RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780818|ref|YP_003065231.1| DNA polymerase III subunit
epsilon [Candidatus Liberibacter asiaticus str. psy62]
(245 letters)
>gnl|CDD|99835 cd06131, DNA_pol_III_epsilon_Ecoli_like, DEDDh 3'-5' exonuclease
domain of the epsilon subunit of Escherichia coli DNA
polymerase III and similar proteins. This subfamily is
composed of the epsilon subunit of Escherichia coli DNA
polymerase III (Pol III) and similar proteins. Pol III
is the main DNA replicating enzyme in bacteria,
functioning as the chromosomal replicase. It is a
holoenzyme complex of ten different subunits, three of
which (alpha, epsilon, and theta) compose the catalytic
core. The Pol III epsilon subunit, encoded by the dnaQ
gene, is a DEDDh-type 3'-5' exonuclease which is
responsible for the proofreading activity of the
polymerase, increasing the fidelity of DNA synthesis. It
contains three conserved sequence motifs termed ExoI,
ExoII and ExoIII, with a specific Hx(4)D conserved
pattern at ExoIII. These motifs are clustered around the
active site and contain four conserved acidic residues
that serve as ligands for the two metal ions required
for catalysis. The epsilon subunit of Pol III also
functions as a stabilizer of the holoenzyme complex.
Length = 167
Score = 233 bits (596), Expect = 4e-62
Identities = 90/170 (52%), Positives = 116/170 (68%), Gaps = 6/170 (3%)
Query: 9 KIVFDIETTGLDSK-NDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITD 67
+IV D ETTGLD + RIIEIG VEL++ T TF V++ P R EA K+HGITD
Sbjct: 1 QIVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPE-RDIPEEAFKVHGITD 59
Query: 68 EFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRI--NKDPLDPSRIID 125
EFL DKP F+ I EF DF AE + HNA FDVGF+NAEL + K +D R+ID
Sbjct: 60 EFLADKPKFAEIADEFLDFIR--GAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVID 117
Query: 126 TLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMM 175
TL++AR+K P N L++LCKR+GI SHR+ HGALLD+ LL++VY+++
Sbjct: 118 TLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAELLAEVYLELT 167
>gnl|CDD|31188 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related
3'-5' exonucleases [DNA replication, recombination, and
repair].
Length = 243
Score = 148 bits (373), Expect = 2e-36
Identities = 80/240 (33%), Positives = 115/240 (47%), Gaps = 13/240 (5%)
Query: 6 KMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGI 65
R +V D+ETTGL+ K DRIIEIGAV L D R+F + P R PE K+HGI
Sbjct: 12 PTRFVVIDLETTGLNPKKDRIIEIGAVTLEDGRIVERSFHTLVNPE-RPIPPEIFKIHGI 70
Query: 66 TDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIID 125
TDE L D P F+ + EF DF +AHNA FDVGF+ E +R+ + ++D
Sbjct: 71 TDEMLADAPKFAEVLPEFLDFIGG-LRLLVAHNAAFDVGFLRVESERLGIEIPGD-PVLD 128
Query: 126 TLSIARRKHPSS-RNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMMVGGSQINFG 184
TL++ARR P R+ L++L +R GI + H AL D+ L+++++ + G +
Sbjct: 129 TLALARRHFPGFDRSSLDALAERLGIDRNPFHPHRALFDALALAELFLL-LQTGLLLKAP 187
Query: 185 FKTNEDRFFKEEKKTVPNISLLKRDKPLFTRITKEELDEH----DKTIQTLGKNAIWDRY 240
D K + + EL H D + L + +W Y
Sbjct: 188 LTAILDLDKLAHKALYD----TLKTAARLFCGIENELKAHGSWLDALAKELLEKKLWKEY 243
>gnl|CDD|176648 cd06127, DEDDh, DEDDh 3'-5' exonuclease domain family. DEDDh
exonucleases, part of the DnaQ-like (or DEDD)
exonuclease superfamily, catalyze the excision of
nucleoside monophosphates at the DNA or RNA termini in
the 3'-5' direction. These proteins contain four
invariant acidic residues in three conserved sequence
motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases
are classified as such because of the presence of
specific Hx(4)D conserved pattern at the ExoIII motif.
The four conserved acidic residues are clustered around
the active site and serve as ligands for the two metal
ions required for catalysis. Most DEDDh exonucleases are
the proofreading subunits (epsilon) or domains of
bacterial DNA polymerase III, the main replicating
enzyme in bacteria, which functions as the chromosomal
replicase. Other members include other DNA and RNA
exonucleases such as RNase T, Oligoribonuclease, and RNA
exonuclease (REX), among others.
Length = 159
Score = 143 bits (363), Expect = 4e-35
Identities = 71/165 (43%), Positives = 94/165 (56%), Gaps = 8/165 (4%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69
+VFD ETTGLD K DRIIEIGAV++ + F+ + P GR PEA +HGITDE
Sbjct: 1 VVFDTETTGLDPKKDRIIEIGAVKVDGGIEIVERFETLVNP-GRPIPPEATAIHGITDEM 59
Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSI 129
L D P F + EF +F +AHNA FD+ F+N EL+R+ PL P+ IDTL +
Sbjct: 60 LADAPPFEEVLPEFLEFLG--GRVLVAHNASFDLRFLNRELRRLGGPPL-PNPWIDTLRL 116
Query: 130 ARRKHP--SSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYI 172
ARR P S L +RYGI + H AL D+ +++ +
Sbjct: 117 ARRLLPGLRSHRLGLLLAERYGIPLEGA--HRALADALATAELLL 159
>gnl|CDD|144506 pfam00929, Exonuc_X-T, Exonuclease. This family includes a variety
of exonuclease proteins, such as ribonuclease T and the
epsilon subunit of DNA polymerase III.;.
Length = 162
Score = 112 bits (283), Expect = 7e-26
Identities = 57/164 (34%), Positives = 87/164 (53%), Gaps = 5/164 (3%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69
+V D ETTGLD + DRIIEI AV ++ F ++ P R + EA K HGIT E
Sbjct: 2 VVIDCETTGLDPEKDRIIEIAAVSIVGGENIGPVFDTYVKPE-RLITDEATKFHGITPEM 60
Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPL-DPSRIIDTLS 128
L++ PSF + F +F + + HNA FDVGF+ + R K P + +IDTL
Sbjct: 61 LRNAPSFEEVLEAFLEFLKKLK-ILVGHNASFDVGFLLYDDLRFLKLPHPKLNDVIDTLI 119
Query: 129 IARRKHPSS-RNDLNSLCKRYGITISHRSKHGALLDSHLLSDVY 171
+ + + R L++L ++ G+ R H AL D+ ++++
Sbjct: 120 LDKATYKGFKRRSLDALAEKLGLEKIQR-AHRALDDARATAELF 162
>gnl|CDD|32359 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive
type) [DNA replication, recombination, and repair].
Length = 1444
Score = 107 bits (269), Expect = 2e-24
Identities = 62/170 (36%), Positives = 93/170 (54%), Gaps = 14/170 (8%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNR---TFQVFLCPNGRKNSPEALKLHGIT 66
+VFDIETTGL D IIEI AV++ K R FQ F+ P GR S +L GIT
Sbjct: 424 VVFDIETTGLSPVYDEIIEIAAVKI----KNGRIIDKFQFFIKP-GRPLSATITELTGIT 478
Query: 67 DEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDT 126
DE L++ P + +F +F ++ +AHNA FD+GF+N ++ +PL +IDT
Sbjct: 479 DEMLENAPEIEEVLEKFREFI--GDSILVAHNASFDMGFLNTNYEKYGLEPLTNP-VIDT 535
Query: 127 LSIARRKHPSSRN-DLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMM 175
L +AR +P ++ L +LCK+ G+ + H A D+ + V+ +
Sbjct: 536 LELARALNPEFKSHRLGTLCKKLGVELERH--HRADYDAEATAKVFFVFL 583
>gnl|CDD|99834 cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial
subgroup of the DEDDh 3'-5' exonuclease domain family
with similarity to the epsilon subunit of DNA polymerase
III. This subfamily is composed of uncharacterized
bacterial proteins with similarity to the epsilon
subunit of DNA polymerase III (Pol III), a multisubunit
polymerase which is the main DNA replicating enzyme in
bacteria, functioning as the chromosomal replicase. The
Pol III holoenzyme is a complex of ten different
subunits, three of which (alpha, epsilon, and theta)
compose the catalytic core. The Pol III epsilon subunit,
encoded by the dnaQ gene, is a DEDDh-type 3'-5'
exonuclease which is responsible for the proofreading
activity of the polymerase, increasing the fidelity of
DNA synthesis. It contains three conserved sequence
motifs termed ExoI, ExoII and ExoIII, with a specific
Hx(4)D conserved pattern at ExoIII. These motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. The epsilon
subunit of Pol III also functions as a stabilizer of the
holoenzyme complex.
Length = 156
Score = 76.0 bits (188), Expect = 1e-14
Identities = 36/110 (32%), Positives = 56/110 (50%), Gaps = 7/110 (6%)
Query: 56 SPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINK 115
P + +HGIT E + D P+F ++ E F + +AHNA FD + A L+
Sbjct: 44 DPFNIAIHGITPEDVADAPTFPEVWPEIKPFL--GGSLVVAHNASFDRSVLRAALEAYGL 101
Query: 116 DPLDPSRIIDTLSIARRKHPSSRN-DLNSLCKRYGITISHRSKHGALLDS 164
P P + + T+ +ARR P N LN++ + GI ++H H AL D+
Sbjct: 102 PP-PPYQYLCTVRLARRVWPLLPNHKLNTVAEHLGIELNH---HDALEDA 147
>gnl|CDD|99837 cd06134, RNaseT, DEDDh 3'-5' exonuclease domain of RNase T. RNase
T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E
implicated in the 3' maturation of small stable RNAs and
23srRNA, and in the end turnover of tRNA. It contains
three conserved sequence motifs termed ExoI, ExoII and
ExoIII, with a specific Hx(4)D conserved pattern at
ExoIII. These motifs are clustered around the active
site and contain four conserved acidic residues that
serve as ligands for the two metal ions required for
catalysis. RNase T is related to the proofreading domain
of DNA polymerase III. Despite its important role, RNase
T is mainly found only in gammaproteobacteria. It is
speculated that it might have originated from DNA
polymerase III at the time the gamma division of
proteobacteria diverged from other bacteria. RNase T is
a homodimer with the catalytic residues of one monomer
contacting a large basic patch on the other monomer to
form a functional active site.
Length = 189
Score = 63.5 bits (155), Expect = 6e-11
Identities = 52/183 (28%), Positives = 86/183 (46%), Gaps = 21/183 (11%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTN-----RTFQVFLCP-NGRKNSPEALKLH 63
+V D+ET G + + D ++EI AV L+ + TF + P G P AL+ +
Sbjct: 8 VVVDVETGGFNPQTDALLEIAAV-TLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFN 66
Query: 64 GITDEF------LKDKPSFSSIFSEFWDFFNEQN---AEWIAHNAKFDVGFINAELQR-- 112
GI D F + +K + IF Q A + HNA FD+GF+NA + R
Sbjct: 67 GI-DPFHPFRFAVDEKEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAVARCK 125
Query: 113 INKDPLDPSRIIDTLSIARRKHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYI 172
I ++P P DT ++A + + L C+ GI ++ H AL D+ ++++
Sbjct: 126 IKRNPFHPFSTFDTATLAGLAY--GQTVLAKACQAAGIEFDNKEAHSALYDTQKTAELFC 183
Query: 173 KMM 175
K++
Sbjct: 184 KIV 186
>gnl|CDD|99836 cd06133, ERI-1_3'hExo_like, DEDDh 3'-5' exonuclease domain of
Caenorhabditis elegans ERI-1, human 3' exonuclease, and
similar proteins. This subfamily is composed of
Caenorhabditis elegans ERI-1, human 3' exonuclease
(3'hExo), Drosophila exonuclease snipper (snp), and
similar proteins from eukaryotes and bacteria. These are
DEDDh-type DnaQ-like 3'-5' exonucleases containing three
conserved sequence motifs termed ExoI, ExoII and ExoIII,
with a specific Hx(4)D conserved pattern at ExoIII.
These motifs are clustered around the active site and
contain four conserved acidic residues that serve as
ligands for the two metal ions required for catalysis.
ERI-1 has been implicated in the degradation of small
interfering RNAs (RNAi). 3'hExo participates in the
degradation of histone mRNAs. Snp is a non-essential
exonuclease that efficiently degrades structured RNA and
DNA substrates as long as there is a minimum of 2
nucleotides in the 3' overhang to initiate degradation.
Snp is not a functional homolog of either ERI-1 or
3'hExo.
Length = 176
Score = 53.4 bits (129), Expect = 6e-08
Identities = 37/177 (20%), Positives = 72/177 (40%), Gaps = 13/177 (7%)
Query: 10 IVFDIETTGLDSKNDR-----IIEIGAVEL-LDYSKTNRTFQVFLCP-NGRKNSPEALKL 62
+V D E T + + IIEIGAV + + + TF ++ P K S +L
Sbjct: 2 LVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTEL 61
Query: 63 HGITDEFLKDKPSFSSIFSEFWDFFNE-QNAEWIAHNAKFDVGFINAELQRINKDPLDP- 120
GIT E + + PSF + EF ++ + ++ +D+ + + L P
Sbjct: 62 TGITQEDVDNAPSFPEVLKEFLEWLGKNGKYAFVT-WGDWDLKDLLQNQCKYKIINLPPF 120
Query: 121 -SRIIDTLSIARRKHPSSRN-DLNSLCKRYGITISHRSKHGALLDSHLLSDVYIKMM 175
+ ID + + + L+ + G+ R H L D+ ++ + +++
Sbjct: 121 FRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGR-HHRGLDDARNIARILKRLL 176
>gnl|CDD|99839 cd06136, TREX1_2, DEDDh 3'-5' exonuclease domain of three prime
repair exonuclease (TREX)1, TREX2, and similar proteins.
Three prime repair exonuclease (TREX)1 and TREX2 are
closely related DEDDh-type DnaQ-like 3'-5' exonucleases.
They contain three conserved sequence motifs known as
ExoI, II, and III, with a specific Hx(4)D conserved
pattern at ExoIII. These motifs contain four conserved
acidic residues that participate in coordination of
divalent metal ions required for catalysis. Both
proteins play a role in the metabolism and clearance of
DNA. TREX1 is the major 3'-5' exonuclease activity
detected in mammalian cells. Mutations in the human
TREX1 gene can cause Aicardi-Goutieres syndrome (AGS),
which is characterized by perturbed innate immunity and
presents itself as a severe neurological disease. TREX1
degrades ssDNA generated by aberrant replication
intermediates to prevent checkpoint activation and
autoimmune disease. There are distinct structural
differences between TREX1 and TREX2 that point to
different biological roles for these proteins. The main
difference is the presence of about 70 amino acids at
the C-terminus of TREX1. In addition, TREX1 has a
nonrepetitive proline-rich region that is not present in
the TREX2 protein. Furthermore, TREX2 contains a
conserved DNA binding loop positioned adjacent to the
active site that has a sequence distinct from the
corresponding loop in TREX1. Truncations in the
C-terminus of human TREX1 cause autosomal dominant
retinal vasculopathy with cerebral leukodystrophy
(RVCL), a neurovascular syndrome featuring a progressive
loss of visual acuity combined with a variable
neurological picture.
Length = 177
Score = 42.3 bits (100), Expect = 1e-04
Identities = 49/184 (26%), Positives = 77/184 (41%), Gaps = 27/184 (14%)
Query: 10 IVFDIETTGL-DSKNDRIIEIGAV-----ELLDYSKTNRTF-----QVFLCPNGRKN-SP 57
+ D+ETTGL I E+ V LL+ S+ ++ LC N + SP
Sbjct: 2 VFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISP 61
Query: 58 EALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWI---AHNA-KFDVGFINAELQRI 113
A ++ G++++ L+ K F S + F + + I AHN +FD + +EL+R+
Sbjct: 62 GASEITGLSNDLLEHKAPFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERL 121
Query: 114 NKDPLDPSRI--IDTLSIARRKHPSSRNDLNSLCKR-YGITISHRSKHGALLDSHLLSDV 170
P I +D+L R S L SL KR +G + H A D L
Sbjct: 122 GTK--LPDDILCVDSLPAFRELDQS----LGSLYKRLFGQEPKN--SHTAEGDVLALLKC 173
Query: 171 YIKM 174
+
Sbjct: 174 ALHK 177
>gnl|CDD|176647 cd06125, DnaQ_like_exo, DnaQ-like (or DEDD) 3'-5' exonuclease
domain superfamily. The DnaQ-like exonuclease
superfamily is a structurally conserved group of 3'-5'
exonucleases, which catalyze the excision of nucleoside
monophosphates at the DNA or RNA termini in the 3'-5'
direction. It is also called the DEDD superfamily, after
the four invariant acidic residues present in the
catalytic site of its members. The superfamily consists
of DNA- and RNA-processing enzymes such as the
proofreading domains of DNA polymerases, other DNA
exonucleases, RNase D, RNase T, Oligoribonuclease and
RNA exonucleases (REX). The DnaQ-like exonuclease domain
contains three conserved sequence motifs termed ExoI,
ExoII and ExoIII, which are clustered around the active
site and contain four conserved acidic residues that
serve as ligands for the two metal ions required for
catalysis. The conservation patterns of the three motifs
may vary among different subfamilies. DnaQ-like
exonucleases are classified as DEDDy or DEDDh
exonucleases depending on the variation of motif III as
YX(3)D or HX(4)D, respectively. The significance of the
motif differences is still unclear. Almost all RNase
families in this superfamily are present only in
eukaryotes and bacteria, but not in archaea, suggesting
a later origin, which in some cases are accompanied by
horizontal gene transfer.
Length = 96
Score = 40.5 bits (95), Expect = 4e-04
Identities = 30/124 (24%), Positives = 40/124 (32%), Gaps = 39/124 (31%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69
I D E TGLD IIEI ++ T + L
Sbjct: 1 IAIDTEATGLDGAVHEIIEIALADVNP----EDTAVIDLKD------------------I 38
Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRIN-KDPLDPSRIIDTLS 128
L+DKP + HN FD+ F+N + K PL IDT+
Sbjct: 39 LRDKPLAILV----------------GHNGSFDLPFLNNRCAELGLKYPLLAGSWIDTIK 82
Query: 129 IARR 132
+A
Sbjct: 83 LAAD 86
>gnl|CDD|99841 cd06138, ExoI_N, N-terminal DEDDh 3'-5' exonuclease domain of
Escherichia coli exonuclease I and similar proteins.
This subfamily is composed of the N-terminal domain of
Escherichia coli exonuclease I (ExoI) and similar
proteins. ExoI is a monomeric enzyme that hydrolyzes
single stranded DNA in the 3' to 5' direction. It plays
a role in DNA recombination and repair. It primarily
functions in repairing frameshift mutations. The
N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5
exonuclease containing three conserved sequence motifs
termed ExoI, ExoII and ExoIII, with a specific Hx(4)D
conserved pattern at ExoIII. These motifs are clustered
around the active site and contain four conserved acidic
residues that serve as ligands for the two metal ions
required for catalysis. The ExoI structure is unique
among DnaQ family enzymes in that there is a large
distance between the two metal ions required for
catalysis and the catalytic histidine is oriented away
from the active site.
Length = 183
Score = 39.6 bits (93), Expect = 9e-04
Identities = 35/134 (26%), Positives = 54/134 (40%), Gaps = 20/134 (14%)
Query: 12 FDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQV-----FLC--PNGRKNSPEALKLHG 64
+D ET GL+ D+I++ A+ T+ F C P SPEAL + G
Sbjct: 3 YDYETFGLNPSFDQILQFAAIR------TDENFNEIEPFNIFCRLPPDVLPSPEALIVTG 56
Query: 65 IT-DEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNA-KFDVGFINAELQRINKDP----- 117
IT + LK+ S ++ FN + +N +FD F+ R DP
Sbjct: 57 ITPQQLLKEGLSEYEFIAKIHRLFNTPGTCIVGYNNIRFDDEFLRFAFYRNLYDPYTWEW 116
Query: 118 LDPSRIIDTLSIAR 131
+ + D L + R
Sbjct: 117 KNGNSRWDLLDVVR 130
>gnl|CDD|99838 cd06135, Orn, DEDDh 3'-5' exonuclease domain of oligoribonuclease
and similar proteins. Oligoribonuclease (Orn) is a
DEDDh-type DnaQ-like 3'-5' exoribonuclease that is
responsible for degrading small oligoribonucleotides to
mononucleotides. It contains three conserved sequence
motifs termed ExoI, ExoII and ExoIII, with a specific
Hx(4)D conserved pattern at ExoIII. These motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. Orn is essential
for Escherichia coli survival. The human homolog, also
called Sfn (small fragment nuclease), is able to
hydrolyze short single-stranded RNA and DNA oligomers.
It plays a role in cellular nucleotide recycling.
Length = 173
Score = 37.5 bits (88), Expect = 0.004
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 13 DIETTGLDSKNDRIIEIGAV 32
D+E TGLD + DRI+EI +
Sbjct: 5 DLEMTGLDPEKDRILEIACI 24
>gnl|CDD|176651 cd06139, DNA_polA_I_Ecoli_like_exo, DEDDy 3'-5' exonuclease domain
of Escherichia coli DNA polymerase I and similar
bacterial family-A DNA polymerases. Escherichia
coli-like Polymerase I (Pol I), a subgroup of family-A
DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5'
exonuclease domain in the same polypeptide chain as the
polymerase domain. The exonuclease domain contains three
conserved sequence motifs termed ExoI, ExoII and ExoIII,
with a specific YX(3)D pattern at ExoIII. These motifs
are clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. The 3'-5'
exonuclease domain of DNA polymerases has a fundamental
role in reducing polymerase errors and is involved in
proofreading activity. E. coli DNA Pol I is involved in
genome replication but is not the main replicating
enzyme. It is also implicated in DNA repair.
Length = 193
Score = 35.6 bits (83), Expect = 0.014
Identities = 34/150 (22%), Positives = 54/150 (36%), Gaps = 35/150 (23%)
Query: 3 RKNKMRKIVFDIETTGLDSKNDRIIEIG-AVELLDYSKTNRTFQVFLCPNGRKNSPEALK 61
K + FD ETT LD ++ I AVE + + P G E L
Sbjct: 1 ELEKAKVFAFDTETTSLDPMQAELVGISFAVEP------GEAYYI---PLGHDYGGEQLP 51
Query: 62 LHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFI-NA--ELQRINKDPL 118
+ KP + + + + N KFD+ + N EL+ D +
Sbjct: 52 REEVLAAL---KP-----------LLEDPSIKKVGQNLKFDLHVLANHGIELRGPAFDTM 97
Query: 119 DPSRIIDTLSIARRKHPSSRNDLNSLCKRY 148
S +++ RR+H L+ L +RY
Sbjct: 98 LASYLLNP---GRRRH-----GLDDLAERY 119
>gnl|CDD|35762 KOG0542, KOG0542, KOG0542, Predicted exonuclease [Replication,
recombination and repair].
Length = 280
Score = 34.9 bits (80), Expect = 0.023
Identities = 42/208 (20%), Positives = 80/208 (38%), Gaps = 21/208 (10%)
Query: 10 IVFDIETTGLD----SKNDRIIEIGAVELL--DYSKTNRTFQVFLCPN-GRKNSPEALKL 62
++ D E T + IIE AV L + S F ++ P + S L
Sbjct: 59 LILDFEATCEEGNKPHYVQEIIEFPAVLLDNTETSIIEDEFHQYVRPVENPRLSDFCTSL 118
Query: 63 HGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKF------DVG-FINAELQRIN- 114
GI E + + P+F + SEF + + + F D+ F+ + + N
Sbjct: 119 TGIQQETVDEAPTFPQVLSEFDSWLRKDSLGDKNGKFAFVTDGDWDLWVFLQYQCKLKNI 178
Query: 115 KDPLDPSRIIDTLSIARR--KHPSSRNDLNSLCKRYGITISHRSKHGALLDSHLLSDVYI 172
+ P ++ I+ I + P+ N + + + YG+ R H + D+ ++ +
Sbjct: 179 RIPAFFNQWINIRKIYKNFYNRPAPTN-ITGMLEHYGLQFEGR-AHSGIDDARNIARIAQ 236
Query: 173 KMMVGGS--QINFGFKTNEDRFFKEEKK 198
KM+ G+ +IN E + +
Sbjct: 237 KMIRDGAEFRINELCDLWERQPLVPNRS 264
>gnl|CDD|176654 cd06142, RNaseD_exo, DEDDy 3'-5' exonuclease domain of Ribonuclease
D and similar proteins. Ribonuclease (RNase) D is a
bacterial enzyme involved in the maturation of small
stable RNAs and the 3' maturation of tRNA. It contains a
DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing
three conserved sequence motifs termed ExoI, ExoII and
ExoIII, with a specific YX(3)D pattern at ExoIII. These
motifs are clustered around the active site and contain
four conserved acidic residues that serve as ligands for
the two metal ions required for catalysis. In vivo,
RNase D only becomes essential upon removal of other
ribonucleases. Eukaryotic RNase D homologs include yeast
Rrp6p, human PM/Scl-100, and the Drosophila melanogaster
egalitarian protein.
Length = 178
Score = 34.8 bits (81), Expect = 0.023
Identities = 21/111 (18%), Positives = 36/111 (32%), Gaps = 21/111 (18%)
Query: 80 FSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRN 139
S + + N + H A+ D+ + + + P + DT AR
Sbjct: 53 LSPLKELLADPNIVKVFHAAREDLELLKRDFGIL------PQNLFDTQIAARLLGLGDSV 106
Query: 140 DLNSLCKRY-GITI---------SHRS-----KHGALLDSHLLSDVYIKMM 175
L +L + G+ + S R A LD L +Y K+
Sbjct: 107 GLAALVEELLGVELDKGEQRSDWSKRPLTDEQLEYAALDVRYLLPLYEKLK 157
>gnl|CDD|32132 COG1949, Orn, Oligoribonuclease (3'->5' exoribonuclease) [RNA
processing and modification].
Length = 184
Score = 34.5 bits (79), Expect = 0.025
Identities = 15/29 (51%), Positives = 18/29 (62%)
Query: 4 KNKMRKIVFDIETTGLDSKNDRIIEIGAV 32
NK I D+E TGLD + DRIIEI +
Sbjct: 3 ANKNNLIWIDLEMTGLDPERDRIIEIATI 31
>gnl|CDD|28891 cd00007, 35EXOc, 3'-5' exonuclease. The 35EXOc domain is
responsible for the 3'-5' exonuclease proofreading
activity of prokaryotic DNA polymerase I (pol I) and
other enzymes, it catalyses the hydrolysis of unpaired
or mismatched nucleotides. This domain consists of the
amino-terminal half of the Klenow fragment in E. coli
pol I. 35EXOc is also found in the Werner syndrome
helicase (WRN), focus forming activity 1 protein (FFA-1)
and ribonuclease D (RNase D)..
Length = 155
Score = 33.1 bits (75), Expect = 0.074
Identities = 27/141 (19%), Positives = 49/141 (34%), Gaps = 37/141 (26%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEF 69
+ FD ETTGL+ +++ I Q+ + EA +
Sbjct: 3 VAFDTETTGLNYHRGKLVGI---------------QIA-------TAGEAA--------Y 32
Query: 70 LKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSI 129
+ D+ + +++ + H+AKFD+ + P I DT+
Sbjct: 33 IPDELELEEDLEALKELLEDEDITKVGHDAKFDLVVLA------RDGIELPGNIFDTMLA 86
Query: 130 ARRKHPS-SRNDLNSLCKRYG 149
A +P + L+ L K Y
Sbjct: 87 AYLLNPGEGSHSLDDLAKEYL 107
>gnl|CDD|144991 pfam01612, 3_5_exonuc, 3'-5' exonuclease. This domain is
responsible for the 3'-5' exonuclease proofreading
activity of E. coli DNA polymerase I (polI) and other
enzymes, it catalyses the hydrolysis of unpaired or
mismatched nucleotides. This domain consists of the
amino-terminal half of the Klenow fragment in E. coli
polI it is also found in the Werner syndrome helicase
(WRN), focus forming activity 1 protein (FFA-1) and
ribonuclease D (RNase D). Werner syndrome is a human
genetic disorder causing premature aging; the WRN
protein has helicase activity in the 3'-5' direction.
The FFA-1 protein is required for formation of a
replication foci and also has helicase activity; it is a
homologue of the WRN protein. RNase D is a 3'-5'
exonuclease involved in tRNA processing. Also found in
this family is the autoantigen PM/Scl thought to be
involved in polymyositis-scleroderma overlap syndrome.
Length = 172
Score = 32.3 bits (74), Expect = 0.12
Identities = 15/63 (23%), Positives = 25/63 (39%), Gaps = 6/63 (9%)
Query: 86 FFNEQNAEWIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPSSRNDLNSLC 145
+ N + HNAKFD+ L R + + DT+ A + L+ L
Sbjct: 70 LLEDPNITKVGHNAKFDLEV----LARDFG--IKLENLFDTMLAAYLLGYPRSHSLDDLA 123
Query: 146 KRY 148
++Y
Sbjct: 124 EKY 126
>gnl|CDD|38452 KOG3242, KOG3242, KOG3242, Oligoribonuclease (3'->5'
exoribonuclease) [RNA processing and modification].
Length = 208
Score = 31.5 bits (71), Expect = 0.21
Identities = 33/144 (22%), Positives = 57/144 (39%), Gaps = 16/144 (11%)
Query: 6 KMRKIVFDIETTGLDSKNDRIIEIGAV---ELLDYSKTNRTFQVFLCPNGRKNSPEALKL 62
K + D E TGLD + DRIIEI + L+ + E
Sbjct: 25 KQPLVWIDCEMTGLDVEKDRIIEIACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIE 84
Query: 63 H----GITDEFLKDKPSFSSIFSEFWDFFNEQ---NAEWIAHNAKF-DVGFINAELQRIN 114
H G+T++ L K + + +E ++ + +A N+ + D F+ + ++
Sbjct: 85 HHGNSGLTEKVLASKITLADAENEVLEYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKL- 143
Query: 115 KDPLDPSRIIDTLSI---ARRKHP 135
RI+D +I ARR +P
Sbjct: 144 -IKHLHYRIVDVSTIKELARRWYP 166
>gnl|CDD|33167 COG3359, COG3359, Predicted exonuclease [DNA replication,
recombination, and repair].
Length = 278
Score = 30.7 bits (69), Expect = 0.33
Identities = 39/151 (25%), Positives = 55/151 (36%), Gaps = 34/151 (22%)
Query: 5 NKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTFQVFLCPNGRKNSPEALKLHG 64
FDIETTGLD + I +G +D + R Q FL A +
Sbjct: 96 EAEDVAFFDIETTGLDRAGNTITLVGGARGVDDTMHVR--QHFL---------PAPEEEV 144
Query: 65 ITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLD---PS 121
E P F+ + S FN FD+ FI +R+ +D L+
Sbjct: 145 AVLENFLHDPDFNMLVS-----FN---------GKAFDIPFI----KRMVRDRLELSLEF 186
Query: 122 RIIDTLSIARR--KHPSSRNDLNSLCKRYGI 150
D +RR KH R L ++ + GI
Sbjct: 187 GHFDLYHPSRRLWKHLLPRCGLKTVERILGI 217
>gnl|CDD|99825 cd05782, DNA_polB_like1_exo, Uncharacterized bacterial subgroup of
the DEDDy 3'-5' exonuclease domain of family-B DNA
polymerases. A subfamily of the 3'-5' exonuclease
domain of family-B DNA polymerases. This subfamily is
composed of uncharacterized bacterial family-B DNA
polymerases. Family-B DNA polymerases contain an
N-terminal DEDDy DnaQ-like exonuclease domain in the
same polypeptide chain as the polymerase domain, similar
to family-A DNA polymerases. This exonuclease domain
contains three sequence motifs termed ExoI, ExoII and
ExoIII, with a specific YX(3)D pattern at ExoIII. These
motifs are involved in metal binding and catalysis. The
exonuclease domain of family-B DNA polymerases has a
fundamental role in proofreading activity. It contains a
beta hairpin structure that plays an important role in
active site switching in the event of a nucleotide
misincorporation. Family-B DNA polymerases are
predominantly involved in DNA replication and DNA
repair.
Length = 208
Score = 30.7 bits (70), Expect = 0.36
Identities = 34/197 (17%), Positives = 58/197 (29%), Gaps = 86/197 (43%)
Query: 10 IVFDIET----------------------------TGLDSKND-------RIIEIGAVEL 34
+VFDIET S +D +++ I A+
Sbjct: 2 LVFDIETVPDVDLGRRLYLLLELDDLEVLEKRFAQRLEKSGSDFLPLPFHKVVSISALYR 61
Query: 35 LDYSKTNRTFQVFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEW 94
D +V + E E L+D F+ ++N
Sbjct: 62 DDDGGF---LKVR----TLDGADEK--------ELLED----------FFQLIEKKNPRL 96
Query: 95 IAHNAK-FDVGFIN-----------AELQRINKDPLDPSR----IIDTLSI-----ARRK 133
++ N + FD+ ++ A NKD +R +D + + AR +
Sbjct: 97 VSFNGRGFDLPVLHLRALIHGVSAPAYFDLGNKDWNYRNRYSERHLDLMDLLAFYGARAR 156
Query: 134 HPSSRNDLNSLCKRYGI 150
L+ L K GI
Sbjct: 157 AS-----LDLLAKLLGI 168
>gnl|CDD|36229 KOG1011, KOG1011, KOG1011, Neurotransmitter release regulator,
UNC-13 [Signal transduction mechanisms, Intracellular
trafficking, secretion, and vesicular transport].
Length = 1283
Score = 30.0 bits (67), Expect = 0.56
Identities = 16/65 (24%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 56 SPEALKLH----GITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQ 111
S + + LH + +E++ D P++ S E+ +F +W+ N + + F+ L+
Sbjct: 707 SADYMNLHFKVKWLYNEYVADLPTYKSSVPEYPAWFEPFVMQWLDENEEVSMDFLRGALE 766
Query: 112 RINKD 116
R KD
Sbjct: 767 RDKKD 771
>gnl|CDD|33213 COG3407, MVD1, Mevalonate pyrophosphate decarboxylase [Lipid
metabolism].
Length = 329
Score = 28.3 bits (63), Expect = 2.1
Identities = 20/68 (29%), Positives = 27/68 (39%), Gaps = 3/68 (4%)
Query: 60 LKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGFINAELQRINKDPLD 119
+K G DE L P SSI DF AE + N + D +N EL +
Sbjct: 17 IKYWGKRDEALN-IPLNSSISVTLEDFSTTTTAEELTENDEEDTFILNGELSEDENEKA- 74
Query: 120 PSRIIDTL 127
R++D
Sbjct: 75 -RRVLDRF 81
>gnl|CDD|176237 cd08276, MDR7, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 336
Score = 27.9 bits (63), Expect = 2.8
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 14 IETTGLDSKNDRIIEIGAVELLDYSKT 40
I T+ D K +R +GA +++Y T
Sbjct: 188 IATSSSDEKLERAKALGADHVINYRTT 214
>gnl|CDD|32342 COG2159, COG2159, Predicted metal-dependent hydrolase of the
TIM-barrel fold [General function prediction only].
Length = 293
Score = 27.3 bits (60), Expect = 4.2
Identities = 12/67 (17%), Positives = 19/67 (28%)
Query: 46 VFLCPNGRKNSPEALKLHGITDEFLKDKPSFSSIFSEFWDFFNEQNAEWIAHNAKFDVGF 105
F+ R+ + GI L + I N+ A A VGF
Sbjct: 44 YFINGKLRRVDLAFMDAAGIDLFVLSGMGEVAIIPDLRRALANDDLAALAAEYPDRFVGF 103
Query: 106 INAELQR 112
+ +
Sbjct: 104 ARVDPRD 110
>gnl|CDD|99848 cd06145, REX1_like, DEDDh 3'-5' exonuclease domain of RNA
exonuclease 1, -3 and similar eukaryotic proteins. This
subfamily is composed of RNA exonuclease 1 (REX1 or
Rex1p), REX3 (or Rex3p), and similar eukaryotic
proteins. In yeast, REX1 and REX3 are required for 5S
rRNA and MRP (mitochondrial RNA processing) RNA
maturation, respectively. They are DEDDh-type DnaQ-like
3'-5' exonucleases containing three conserved sequence
motifs termed ExoI, ExoII and ExoIII, with a specific
Hx(4)D conserved pattern at ExoIII. These motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. REX1 is the major
exonuclease responsible for pre-tRNA trail trimming and
may also be involved in nuclear CCA turnover. REX
proteins function in the processing and maturation of
many RNA species, similar to the function of Escherichia
coli RNase T.
Length = 150
Score = 26.7 bits (60), Expect = 6.3
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 118 LDPSRIIDTLSI--ARRKHPSSRNDLNSLCKRY 148
L R+IDT +I + P + L +L K+Y
Sbjct: 93 LIHPRVIDT-AILFPHPRGPPYKPSLKNLAKKY 124
>gnl|CDD|153225 cd03131, GATase1_HTS, Type 1 glutamine amidotransferase
(GATase1)-like domain found in homoserine
trans-succinylase (HTS). Type 1 glutamine
amidotransferase (GATase1)-like domain found in
homoserine trans-succinylase (HTS). HTS, the first
enzyme in methionine biosynthesis in Escherichia coli,
transfers a succinyl group from succinyl-CoA to
homoserine forming succinyl homoserine. It has been
suggested that the succinyl group of succinyl-CoA is
initially transferred to an enzyme nucleophile before
subsequent transfer to homoserine. The catalytic triad
typical of GATase1 domains is not conserved in this
GATase1-like domain. However, in common with GATase1
domains a reactive cys residue is found in the sharp
turn between a beta strand and an alpha helix termed the
nucleophile elbow. It has been proposed that this cys is
in the active site of the molecule. However, as succinyl
has been found bound to a conserved lysine residue, this
conserved cys may play a role in dimer formation. HTS
activity is tightly regulated by several mechanisms
including feedback inhibition and proteolysis. It
represents a critical control point for cell growth and
viability.
Length = 175
Score = 26.5 bits (59), Expect = 6.9
Identities = 8/18 (44%), Positives = 13/18 (72%)
Query: 32 VELLDYSKTNRTFQVFLC 49
E+LD++KT+ T +F C
Sbjct: 88 TEILDWAKTHVTSTLFSC 105
>gnl|CDD|35403 KOG0182, KOG0182, KOG0182, 20S proteasome, regulatory subunit alpha
type PSMA6/SCL1 [Posttranslational modification, protein
turnover, chaperones].
Length = 246
Score = 26.5 bits (58), Expect = 7.0
Identities = 8/28 (28%), Positives = 16/28 (57%)
Query: 197 KKTVPNISLLKRDKPLFTRITKEELDEH 224
K + + ++ D P F ++ EE++EH
Sbjct: 211 KSSELEVGVVTVDNPEFRILSAEEIEEH 238
>gnl|CDD|32749 COG2925, SbcB, Exonuclease I [DNA replication, recombination, and
repair].
Length = 475
Score = 26.0 bits (57), Expect = 8.8
Identities = 20/87 (22%), Positives = 37/87 (42%), Gaps = 19/87 (21%)
Query: 10 IVFDIETTGLDSKNDRIIEIGAVELLDYSKTNRTF------QVFLC--PNGRKNSPEALK 61
+ +D ET G+ DR + + +T+ F VF C + P A+
Sbjct: 12 LFYDYETFGVHPALDRPAQFAGI------RTDIEFNIIGEPIVFYCKPADDYLPQPGAVL 65
Query: 62 LHGITDEFLKDK----PSFSS-IFSEF 83
+ GIT + ++K +F++ I +E
Sbjct: 66 ITGITPQEAREKGINEAAFAARIHAEL 92
>gnl|CDD|36671 KOG1458, KOG1458, KOG1458, Fructose-1,6-bisphosphatase
[Carbohydrate transport and metabolism].
Length = 343
Score = 26.0 bits (57), Expect = 9.1
Identities = 11/36 (30%), Positives = 12/36 (33%), Gaps = 7/36 (19%)
Query: 116 DPLDPSRIIDTL-------SIARRKHPSSRNDLNSL 144
DPLD S ID L I R + L
Sbjct: 129 DPLDGSSNIDALVSVGTIFGIYRLLSDDEPTIKDVL 164
>gnl|CDD|34109 COG4403, LcnDR2, Lantibiotic modifying enzyme [Defense mechanisms].
Length = 963
Score = 26.1 bits (57), Expect = 9.3
Identities = 15/71 (21%), Positives = 19/71 (26%), Gaps = 9/71 (12%)
Query: 1 MIRKNKMRKIVFDIETTGLDSKNDRIIEIGAVELLDYSKTN----RTFQVFLCPNGRKNS 56
I N + KN ELLDY K R + LC +
Sbjct: 382 NINLNTDEMKIVKEPYMFESEKNLPTFNGKDKELLDYIKEITEGFRNMYLLLCSGISE-- 439
Query: 57 PEALKLHGITD 67
+K I
Sbjct: 440 ---IKEKNILA 447
>gnl|CDD|176650 cd06129, RNaseD_like, DEDDy 3'-5' exonuclease domain of RNase D,
WRN, and similar proteins. The RNase D-like group is
composed of RNase D, WRN, and similar proteins. They
contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease
domain that contains three conserved sequence motifs
termed ExoI, ExoII and ExoIII, with a specific YX(3)D
pattern at ExoIII. These motifs are clustered around the
active site and contain four conserved acidic residues
that serve as ligands for the two metal ions required
for catalysis. RNase D is involved in the 3'-end
processing of tRNA precursors. RNase D-like proteins in
eukaryotes include yeast Rrp6p, human PM/Scl-100 and
Drosophila melanogaster egalitarian (Egl) protein. WRN
is a unique DNA helicase possessing exonuclease
activity. Mutation in the WRN gene is implicated in
Werner syndrome, a disease associated with premature
aging and increased predisposition to cancer. Yeast
Rrp6p and the human Polymyositis/scleroderma autoantigen
100kDa (PM/Scl-100) are exosome-associated proteins
involved in the degradation and processing of precursors
to stable RNAs. Egl is a component of an mRNA-binding
complex which is required for oocyte specification. The
Egl subfamily does not possess a completely conserved
YX(3)D pattern at the ExoIII motif.
Length = 161
Score = 25.9 bits (57), Expect = 9.4
Identities = 24/115 (20%), Positives = 37/115 (32%), Gaps = 25/115 (21%)
Query: 81 SEFWDFFNE--QNAE--WIAHNAKFDVGFINAELQRINKDPLDPSRIIDTLSIARRKHPS 136
S W +N H + D+ +L R + R+ DT A K
Sbjct: 53 SVDWQGLKMLLENPSIVKALHGIEGDL----WKLLRDFGEK--LQRLFDTTIAANLKGLP 106
Query: 137 SRNDLNSLCKRY-GIT--------------ISHRSKHGALLDSHLLSDVYIKMMV 176
R L SL + + G T ++ K A D + L +Y K+
Sbjct: 107 ERWSLASLVEHFLGKTLDKSISCADWSYRPLTEDQKLYAAADVYALLIIYTKLRN 161
>gnl|CDD|58113 cd03782, MATH_Meprin_Beta, Meprin family, Beta subunit, MATH
domain; Meprins are multidomain extracellular
metalloproteases capable of cleaving growth factors,
cytokines, extracellular matrix proteins, and
biologically active peptides. They are composed of two
related subunits, alpha and beta, which form homo- or
hetro-complexes where the basic unit is a
disulfide-linked dimer. The beta subunit is a type I
membrane protein, which forms homodimers or
heterotetramers (alpha2beta2 or alpha3beta). Meprin
beta shows preference for acidic residues at the P1 and
P1' sites of its substrate. Among its best substrates
are growth factors and chemokines such as gastrin and
osteopontin. Both alpha and beta subunits contain a
catalytic astacin (M12 family) protease domain followed
by the adhesion or interaction domains MAM, MATH and
AM. The MATH and MAM domains provide symmetrical
intersubunit disulfide bonds necessary for the
dimerization of meprin subunits. The MATH domain may
also be required for folding of an activable zymogen..
Length = 167
Score = 26.1 bits (57), Expect = 9.4
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 37 YSKTNRTFQVFLCPNGRKNSPEALKLH 63
S T +FQV L NG + P L ++
Sbjct: 30 LSSTGYSFQVGLYLNGTDDYPGNLAIY 56
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.319 0.136 0.398
Gapped
Lambda K H
0.267 0.0761 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,010,136
Number of extensions: 155648
Number of successful extensions: 457
Number of sequences better than 10.0: 1
Number of HSP's gapped: 431
Number of HSP's successfully gapped: 42
Length of query: 245
Length of database: 6,263,737
Length adjustment: 91
Effective length of query: 154
Effective length of database: 4,297,318
Effective search space: 661786972
Effective search space used: 661786972
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)