RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14581
(124 letters)
>gnl|CDD|153436 cd07967, OBF_DNA_ligase_III, The Oligonucleotide/oligosaccharide
binding (OB)-fold domain of ATP-dependent DNA ligase III
is a DNA-binding module that is part of the catalytic
core unit. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three step reaction mechanism.
DNA ligases play a vital role in the diverse processes
of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms such
as viruses, bacteriohages, eukarya, archaea and
bacteria. There are three classes of ATP-dependent DNA
ligases in eukaryotic cells (I, III and IV). DNA ligase
III is not found in lower eukaryotes and is present both
in the nucleus and mitochondria. It has several
isoforms; two splice forms, III-alpha and III-beta,
differ in their carboxy-terminal sequences. DNA ligase
III-beta is believed to play a role in homologous
recombination during meiotic prophase. DNA ligase
III-alpha interacts with X-ray Cross Complementing
factor 1 (XRCC1) and functions in single nucleotide Base
Excision Repair (BER). The mitochondrial form of DNA
ligase III originates from the nucleolus and is involved
in the mitochondrial DNA repair pathway. This isoform is
expressed by a second start site on the DNA ligase III
gene. DNA ligases have a highly modular architecture
consisting of a unique arrangement of two or more
discrete domains. The adenylation and C-terminal
oligouncleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common to
most members of the ATP-dependent DNA ligase family. The
catalytic core unit contains six conserved sequence
motifs (I, III, IIIa, IV, V and VI) that define this
family of related nucleotidyltransferases. The OB-fold
domain contacts the nicked DNA substrate and is required
for the ATP-dependent DNA ligase nucleotidylation step.
The RxDK motif (motif VI), which is essential for ATP
hydrolysis, is located in the OB-fold domain.
Length = 139
Score = 105 bits (265), Expect = 1e-30
Identities = 44/61 (72%), Positives = 52/61 (85%), Gaps = 3/61 (4%)
Query: 31 SRSLKP---VLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLP 87
++SL P V + K PVWEI+GAEFS++E HTADGISIRFPRVT+IRDDKDWKTAT+LP
Sbjct: 79 NKSLVPDFIVKDPKKAPVWEITGAEFSKSEAHTADGISIRFPRVTRIRDDKDWKTATSLP 138
Query: 88 E 88
E
Sbjct: 139 E 139
>gnl|CDD|185712 cd07902, Adenylation_DNA_ligase_III, Adenylation domain of DNA
Ligase III. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three-step reaction
mechanism. DNA ligases play a vital role in the diverse
processes of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms
such as viruses, bacteriophages, eukarya, archaea and
bacteria. There are three classes of ATP-dependent DNA
ligases in eukaryotic cells (I, III and IV). DNA ligase
III is not found in lower eukaryotes and is present
both in the nucleus and mitochondria. It has several
isoforms; two splice forms, III-alpha and III-beta,
differ in their carboxy-terminal sequences. DNA ligase
III-beta is believed to play a role in homologous
recombination during meiotic prophase. DNA ligase
III-alpha interacts with X-ray Cross Complementing
factor 1 (XRCC1) and functions in single nucleotide
Base Excision Repair (BER). The mitochondrial form of
DNA ligase III originates from the nucleolus and is
involved in the mitochondrial DNA repair pathway. This
isoform is expressed by a second start site on the DNA
ligase III gene. DNA ligases have a highly modular
architecture consisting of a unique arrangement of two
or more discrete domains. The adenylation and
C-terminal oligonucleotide/oligosaccharide binding
(OB)-fold domains comprise a catalytic core unit that
is common to most members of the ATP-dependent DNA
ligase family. The adenylation domain binds ATP and
contains many active site residues. The common
catalytic core unit comprises six conserved sequence
motifs (I, III, IIIa, IV, V and VI) that define this
family of related nucleotidyltransferases.
Length = 213
Score = 78.9 bits (195), Expect = 2e-19
Identities = 28/34 (82%), Positives = 32/34 (94%)
Query: 8 YSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHK 41
Y+EIKYDGERVQVHK+G+ FK+FSRSLKPVL HK
Sbjct: 37 YAEIKYDGERVQVHKQGDNFKFFSRSLKPVLPHK 70
>gnl|CDD|233029 TIGR00574, dnl1, DNA ligase I, ATP-dependent (dnl1). All proteins
in this family with known functions are ATP-dependent
DNA ligases. Functions include DNA repair, DNA
replication, and DNA recombination (or any process
requiring ligation of two single-stranded DNA sections).
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 514
Score = 72.7 bits (179), Expect = 4e-16
Identities = 26/82 (31%), Positives = 46/82 (56%), Gaps = 2/82 (2%)
Query: 15 GERVQVHKKGNEFKYFSRSLKPVLEHKAQP--VWEISGAEFSQAEIHTADGISIRFPRVT 72
G+++ L + P VWE++GAE +++ + A+GIS+RFPR +
Sbjct: 433 GKKLPPLWIDPPGSRVPSILPDEPDIWPDPAIVWEVTGAEITKSPAYKANGISLRFPRFS 492
Query: 73 KIRDDKDWKTATNLPELKVLFK 94
+IRDDK + AT + ++K L++
Sbjct: 493 RIRDDKGPEDATTIEQIKELYE 514
Score = 64.3 bits (157), Expect = 3e-13
Identities = 21/39 (53%), Positives = 24/39 (61%)
Query: 3 KNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHK 41
K Y E KYDGERVQVHK G++FK FSR L+
Sbjct: 185 KGNGFYVEYKYDGERVQVHKDGDKFKIFSRRLENYTYAY 223
>gnl|CDD|153435 cd07893, OBF_DNA_ligase, The Oligonucleotide/oligosaccharide
binding (OB)-fold domain is a DNA-binding module that is
part of the catalytic core unit of ATP dependent DNA
ligases. ATP-dependent polynucleotide ligases catalyze
phosphodiester bond formation using nicked nucleic acid
substrates with the high energy nucleotide of ATP as a
cofactor in a three step reaction mechanism. DNA ligases
play a vital role in the diverse processes of DNA
replication, recombination and repair. ATP dependent DNA
ligases have a highly modular architecture consisting of
a unique arrangement of two or more discrete domains
including a DNA-binding domain, an adenylation
(nucleotidyltransferase (NTase)) domain, and an
oligonucleotide/oligosaccharide binding (OB)-fold
domain. The adenylation and C-terminal OB-fold domains
comprise a catalytic core unit that is common to most
members of the ATP-dependent DNA ligase family. The
catalytic core unit contains six conserved sequence
motifs (I, III, IIIa, IV, V and VI) that define this
family of related nucleotidyltransferases. The OB-fold
domain contacts the nicked DNA substrate and is required
for the ATP-dependent DNA ligase nucleotidylation step.
The RxDK motif (motif VI), which is essential for ATP
hydrolysis, is located in the OB-fold domain.
Length = 129
Score = 58.9 bits (143), Expect = 3e-12
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 6/46 (13%)
Query: 44 PVWEISGAEFSQAEIHTAD------GISIRFPRVTKIRDDKDWKTA 83
V E+ E +++ +HTA G ++RFPR +IRDDK + A
Sbjct: 84 VVVEVLADEITRSPMHTAGRGEEEEGYALRFPRFVRIRDDKGPEDA 129
>gnl|CDD|153438 cd07969, OBF_DNA_ligase_I, The Oligonucleotide/oligosaccharide
binding (OB)-fold domain of ATP-dependent DNA ligase I
is a DNA-binding module that is part of the catalytic
core unit. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three step reaction mechanism.
DNA ligases play a vital role in the diverse processes
of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms such
as viruses, bacteriohages, eukarya, archaea and
bacteria. There are three classes of ATP-dependent DNA
ligases in eukaryotic cells (I, III and IV). This group
is composed of eukaryotic DNA ligase I, Sulfolobus
solfataricus DNA ligase and similar proteins. DNA ligase
I is required for the ligation of Okazaki fragments
during lagging-strand DNA synthesis and for base
excision repair (BER). ATP dependent DNA ligases have a
highly modular architecture consisting of a unique
arrangement of two or more discrete domains including a
DNA-binding domain, an adenylation
(nucleotidyltransferase (NTase)) domain, and an
oligonucleotide/oligosaccharide binding (OB)-fold
domain. The adenylation and C-terminal OB-fold domains
comprise a catalytic core unit that is common to most
members of the ATP-dependent DNA ligase family. The
catalytic core unit contains six conserved sequence
motifs (I, III, IIIa, IV, V and VI) that define this
family of related nucleotidyltransferases. The OB-fold
domain contacts the nicked DNA substrate and is required
for the ATP-dependent DNA ligase nucleotidylation step.
The RxDK motif (motif VI), which is essential for ATP
hydrolysis, is located in the OB-fold domain.
Length = 144
Score = 58.3 bits (142), Expect = 6e-12
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 8/75 (10%)
Query: 29 YFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTA--------DGISIRFPRVTKIRDDKDW 80
SL+P + + + VWE+ A+ + + +HTA GIS+RFPR ++RDDK
Sbjct: 70 RVDSSLEPDVWFEPKEVWEVKAADLTLSPVHTAAIGLVDEEKGISLRFPRFIRVRDDKKP 129
Query: 81 KTATNLPELKVLFKK 95
+ AT ++ ++KK
Sbjct: 130 EDATTSEQIAEMYKK 144
>gnl|CDD|216280 pfam01068, DNA_ligase_A_M, ATP dependent DNA ligase domain. This
domain belongs to a more diverse superfamily, including
pfam01331 and pfam01653.
Length = 195
Score = 57.3 bits (139), Expect = 3e-11
Identities = 18/39 (46%), Positives = 21/39 (53%)
Query: 3 KNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHK 41
E KYDGERVQ+HK G E K SR+ KP+
Sbjct: 17 GGGAFIVEEKYDGERVQIHKDGGEVKLLSRNGKPITATY 55
>gnl|CDD|185709 cd07898, Adenylation_DNA_ligase, Adenylation domain of
ATP-dependent DNA Ligases. ATP-dependent
polynucleotide ligases catalyze phosphodiester bond
formation using nicked nucleic acid substrates with the
high energy nucleotide of ATP as a cofactor in a three
step reaction mechanism. DNA ligases play a vital role
in the diverse processes of DNA replication,
recombination and repair. ATP-dependent ligases are
present in many organisms such as viruses,
bacteriophages, eukarya, archaea and bacteria. Some
organisms express a variety of different ligases which
appear to be targeted to specific functions.
ATP-dependent DNA ligases have a highly modular
architecture consisting of a unique arrangement of two
or more discrete domains including a DNA-binding
domain, an adenylation (nucleotidyltransferase (NTase))
domain, and an oligonucleotide/oligosaccharide binding
(OB)-fold domain. The adenylation domain binds ATP and
contains many of the active-site residues. The
adenylation and C-terminal OB-fold domains comprise a
catalytic core unit that is common to most members of
the ATP-dependent DNA ligase family. The catalytic core
unit contains six conserved sequence motifs (I, III,
IIIa, IV, V and VI) that define this family of related
nucleotidyltransferases.
Length = 201
Score = 55.8 bits (135), Expect = 1e-10
Identities = 17/43 (39%), Positives = 23/43 (53%)
Query: 1 MAKNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQ 43
K + E KYDG R QVHK G + FSRSL+ + + +
Sbjct: 17 AKKPAAAWVEDKYDGIRAQVHKDGGRVEIFSRSLEDITDQFPE 59
>gnl|CDD|185713 cd07903, Adenylation_DNA_ligase_IV, Adenylation domain of DNA
Ligase IV. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three step reaction
mechanism. DNA ligases play a vital role in the diverse
processes of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms
such as viruses, bacteriophages, eukarya, archaea and
bacteria. There are three classes of ATP-dependent DNA
ligase in eukaryotic cells (I, III and IV). DNA ligase
IV is required for DNA non-homologous end joining
pathways, including recombination of the V(D)J
immunoglobulin gene segments in cells of the mammalian
immune system. DNA ligase IV is stabilized by forming a
complex with XRCC4, a nuclear phosphoprotein, which is
phosphorylated by DNA-dependent protein kinase. DNA
ligases have a highly modular architecture consisting
of a unique arrangement of two or more discrete
domains. The adenylation and C-terminal
oligonucleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common
to all members of the ATP-dependent DNA ligase family.
The adenylation domain binds ATP and contains many of
the active-site residues. The common catalytic unit
comprises six conserved sequence motifs (I, III, IIIa,
IV, V and VI) that define this family of related
nucleotidyltransferases.
Length = 225
Score = 53.7 bits (130), Expect = 9e-10
Identities = 19/26 (73%), Positives = 22/26 (84%)
Query: 8 YSEIKYDGERVQVHKKGNEFKYFSRS 33
Y E K DGER+Q+HK GNEFKYFSR+
Sbjct: 36 YIETKLDGERIQLHKDGNEFKYFSRN 61
>gnl|CDD|185711 cd07901, Adenylation_DNA_ligase_Arch_LigB, Adenylation domain of
archaeal and bacterial LigB-like DNA ligases.
ATP-dependent polynucleotide ligases catalyze
phosphodiester bond formation using nicked nucleic acid
substrates with the high energy nucleotide of ATP as a
cofactor in a three step reaction mechanism. DNA
ligases play a vital role in the diverse processes of
DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms
such as viruses, bacteriophages, eukarya, archaea and
bacteria. Bacterial DNA ligases are divided into two
broad classes: NAD-dependent and ATP-dependent. All
bacterial species have a NAD-dependent DNA ligase
(LigA). Some bacterial genomes contain multiple genes
for DNA ligases that are predicted to use ATP as their
cofactor, including Mycobacterium tuberculosis LigB,
LigC, and LigD. This group is composed of archaeal DNA
ligases and bacterial proteins similar to Mycobacterium
tuberculosis LigB. Members of this group contain
adenylation and C-terminal
oligonucleotide/oligosaccharide binding (OB)-fold
domains, comprising a catalytic core unit that is
common to most members of the ATP-dependent DNA ligase
family. The adenylation domain binds ATP and contains
many of the active-site residues. The common catalytic
core unit comprises six conserved sequence motifs (I,
III, IIIa, IV, V and VI) that define this family of
related nucleotidyltransferases.
Length = 207
Score = 51.8 bits (125), Expect = 4e-09
Identities = 16/29 (55%), Positives = 19/29 (65%)
Query: 6 RCYSEIKYDGERVQVHKKGNEFKYFSRSL 34
E KYDG RVQ+HK G+E + FSR L
Sbjct: 26 EAAVEYKYDGIRVQIHKDGDEVRIFSRRL 54
>gnl|CDD|234900 PRK01109, PRK01109, ATP-dependent DNA ligase; Provisional.
Length = 590
Score = 49.2 bits (118), Expect = 6e-08
Identities = 17/29 (58%), Positives = 20/29 (68%)
Query: 6 RCYSEIKYDGERVQVHKKGNEFKYFSRSL 34
E KYDGER Q+HKKG++ K FSR L
Sbjct: 249 EALVEYKYDGERAQIHKKGDKVKIFSRRL 277
Score = 43.8 bits (104), Expect = 4e-06
Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 8/75 (10%)
Query: 33 SLKPVLEHKAQPVWEISGAEFSQAEIHTAD--------GISIRFPRVTKIRDDKDWKTAT 84
++P + + + V EI GAE + + +HT G++IRFPR + RDDK + AT
Sbjct: 511 KMEPDVWVEPKLVAEIIGAEITLSPLHTCCLGVVEKGAGLAIRFPRFIRWRDDKSPEDAT 570
Query: 85 NLPELKVLFKKSKET 99
E+ ++K+ K+
Sbjct: 571 TTEEILEMYKRQKKK 585
>gnl|CDD|153437 cd07968, OBF_DNA_ligase_IV, The Oligonucleotide/oligosaccharide
binding (OB)-fold domain of ATP-dependent DNA ligase IV
is a DNA-binding module that is part of the catalytic
core unit. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three step reaction mechanism.
DNA ligases play a vital role in the diverse processes
of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms such
as viruses, bacteriohages, eukarya, archaea and
bacteria. There are three classes of ATP-dependent DNA
ligases in eukaryotic cells (I, III and IV). DNA ligase
IV is required for DNA non-homologous end joining
pathways, including recombination of the V(D)J
immunoglobulin gene segments in cells of the mammalian
immune system. DNA ligase IV is stabilized by forming a
complex with XRCC4, a nuclear phosphoprotein, which is
phosphorylated by DNA-dependent protein kinase. DNA
ligases have a highly modular architecture consisting of
a unique arrangement of two or more discrete domains.
The adenylation and C-terminal
oligouncleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common to
most members of the ATP-dependent DNA ligase family. The
catalytic core unit contains six conserved sequence
motifs (I, III, IIIa, IV, V and VI) that define this
family of related nucleotidyltransferases. The OB-fold
domain contacts the nicked DNA substrate and is required
for the ATP-dependent DNA ligase nucleotidylation step.
The RxDK motif (motif VI), which is essential for ATP
hydrolysis, is located in the OB-fold domain.
Length = 140
Score = 45.2 bits (108), Expect = 5e-07
Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 45 VWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTA 83
V E+ AE ++ + G ++RFPR KIR DKDW
Sbjct: 100 VLEVKAAEIVPSDSYKT-GYTLRFPRCEKIRYDKDWHDC 137
>gnl|CDD|215584 PLN03113, PLN03113, DNA ligase 1; Provisional.
Length = 744
Score = 46.1 bits (109), Expect = 7e-07
Identities = 25/89 (28%), Positives = 46/89 (51%), Gaps = 8/89 (8%)
Query: 17 RVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTA--------DGISIRF 68
R QV + + S+KP + + VWE+ A+ + + +H A GIS+RF
Sbjct: 643 RSQVIPTPKSYYRYGDSIKPDVWFEPTEVWEVKAADLTISPVHRAAVGIVDPDKGISLRF 702
Query: 69 PRVTKIRDDKDWKTATNLPELKVLFKKSK 97
PR+ ++R+DK + AT+ ++ ++ K
Sbjct: 703 PRLVRVREDKSPEQATSSEQVADMYNAQK 731
Score = 27.6 bits (61), Expect = 2.0
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 10 EIKYDGERVQVHKKGN-EFKYFSRS 33
E KYDGER Q+H + + +SR+
Sbjct: 396 EYKYDGERAQIHFLEDGSVEIYSRN 420
>gnl|CDD|218210 pfam04679, DNA_ligase_A_C, ATP dependent DNA ligase C terminal
region. This region is found in many but not all
ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is
thought to constitute part of the catalytic core of ATP
dependent DNA ligase.
Length = 95
Score = 41.4 bits (98), Expect = 6e-06
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 13/45 (28%)
Query: 34 LKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDK 78
++P L V E+ AE+ TA G +RFPR +R+DK
Sbjct: 64 VEPEL------VAEVEFAEW------TASG-RLRFPRFKGLREDK 95
>gnl|CDD|224706 COG1793, CDC9, ATP-dependent DNA ligase [DNA replication,
recombination, and repair].
Length = 444
Score = 42.7 bits (101), Expect = 1e-05
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRSLKPV 37
E K+DG RVQ+H G + + +SR+ +
Sbjct: 138 EEKFDGYRVQIHIDGGKVRLYSRNGEDW 165
Score = 38.1 bits (89), Expect = 4e-04
Identities = 17/51 (33%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 45 VWEISGAEFSQAEIHT-ADGISIRFPRVTKIRDDKDWKTATNLPELKVLFK 94
V E+ AE +++ A G+ +RFPR ++RDDK + A + E++ L+
Sbjct: 394 VAEVRFAEITKSGRLRHASGLGLRFPRFVRVRDDKLPEDADTIEEIEALYL 444
>gnl|CDD|235108 PRK03180, ligB, ATP-dependent DNA ligase; Reviewed.
Length = 508
Score = 41.9 bits (99), Expect = 2e-05
Identities = 12/28 (42%), Positives = 20/28 (71%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRSLKPV 37
E K DG RVQVH+ G++ + ++R+L +
Sbjct: 209 EAKLDGARVQVHRDGDDVRVYTRTLDDI 236
Score = 28.0 bits (63), Expect = 1.3
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 63 GISIRFPRVTKIRDDKD 79
G+++RF RV + R DK
Sbjct: 476 GVALRFARVLRYRPDKT 492
>gnl|CDD|185710 cd07900, Adenylation_DNA_ligase_I_Euk, Adenylation domain of
eukaryotic DNA Ligase I. ATP-dependent polynucleotide
ligases catalyze phosphodiester bond formation using
nicked nucleic acid substrates with the high energy
nucleotide of ATP as a cofactor in a three step
reaction mechanism. DNA ligases play a vital role in
the diverse processes of DNA replication, recombination
and repair. ATP-dependent ligases are present in many
organisms such as viruses, bacteriophages, eukarya,
archaea and bacteria. Some organisms express a variety
of different ligases which appear to be targeted to
specific functions. There are three classes of
ATP-dependent DNA ligases in eukaryotic cells (I, III
and IV). DNA ligase I is required for the ligation of
Okazaki fragments during lagging-strand DNA synthesis
and for base excision repair (BER). DNA ligases have a
highly modular architecture consisting of a unique
arrangement of two or more discrete domains. The
adenylation and C-terminal
oligonucleotide/oligosaccharide binding (OB)-fold
domains comprise a catalytic core unit that is common
to most members of the ATP-dependent DNA ligase family.
The adenylation domain binds ATP and contains many of
the active-site residues. DNA ligase I is the main
replicative ligase in eukaryotes. The common catalytic
core unit comprises six conserved sequence motifs (I,
III, IIIa, IV, V and VI) that define this family of
related nucleotidyltransferases.
Length = 219
Score = 39.5 bits (93), Expect = 1e-04
Identities = 14/27 (51%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 9 SEIKYDGERVQVHK-KGNEFKYFSRSL 34
E KYDGER Q+H + + K FSR+L
Sbjct: 35 CEYKYDGERAQIHLLEDGKVKIFSRNL 61
>gnl|CDD|153441 cd07972, OBF_DNA_ligase_Arch_LigB, The
Oligonucleotide/oligosaccharide binding (OB)-fold domain
of archaeal and bacterial ATP-dependent DNA ligases is a
DNA-binding module that is part of the catalytic core
unit. ATP-dependent polynucleotide ligases catalyze
phosphodiester bond formation using nicked nucleic acid
substrates with the high energy nucleotide of ATP as a
cofactor in a three step reaction mechanism. DNA ligases
play a vital role in the diverse processes of DNA
replication, recombination and repair. ATP-dependent
ligases are present in many organisms such as viruses,
bacteriohages, eukarya, archaea and bacteria. Bacterial
DNA ligases are divided into two broad classes:
NAD-dependent and ATP-dependent. All bacterial species
have a NAD-dependent DNA ligase (LigA). Some bacterial
genomes contain multiple genes for DNA ligases that are
predicted to use ATP as their cofactor, including
Mycobacterium tuberculosis LigB, LigC, and LigD. This
group is composed of Pyrococcus furiosus DNA ligase,
Mycobacterium tuberculosis LigB, and similar archaeal
and bacterial proteins. ATP dependent DNA ligases have a
highly modular architecture consisting of a unique
arrangement of two or more discrete domains including a
DNA-binding domain, an adenylation
(nucleotidyltransferase (NTase)) domain, and an
oligonucleotide/oligosaccharide binding (OB)-fold
domain. The adenylation and C-terminal OB-fold domains
comprise a catalytic core unit that is common to most
members of the ATP-dependent DNA ligase family. The
catalytic core unit contains six conserved sequence
motifs (I, III, IIIa, IV, V and VI) that define this
family of related nucleotidyltransferases. The OB-fold
domain contacts the nicked DNA substrate and is required
for the ATP-dependent DNA ligase nucleotidylation step.
The RxDK motif (motif VI), which is essential for ATP
hydrolysis, is located in the OB-fold domain.
Length = 122
Score = 34.4 bits (80), Expect = 0.003
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 7/55 (12%)
Query: 32 RSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNL 86
S+KP L V+E++ E ++ + + G ++RFPR+ +IRDDKD A L
Sbjct: 70 VSVKPEL------VFEVAFEEIQRSPRYKS-GYALRFPRIVRIRDDKDPDEADTL 117
>gnl|CDD|185704 cd06846, Adenylation_DNA_ligase_like, Adenylation domain of
proteins similar to ATP-dependent polynucleotide
ligases. ATP-dependent polynucleotide ligases catalyze
the phosphodiester bond formation of nicked nucleic
acid substrates using ATP as a cofactor in a three step
reaction mechanism. This family includes ATP-dependent
DNA and RNA ligases. DNA ligases play a vital role in
the diverse processes of DNA replication, recombination
and repair. ATP-dependent DNA ligases have a highly
modular architecture, consisting of a unique
arrangement of two or more discrete domains, including
a DNA-binding domain, an adenylation or
nucleotidyltransferase (NTase) domain, and an
oligonucleotide/oligosaccharide binding (OB)-fold
domain. The adenylation domain binds ATP and contains
many active site residues. Together with the C-terminal
OB-fold domain, it comprises a catalytic core unit that
is common to most members of the ATP-dependent DNA
ligase family. The catalytic core contains six
conserved sequence motifs (I, III, IIIa, IV, V and VI)
that define this family of related
nucleotidyltransferases including eukaryotic
GRP-dependent mRNA-capping enzymes. The catalytic core
contains both the active site as well as many
DNA-binding residues. The RNA circularization protein
from archaea and bacteria contains the minimal
catalytic unit, the adenylation domain, but does not
contain an OB-fold domain. This family also includes
the m3G-cap binding domain of snurportin, a nuclear
import adaptor that binds m3G-capped spliceosomal U
small nucleoproteins (snRNPs), but doesn't have
enzymatic activity.
Length = 182
Score = 33.2 bits (76), Expect = 0.016
Identities = 9/32 (28%), Positives = 13/32 (40%)
Query: 6 RCYSEIKYDGERVQVHKKGNEFKYFSRSLKPV 37
Y + KYDG+R + SR+ V
Sbjct: 20 EYYVQEKYDGKRALIVALNGGVFAISRTGLEV 51
>gnl|CDD|185715 cd07906, Adenylation_DNA_ligase_LigD_LigC, Adenylation domain of
Mycobacterium tuberculosis LigD and LigC-like
ATP-dependent DNA ligases. Bacterial DNA ligases are
divided into two broad classes: NAD-dependent and
ATP-dependent. All bacterial species have a
NAD-dependent DNA ligase (LigA). Some bacterial genomes
contain multiple genes for DNA ligases that are
predicted to use ATP as their cofactor, including
Mycobacterium tuberculosis LigB, LigC, and LigD. This
group is composed of ATP-dependent DNA ligases similar
to Mycobacterium tuberculosis LigC. ATP-dependent
polynucleotide ligases catalyze phosphodiester bond
formation using nicked nucleic acid substrates with the
high energy nucleotide of ATP as a cofactor in a three
step reaction mechanism. DNA ligases play a vital role
in the diverse processes of DNA replication,
recombination and repair. Members of this group contain
adenylation and C-terminal
oligonucleotide/oligosaccharide binding (OB)-fold
domains, comprising a catalytic core unit that is
common to all members of the ATP-dependent DNA ligase
family. The adenylation domain binds ATP and contains
many of the active-site residues. The common catalytic
core unit comprises six conserved sequence motifs (I,
III, IIIa, IV, V and VI) that define this family of
related nucleotidyltransferases. LigD consists of a
central ATP-dependent DNA ligase catalytic core unit
fused to a C-terminal polymerase domain and an
N-terminal 3'-phosphoesterase (PE) module. LigD
catalyzes the end-healing and end-sealing steps during
non-homologous end joining.
Length = 190
Score = 32.1 bits (74), Expect = 0.034
Identities = 9/28 (32%), Positives = 13/28 (46%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRSLKPV 37
EIK+DG R G + +SR+
Sbjct: 21 EIKWDGYRALARVDGGRVRLYSRNGLDW 48
>gnl|CDD|236428 PRK09247, PRK09247, ATP-dependent DNA ligase; Validated.
Length = 539
Score = 31.7 bits (73), Expect = 0.073
Identities = 13/34 (38%), Positives = 19/34 (55%)
Query: 63 GISIRFPRVTKIRDDKDWKTATNLPELKVLFKKS 96
GI++RFPR+ + R DK + A L L+ L
Sbjct: 505 GIAVRFPRILRWRWDKPAREADTLETLQALLDAE 538
Score = 27.5 bits (62), Expect = 1.7
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRS 33
E K+DG RVQ+ ++G E + +SR
Sbjct: 230 EWKWDGIRVQLVRRGGEVRLWSRG 253
>gnl|CDD|234477 TIGR04120, DNA_lig_bact, DNA ligase, ATP-dependent, PP_1105 family.
This model describes a family of ATP-dependent DNA
ligases present in about 12 % of prokaryotic genomes. It
occurs as part of a four-gene system with an
exonuclease, a helicase and a phosphoesterase, with all
four genes clustered or at least the first two and last
two paired. This family resembles DNA ligase I (see
TIGR00574 and pfam01068), and its presumed function may
be in DNA repair, replication, or recombination.
Length = 526
Score = 31.5 bits (72), Expect = 0.082
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 36 PVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVL 92
PV E K + V+E+ E G+++RFPR+++IR DK A L L+ +
Sbjct: 470 PVREVKPELVFEV-AFEGINRSTRHKSGVAMRFPRISRIRWDKPAAEADRLATLEAM 525
Score = 27.3 bits (61), Expect = 2.1
Identities = 10/24 (41%), Positives = 17/24 (70%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRS 33
E K+DG RVQ+ ++G + +SR+
Sbjct: 226 EWKWDGIRVQLVRRGGGRRLYSRT 249
>gnl|CDD|185716 cd08039, Adenylation_DNA_ligase_Fungal, Adenylation domain of
uncharacterized fungal ATP-dependent DNA ligase-like
proteins. ATP-dependent polynucleotide ligases
catalyze phosphodiester bond formation using nicked
nucleic acid substrates with the high energy nucleotide
of ATP as a cofactor in a three step reaction
mechanism. DNA ligases play a vital role in the diverse
processes of DNA replication, recombination and repair.
ATP-dependent ligases are present in many organisms
such as viruses, bacteriophages, eukarya, archaea and
bacteria. This group is composed of uncharacterized
fungal proteins with similarity to ATP-dependent DNA
ligases. ATP dependent DNA ligases have a highly
modular architecture consisting of a unique arrangement
of two or more discrete domains including a DNA-binding
domain, an adenylation (nucleotidyltransferase (NTase))
domain, and an oligonucleotide/oligosaccharide binding
(OB)-fold domain. The adenylation domain binds ATP and
contains many of the active-site residues. The
adenylation and C-terminal OB-fold domains comprise a
catalytic core unit that is common to most members of
the ATP-dependent DNA ligase family. The catalytic core
unit contains six conserved sequence motifs (I, III,
IIIa, IV, V and VI) that define this family of related
nucleotidyltransferases. This model characterizes the
adenylation domain of this group of uncharacterized
fungal proteins. It is not known whether these proteins
also contain an OB-fold domain.
Length = 235
Score = 31.2 bits (71), Expect = 0.094
Identities = 15/39 (38%), Positives = 21/39 (53%), Gaps = 4/39 (10%)
Query: 1 MAKNERCYSEIKYDGERVQVH----KKGNEFKYFSRSLK 35
M + R + E KYDGE Q+H K + + FS+S K
Sbjct: 18 MIGSRRMWVETKYDGEYCQIHIDLSKDSSPIRIFSKSGK 56
>gnl|CDD|185708 cd07897, Adenylation_DNA_ligase_Bac1, Adenylation domain of
putative bacterial ATP-dependent DNA ligases.
Bacterial DNA ligases are divided into two broad
classes: NAD-dependent and ATP-dependent. All bacterial
species have a NAD-dependent DNA ligase (LigA). Some
bacterial genomes contain multiple genes for DNA
ligases that are predicted to use ATP as their
cofactor, including Mycobacterium tuberculosis LigB,
LigC, and LigD. This group is composed of predicted
bacterial ATP-dependent DNA ligases. ATP-dependent
polynucleotide ligases catalyze phosphodiester bond
formation using nicked nucleic acid substrates with the
high energy nucleotide of ATP as a cofactor in a
three-step reaction mechanism. The adenylation and
C-terminal oligonucleotide/oligosaccharide binding
(OB)-fold domains comprise a catalytic core unit that
is common to most members of the ATP-dependent DNA
ligase family, including this group. The adenylation
domain binds ATP and contains many of the active site
residues.
Length = 207
Score = 29.1 bits (66), Expect = 0.41
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSR 32
E K+DG R Q+ ++G E +SR
Sbjct: 29 EWKWDGIRGQLIRRGGEVFLWSR 51
>gnl|CDD|236505 PRK09419, PRK09419, bifunctional 2',3'-cyclic nucleotide
2'-phosphodiesterase/3'-nucleotidase precursor protein;
Reviewed.
Length = 1163
Score = 29.4 bits (66), Expect = 0.44
Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 9/61 (14%)
Query: 34 LKPVLEHKAQPVWEISGAEFSQAEI-HTADG--------ISIRFPRVTKIRDDKDWKTAT 84
+K LEH PV GA A + +T +R +K+ DK + AT
Sbjct: 1035 IKKALEHGISPVEFGGGAFPQVAGLKYTFTLSAEPGNRITDVRLEDGSKLDKDKTYTVAT 1094
Query: 85 N 85
N
Sbjct: 1095 N 1095
>gnl|CDD|234009 TIGR02779, NHEJ_ligase_lig, DNA polymerase LigD, ligase 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 ligase domain.
Length = 298
Score = 29.2 bits (66), Expect = 0.52
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 10 EIKYDGERVQVHKKGNEFKYFSRSLKP 36
E+KYDG R +G + + SR+
Sbjct: 17 EVKYDGYRCLARIEGGKVRLISRNGHD 43
>gnl|CDD|238582 cd01177, IPT_NFkappaB, IPT domain of the transcription factor
NFkappaB and related transcription factors. NFkappaB is
considered a central regulator of stress responses,
activated by different stressful conditions, including
physical stress, oxidative stress, and exposure to
certain chemicals. NFkappaB blocking cell apoptosis in
several cell types, gives it an important role in cell
proliferation and differentiation.
Length = 102
Score = 26.9 bits (60), Expect = 1.7
Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 9/71 (12%)
Query: 39 EHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSKE 98
E + + VWE + +FSQ ++H I R P + K ++++ E
Sbjct: 38 EDEEETVWE-AFGDFSQTDVHRQYAIVFRTPPYHDPDITEPVKV-----KIQLKRPSDGE 91
Query: 99 TS---DFTLKP 106
S FT P
Sbjct: 92 RSESVPFTYVP 102
>gnl|CDD|139531 PRK13383, PRK13383, acyl-CoA synthetase; Provisional.
Length = 516
Score = 27.7 bits (61), Expect = 2.0
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 51 AEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATN-LPELKVLFKKSKETSDFTLKPKY 108
A +QA +H AD + + +I + A N LP+L+V+ S + D TL ++
Sbjct: 255 AALAQASLHRADAFTAVPVVLARILELPPRVRARNPLPQLRVVM-SSGDRLDPTLGQRF 312
>gnl|CDD|190783 pfam03888, MucB_RseB, MucB/RseB family. Members of this family
are regulators of the anti-sigma E protein RseD.
Length = 285
Score = 27.4 bits (61), Expect = 2.1
Identities = 10/32 (31%), Positives = 15/32 (46%)
Query: 14 DGERVQVHKKGNEFKYFSRSLKPVLEHKAQPV 45
DG R +V ++ NE YF L+P +
Sbjct: 47 DGPRQEVVRRDNEVSYFEPGLEPFTINGGMIA 78
>gnl|CDD|225570 COG3026, RseB, Negative regulator of sigma E activity [Signal
transduction mechanisms].
Length = 320
Score = 27.0 bits (60), Expect = 2.6
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 14 DGERVQVHKKGNEFKYFSRSLKPVLEHKAQPV 45
DG R +V ++GNE YF L+P + V
Sbjct: 77 DGPRREVVRRGNEVSYFEPGLEPFTLNGDYIV 108
>gnl|CDD|153414 cd07960, Anticodon_Ia_Ile_BEm, Anticodon-binding domain of
bacterial and eukaryotic mitochondrial isoleucyl tRNA
synthetases. This domain is found in isoleucyl tRNA
synthetases (IleRS), which belong to the class Ia
aminoacyl tRNA synthetases. It lies C-terminal to the
catalytic core domain, and recognizes and specifically
binds to the tRNA anticodon. This family includes
bacterial and eukaryotic mitochondrial members. IleRS
catalyzes the transfer of isoleucine to the 3'-end of
its tRNA.
Length = 180
Score = 26.7 bits (60), Expect = 3.1
Identities = 13/64 (20%), Positives = 23/64 (35%), Gaps = 9/64 (14%)
Query: 27 FKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDD----KDWKT 82
+ L P+L A+ VWE E + + D +P + + D + W+
Sbjct: 117 LDALLKLLAPILPFTAEEVWEHLPGEKKEESVFLED-----WPELPEEWKDEELEEKWEK 171
Query: 83 ATNL 86
L
Sbjct: 172 LLAL 175
>gnl|CDD|216405 pfam01274, Malate_synthase, Malate synthase.
Length = 517
Score = 26.5 bits (59), Expect = 3.8
Identities = 17/37 (45%), Positives = 18/37 (48%), Gaps = 3/37 (8%)
Query: 55 QAEIHTADGISIRFPRVTK-IRDDKDWKTATNLPELK 90
QA I G F T IR D DWK AT PEL+
Sbjct: 45 QARI--DKGHLPDFLPETGYIRPDPDWKGATLPPELQ 79
>gnl|CDD|149907 pfam08989, DUF1896, Domain of unknown function (DUF1896). This
domain is found in a set of hypothetical bacterial
proteins.
Length = 144
Score = 26.2 bits (58), Expect = 4.4
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 86 LPELKVLFKKSKETSDFTLKPKYDRI 111
LPE++ +F K + DF P+YD +
Sbjct: 102 LPEVEAVFAKYPLSDDFEFSPEYDTL 127
>gnl|CDD|132408 TIGR03365, Bsubt_queE, 7-cyano-7-deazaguanosine (preQ0)
biosynthesis protein QueE. This uncharacterized enzyme,
designated QueE, participates in the biosynthesis, from
GTP, of 7-cyano-7-deazaguanosine, also called preQ0
because in many species it is a precursor of queuosine.
In most Archaea, it is instead the precursor of a
different tRNA modified base, archaeosine [Protein
synthesis, tRNA and rRNA base modification].
Length = 238
Score = 25.8 bits (57), Expect = 6.3
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 71 VTKIRDDKDWKTATNLPELKVL 92
V K+ D++W LP+L VL
Sbjct: 209 VEKVAADREWFDVRVLPQLHVL 230
>gnl|CDD|130302 TIGR01235, pyruv_carbox, pyruvate carboxylase. This enzyme plays a
role in gluconeogensis but not glycolysis [Energy
metabolism, Glycolysis/gluconeogenesis].
Length = 1143
Score = 25.9 bits (57), Expect = 7.0
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 47 EISGAEFSQAEIHTADGISIRFPRV 71
EI+G + QA+IH ADG S+ P++
Sbjct: 302 EITGIDIVQAQIHIADGASLPTPQL 326
>gnl|CDD|147308 pfam05059, Orbi_VP4, Orbivirus VP4 core protein. Orbiviruses are
double stranded RNA retroviruses of which the
bluetongue virus is a member. The core of bluetongue
virus (BTV) is a multienzyme complex composed of two
major proteins (VP7 and VP3) and three minor proteins
(VP1, VP4 and VP6) in addition to the viral genome. VP4
has been shown to perform all RNA capping activities
and has both methyltransferase type 1 and type 2
activities associated with it.
Length = 642
Score = 25.5 bits (56), Expect = 8.7
Identities = 8/24 (33%), Positives = 16/24 (66%)
Query: 29 YFSRSLKPVLEHKAQPVWEISGAE 52
Y +R L+P+L+ P+ +++G E
Sbjct: 9 YVTRELEPLLKDGFLPILKLTGIE 32
>gnl|CDD|173544 PTZ00351, PTZ00351, adenylosuccinate synthetase; Provisional.
Length = 710
Score = 25.8 bits (56), Expect = 8.8
Identities = 10/36 (27%), Positives = 21/36 (58%)
Query: 86 LPELKVLFKKSKETSDFTLKPKYDRIKNLKLQKARC 121
+P+ + F ++K+ +F +K DR+++ ARC
Sbjct: 364 VPDYVIAFAQAKDKVEFLVKLYRDRVRHNPDFPARC 399
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
0.317 0.132 0.389
Gapped
Lambda K H
0.267 0.0687 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,017,448
Number of extensions: 502113
Number of successful extensions: 459
Number of sequences better than 10.0: 1
Number of HSP's gapped: 454
Number of HSP's successfully gapped: 54
Length of query: 124
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 39
Effective length of database: 7,167,512
Effective search space: 279532968
Effective search space used: 279532968
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 (24.3 bits)