RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6232
(100 letters)
>gnl|CDD|240131 cd04861, LigD_Pol_like, LigD_Pol_like: Polymerase (Pol) domain of
bacterial LigD proteins similar to Pseudomonas
aeruginosa (Pae) LigD. The LigD Pol domain belongs to
the archaeal/eukaryal primase (AEP) superfamily. In
prokaryotes, LigD along with Ku is required for
non-homologous end joining (NHEJ)-mediated repair of DNA
double-strand breaks (DSB). NHEJ-mediated DNA DSB repair
is error-prone. PaeLigD is monomeric, containing an
N-terminal phosphoesterase module, a central polymerase
(Pol) domain, and a C-terminal ATP-dependent ligase
domain. Mycobacterium tuberculosis (Mt)LigD, also found
in this group, is monomeric and contains the same
modules but these are arranged differently: an
N-terminal Pol domain, a central phosphoesterase module,
and a C-terminal ligase domain. It has been suggested
that LigD Pol contributes to NHEJ-mediated DNA DSB
repair in vivo, by filling in short 5'-overhangs with
ribonucleotides; the filled in termini would then be
sealed by the associated LigD ligase domain, resulting
in short stretches of RNA incorporated into the genomic
DNA. The PaeLigD Pol domain in vitro, in a
manganese-dependent fashion, catalyzes templated
extensions of 5'-overhang duplex DNA, and nontemplated
single-nucleotide additions to blunt-end duplex DNA; it
preferentially adds single ribonucleotides at blunt DNA
ends. PaeLigD Pol adds a correctly paired rNTP to the
DNA primer termini more rapidly than it does a correctly
paired dNTP; it has higher infidelity as an RNA
polymerase than it does as a DNA polymerase, which is in
keeping with the mutagenic property of NHEJ-mediated DNA
DSB repair. The MtLigD Pol domain similarly is
stimulated by manganese, is error-prone, and prefers
adding rNTPs to dNTPs in vitro. The MtLigD Pol domain
has been shown to prefer DNA gapped substrates
containing a 5'-phosphate group at the gap.
Length = 227
Score = 29.8 bits (68), Expect = 0.17
Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 15/81 (18%)
Query: 7 DDPCFFQNSIPDYL--FFVSPSIYFLD---DFILKQHAWVWLLWLLSQTWITLHIWTPKC 61
D FFQ P + + + +++L A L+WL + I LH W +
Sbjct: 34 DGESFFQKHAPAGAPDWVRTVEVESEGGTINYLLVNDAAG-LVWLANLGAIELHPWLSRA 92
Query: 62 ERLATTEKLFVRPMYDALLID 82
+ L RP D L+ D
Sbjct: 93 DDLE-------RP--DRLVFD 104
>gnl|CDD|220637 pfam10223, DUF2181, Uncharacterized conserved protein (DUF2181).
This is region of approximately 250 residues conserved
from worms to humans. Its function is unknown.
Length = 244
Score = 29.0 bits (65), Expect = 0.38
Identities = 12/37 (32%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 38 HAWVWLLWLLSQTW-ITLHIWTPKCERLATTEKLFVR 73
++W LLWLLSQ+ +L +W+ + ++ + L +R
Sbjct: 189 NSWPQLLWLLSQSNRYSLTLWSGAEDAVSVEDLLELR 225
>gnl|CDD|240136 cd04866, LigD_Pol_like_3, LigD_Pol_like_3: Polymerase (Pol)
domain of bacterial LigD proteins similar to
Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD
Pol domain belongs to the archaeal/eukaryal primase
(AEP) superfamily. In prokaryotes, LigD along with Ku
is required for non-homologous end joining
(NHEJ)-mediated repair of DNA double-strand breaks
(DSB). NHEJ-mediated DNA DSB repair is error-prone. It
has been suggested that LigD Pol contributes to
NHEJ-mediated repair DSB repair in vivo, by filling in
short 5'-overhangs with ribonucleotides; the filled in
termini would then be sealed by the associated LigD
ligase domain, resulting in short stretches of RNA
incorporated into the genomic DNA. The Pol domains of
PaeLigD and Mycobacterium tuberculosis (Mt)LigD are
stimulated by manganese, are error-prone, and prefer
adding rNTPs to dNTPs in vitro; however PaeLigD and
MtLigD belong to other subgroups, proteins in this
subgroup await functional characterization.
Length = 223
Score = 27.8 bits (62), Expect = 0.81
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 11 FFQNSIPDYL-FFVSPSIYFLDDFILKQHAWVWLLWLLSQTWITLHI 56
FFQ + PDY FV + ++I+ + L+WL +Q + LHI
Sbjct: 38 FFQKNKPDYAPEFVETVMLDEINYIVCNNLET-LVWLGNQLALELHI 83
>gnl|CDD|182006 PRK09633, ligD, ATP-dependent DNA ligase; Reviewed.
Length = 610
Score = 27.7 bits (62), Expect = 0.92
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 12/52 (23%)
Query: 11 FFQNSIPDYLFFVSPSIYFLDDFILKQHAWVW------LLWLLSQTWITLHI 56
F+Q + PDY P F+ + ++ LLWL +Q + HI
Sbjct: 377 FYQKNKPDYA----PD--FVQSARDDEIEYIVCNDLSTLLWLGNQLALEFHI 422
>gnl|CDD|234007 TIGR02776, NHEJ_ligase_prk, DNA ligase D. Members of this protein
family are DNA ligases involved in the repair of DNA
double-stranded breaks by non-homologous end joining
(NHEJ). The system of the bacterial Ku protein
(TIGR02772) plus this DNA ligase is seen in about 20 %
of bacterial genomes to date and at least one archaeon
(Archeoglobus fulgidus). This model describes a central
and a C-terminal domain. These two domains may be
permuted, as in genus Mycobacterium, or divided into
tandem ORFs, and therefore not be identified by This
model. An additional N-terminal 3'-phosphoesterase (PE)
domain present in some but not all examples of this
ligase is not included in the seed alignment for this
model; This model models only the central ATP-dependent
ligase domain and the C-terminal polymerase domain. Most
examples of genes for this ligase are adjacent to the
gene for Ku [DNA metabolism, DNA replication,
recombination, and repair].
Length = 552
Score = 27.7 bits (62), Expect = 1.1
Identities = 18/53 (33%), Positives = 22/53 (41%), Gaps = 7/53 (13%)
Query: 9 PCFFQNSIPDYLFFVSPSIYFLDDFILKQHAWV----WLLWLLSQTWITLHIW 57
CFFQ PDY P + D K++ LLWL Q + HIW
Sbjct: 332 ECFFQKHAPDYA---PPFVASFKDGDEKEYLVCNDAEGLLWLAQQGALEFHIW 381
>gnl|CDD|240135 cd04865, LigD_Pol_like_2, LigD_Pol_like_2: Polymerase (Pol) domain
of bacterial LigD proteins similar to Pseudomonas
aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain
belongs to the archaeal/eukaryal primase (AEP)
superfamily. In prokaryotes, LigD along with Ku is
required for non-homologous end joining (NHEJ)-mediated
repair of DNA double-strand breaks (DSB). NHEJ-mediated
DNA DSB repair is error-prone. It has been suggested
that LigD Pol contributes to NHEJ-mediated DNA DSB
repair in vivo, by filling in short 5'-overhangs with
ribonucleotides; the filled in termini would then be
sealed by the associated LigD ligase domain, resulting
in short stretches of RNA incorporated into the genomic
DNA. The Pol domains of PaeLigD and Mycobacterium
tuberculosis (Mt)LigD are stimulated by manganese, are
error-prone, and prefer adding rNTPs to dNTPs in vitro;
however PaeLigD and MtLigD belong to other subgroups,
proteins in this subgroup await functional
characterization.
Length = 228
Score = 27.2 bits (61), Expect = 1.4
Identities = 20/82 (24%), Positives = 31/82 (37%), Gaps = 16/82 (19%)
Query: 7 DDPCFFQNSIPDYL--FFVSPSIYFLD----DFILKQHAWVWLLWLLSQTWITLHIWTPK 60
D F+Q +P + + I ++++ Q LLWL + I LH W +
Sbjct: 34 DGKGFYQKDVPAGAPDWLRTVRITSESGRTINYLIVQDPAA-LLWLANLGCIELHPWPSR 92
Query: 61 CERLATTEKLFVRPMYDALLID 82
L P D L+ID
Sbjct: 93 AGDLD-------HP--DELVID 105
>gnl|CDD|225823 COG3285, COG3285, Predicted eukaryotic-type DNA primase [DNA
replication, recombination, and repair].
Length = 299
Score = 27.0 bits (60), Expect = 1.6
Identities = 14/74 (18%), Positives = 22/74 (29%), Gaps = 11/74 (14%)
Query: 7 DDPCFFQNSIPDYLFFVSPSIYFLDDF----ILKQHAWV----WLLWLLSQTWITLHIWT 58
FFQ P P + + K + + L WL Q + H W
Sbjct: 59 GGEAFFQKHAPRG---APPWVQTVRVTKDSGRTKPYLVIDDAAGLAWLAQQGALEFHPWG 115
Query: 59 PKCERLATTEKLFV 72
+ L ++ V
Sbjct: 116 ATIDDLEHPDERIV 129
>gnl|CDD|234008 TIGR02778, ligD_pol, DNA polymerase LigD, polymerase domain. DNA
repair of double-stranded breaks by non-homologous end
joining (NHEJ) is accomplished by a two-protein system
that is present in a minority of prokaryotes. One
component is the Ku protein (see TIGR02772), which binds
DNA ends. The other is a DNA ligase, a protein that is a
multidomain polypeptide in most of those bacteria that
have NHEJ, a permuted polypeptide in Mycobacterium
tuberculosis and a few other species, and the product of
tandem genes in some other bacteria. This model
represents the polymerase domain.
Length = 245
Score = 26.5 bits (59), Expect = 2.5
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 11/56 (19%)
Query: 9 PCFFQNSIPDYLFFVSPSIYFL-------DDFILKQHAWVWLLWLLSQTWITLHIW 57
CFFQ +P P + + +++ A LLWL+ Q + HIW
Sbjct: 53 ECFFQKHLPQGA---PPFVVSAEVEESDGETYLVINDAEG-LLWLVQQGALEFHIW 104
>gnl|CDD|219656 pfam07947, YhhN, YhhN-like protein. The members of this family are
similar to the hypothetical protein yhhN expressed by E.
coli. Many of the members of this family are annotated
as being possible transmembrane proteins, and in fact
they all have a high proportion of hydrophobic residues.
Length = 182
Score = 25.7 bits (57), Expect = 3.9
Identities = 7/38 (18%), Positives = 15/38 (39%), Gaps = 3/38 (7%)
Query: 20 LFFVSPSIYFLDDFILK---QHAWVWLLWLLSQTWITL 54
LF +S + ++ F+ + + +Q I L
Sbjct: 143 LFVLSDLLLAINRFVGPFPAARLLIMGTYYAAQLLIVL 180
>gnl|CDD|240134 cd04864, LigD_Pol_like_1, LigD_Pol_like_1: Polymerase (Pol)
domain of mostly bacterial LigD proteins similar to
Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD
Pol domain belongs to the archaeal/eukaryal primase
(AEP) superfamily. In prokaryotes, LigD along with Ku
is required for non-homologous end joining
(NHEJ)-mediated repair of DNA double-strand breaks
(DSB). NHEJ-mediated DNA DSB repair is error-prone. It
has been suggested that LigD Pol contributes to
NHEJ-mediated DNA DSB repair in vivo, by filling in
short 5'-overhangs with ribonucleotides; the filled in
termini would then be sealed by the associated LigD
ligase domain, resulting in short stretches of RNA
incorporated into the genomic DNA. The Pol domains of
PaeLigD and Mycobacterium tuberculosis (Mt)LigD are
stimulated by manganese, are error-prone, and prefer
adding rNTPs to dNTPs in vitro; however PaeLigD and
MtLigD belong to other subgroups, proteins in this
subgroup await functional characterization.
Length = 228
Score = 25.1 bits (55), Expect = 7.9
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 43 LLWLLSQTWITLHIWTPKCERL 64
L++L Q IT H+W + + L
Sbjct: 76 LVYLADQASITPHVWLSRADDL 97
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
0.328 0.141 0.490
Gapped
Lambda K H
0.267 0.0791 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,249,157
Number of extensions: 435665
Number of successful extensions: 439
Number of sequences better than 10.0: 1
Number of HSP's gapped: 433
Number of HSP's successfully gapped: 22
Length of query: 100
Length of database: 10,937,602
Length adjustment: 66
Effective length of query: 34
Effective length of database: 8,010,238
Effective search space: 272348092
Effective search space used: 272348092
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.1 bits)