS-------KSANYCPTDEAHGSGLMLLSEVALGDMNELTKADYAEKL 144
Query: 232 PDQVKCQ--------EDTEEN----RRRALAQDSLGGEVPHKYYVVENSALVKVKYVLVY 279
P ED + +A + + YVV N V+ KY+L
Sbjct: 145 PPGKHSVKGLGKTAPEDFVWLDGVPLGKPVATGYDSSVLLYNEYVVYNVNQVRPKYLLEV 204
>gnl|CDD|238651 cd01341, ADP_ribosyl, ADP_ribosylating enzymes catalyze the
transfer of ADP_ribose from NAD+ to substrates.
Bacterial toxins are cytoplasmic and catalyze the
transfer of a single ADP_ribose unit to eukaryotic
elongation factor 2, halting protein synthesis and
killing the cell. Poly(ADP-ribose) polymerases (PARPS
1-3, VPARP, tankyrase) catalyze the addition of up to
100 ADP_ribose units from NAD+. PARPs 1 and 2 are
localized in the nucleaus, bind DNA, and are activated
by DNA damage. VPARP is part of the vault
ribonucleoprotein complex. Tankyrases regulates telomere
length in part through poy(ADP_ribosylation) of telomere
repeat binding factor 1 (TRF1). Poly(ADP-ribose)
polymerase catalyses the covalent attachment of
ADP-ribose units from NAD+ to itself and to a limited
number of other DNA binding proteins, which decreases
their affinity for DNA. Poly(ADP-ribose) polymerase is a
regulatory component induced by DNA damage. The
carboxyl-terminal region is the most highly conserved
region of the protein. Experiments have shown that a
carboxyl 40 kDa fragment is still catalytically active.
Length = 137
Score = 37.5 bits (87), Expect = 0.002
Identities = 20/64 (31%), Positives = 25/64 (39%), Gaps = 14/64 (21%)
Query: 160 HAFHGSRLENFHSILNFGLQQHFNKNSL----FGQGIYLSSQLGICLIYSPYSAGWGGSC 215
FHGS N SIL GL+ L FG+GIY + S G+
Sbjct: 1 FLFHGSPPGNVISILKLGLRPASYGVLLNGGMFGKGIYSAPN-------ISKSNGY---S 50
Query: 216 VGSE 219
VG +
Sbjct: 51 VGCD 54
>gnl|CDD|238717 cd01437, parp_like, Poly(ADP-ribose) polymerase (parp) catalytic
domain catalyses the covalent attachment of ADP-ribose
units from NAD+ to itself and to a limited number of
other DNA binding proteins, which decreases their
affinity for DNA. Poly(ADP-ribose) polymerase is a
regulatory component induced by DNA damage. The
carboxyl-terminal region is the most highly conserved
region of the protein. Experiments have shown that a
carboxyl 40 kDa fragment is still catalytically active.
Poly(ADP-ribose)-like polymerases (PARPS 1-3, VPARP,
tankyrase) catalyze the addition of up to 100 ADP_ribose
units from NAD+. PARPs 1 and 2 are localized in the
nucleaus, bind DNA, and are activated by DNA damage.
VPARP is part of the vault ribonucleoprotein complex.
Tankyrases regulates telomere length through
interactions with telomere repeat binding factor 1.
Length = 347
Score = 36.5 bits (85), Expect = 0.011
Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 6/49 (12%)
Query: 152 SLGRKKILHAFHGSRLENFHSILNFGLQ----QHFNKNSLFGQGIYLSS 196
LG +K+L +HGSRL NF IL+ GL+ + +FG+GIY +
Sbjct: 191 KLGNRKLL--WHGSRLTNFVGILSQGLRIAPPEAPVTGYMFGKGIYFAD 237
>gnl|CDD|143590 cd07566, ScNTA1_like, Saccharomyces cerevisiae N-terminal amidase
NTA1, and related proteins (class 3 nitrilases).
Saccharomyces cerevisiae NTA1 functions in the N-end
rule protein degradation pathway. It specifically
deaminates the N-terminal asparagine and glutamine
residues of substrates of this pathway, to aspartate and
glutamate respectively, these latter are the
destabilizing residues. This subgroup belongs to a
larger nitrilase superfamily comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as 1-13),
this subgroup corresponds to class 3.
Length = 295
Score = 30.8 bits (70), Expect = 0.71
Identities = 18/86 (20%), Positives = 30/86 (34%), Gaps = 17/86 (19%)
Query: 170 FHSILNFGLQQHFNKNSLFGQGIYLSSQLGICLIYSPYS--AGW-----GGSCV--GSEL 220
L F F+ S + L + +GIC+ +PY A + + G+EL
Sbjct: 139 QTFPLPFAKDDDFDGGS---VDVTLKTSIGICMDLNPYKFEAPFTDFEFATHVLDNGTEL 195
Query: 221 SIVS---LCSIVDDPDQVKCQEDTEE 243
I L S P ++ +
Sbjct: 196 IICPMAWLHS--LSPTELTVLPQEPD 219
>gnl|CDD|215590 PLN03123, PLN03123, poly [ADP-ribose] polymerase; Provisional.
Length = 981
Score = 30.9 bits (70), Expect = 0.90
Identities = 18/48 (37%), Positives = 27/48 (56%), Gaps = 6/48 (12%)
Query: 150 KLSLGRKKILHAFHGSRLENFHSILNFGLQ----QHFNKNSLFGQGIY 193
K L + +L +HGSRL NF IL+ GL+ + +FG+G+Y
Sbjct: 820 KEKLKNRMLL--WHGSRLTNFVGILSQGLRIAPPEAPATGYMFGKGVY 865
>gnl|CDD|219831 pfam08416, PTB, Phosphotyrosine-binding domain. The
phosphotyrosine-binding domain (PTB, also
phosphotyrosine-interaction or PI domain) in the protein
tensin tends to be found at the C-terminus. Tensin is a
multi-domain protein that binds to actin filaments and
functions as a focal-adhesion molecule (focal adhesions
are regions of plasma membrane through which cells
attach to the extracellular matrix). Human tensin has
actin-binding sites, an SH2 (pfam00017) domain and a
region similar to the tumour suppressor PTEN. The PTB
domain interacts with the cytoplasmic tails of beta
integrin by binding to an NPXY motif.
Length = 131
Score = 28.9 bits (65), Expect = 1.4
Identities = 20/49 (40%), Positives = 28/49 (57%), Gaps = 5/49 (10%)
Query: 114 YDSVLNLVSCEPNVAKPD-FIFQVQY----SPQSSIESNWSKLSLGRKK 157
Y+S+L V+ EP +KP+ +FQ P IES SK+ LG+KK
Sbjct: 82 YNSLLAFVAQEPGQSKPNVHLFQCDELGAEQPAEDIESALSKVRLGKKK 130
>gnl|CDD|214630 smart00349, KRAB, krueppel associated box.
Length = 61
Score = 26.8 bits (60), Expect = 2.9
Identities = 10/19 (52%), Positives = 12/19 (63%)
Query: 119 NLVSCEPNVAKPDFIFQVQ 137
NLVS V KPD I Q++
Sbjct: 36 NLVSLGFQVPKPDLISQLE 54
>gnl|CDD|241246 cd01210, PTB_EPS8, Epidermal growth factor receptor kinase
substrate (EPS8)-like Phosphotyrosine-binding (PTB)
domain. EPS8 is a regulator of Rac signaling. It
consists of a PTB and an SH3 domain. PTB domains have a
common PH-like fold and are found in various eukaryotic
signaling molecules. This domain was initially shown to
binds peptides with a NPXY motif with differing
requirements for phosphorylation of the tyrosine,
although more recent studies have found that some types
of PTB domains can bind to peptides lack tyrosine
residues altogether. In contrast to SH2 domains, which
recognize phosphotyrosine and adjacent carboxy-terminal
residues, PTB-domain binding specificity is conferred by
residues amino-terminal to the phosphotyrosine. PTB
domains are classified into three groups:
phosphotyrosine-dependent Shc-like,
phosphotyrosine-dependent IRS-like, and
phosphotyrosine-independent Dab-like PTB domains. This
cd is part of the Dab-like subgroup.
Length = 131
Score = 27.1 bits (61), Expect = 6.2
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 110 PRDQYDSVLNLVSCEPNVAKPD-FIFQVQ 137
Y+S+L LV EP+ KP+ +FQ
Sbjct: 81 SDCSYNSLLLLVVQEPDQPKPEMHLFQCD 109
>gnl|CDD|233012 TIGR00535, SAM_DCase, S-adenosylmethionine decarboxylase proenzyme,
eukaryotic form. This enzyme is a key regulatory enzyme
of the polyamine synthetic pathway. This protein is a
pyruvoyl-dependent enzyme. The proenzyme is cleaved at a
Ser residue that becomes a pyruvoyl group active site
[Central intermediary metabolism, Polyamine
biosynthesis].
Length = 334
Score = 27.9 bits (62), Expect = 6.7
Identities = 10/38 (26%), Positives = 19/38 (50%)
Query: 87 KLCDLIYLLHWLLVEQSPSLEEVPRDQYDSVLNLVSCE 124
KL ++ + H +++ L + R Q D +L+L C
Sbjct: 6 KLLEIWFFEHKKFIDEGKGLRAIGRAQIDEILDLARCT 43
>gnl|CDD|131863 TIGR02816, pfaB_fam, PfaB family protein. The protein PfaB is part
of four gene locus, similar to polyketide biosynthesis
systems, responsible for omega-3 polyunsaturated fatty
acid biosynthesis in several high pressure and/or
cold-adapted bacteria. The fairly permissive trusted
cutoff set for this model allows detection of homologs
encoded near homologs to other proteins of the locus:
PfaA, PfaC, and/or PfaD. The likely role in every case
is either polyunsaturated fatty acid or polyketide
biosynthesis.
Length = 538
Score = 27.7 bits (61), Expect = 9.2
Identities = 14/62 (22%), Positives = 29/62 (46%)
Query: 4 SDIDVKITELKQILAWNKLGCDIKWSIFVSACQSYRVSSCLHPFPPMFIKNQHKDISAVL 63
S I K+T +++ + +I+W+ FV C++ + + L FP ++ D +
Sbjct: 304 SAISGKLTAVREAWQLDDTAAEIQWNSFVVRCEAAPIEALLKDFPHAYLAIIQGDTCVIA 363
Query: 64 EC 65
C
Sbjct: 364 GC 365
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 0.135 0.414
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,316,371
Number of extensions: 1298419
Number of successful extensions: 820
Number of sequences better than 10.0: 1
Number of HSP's gapped: 817
Number of HSP's successfully gapped: 14
Length of query: 291
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 195
Effective length of database: 6,679,618
Effective search space: 1302525510
Effective search space used: 1302525510
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: 59 (26.4 bits)