RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8196
(230 letters)
>gnl|CDD|235574 PRK05711, PRK05711, DNA polymerase III subunit epsilon;
Provisional.
Length = 240
Score = 309 bits (793), Expect = e-107
Identities = 119/235 (50%), Positives = 155/235 (65%), Gaps = 9/235 (3%)
Query: 3 RHIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTT 62
R IVLD ETTGLN +GHRIIEIG VE+ NR++TG N H YI P R + ALA+HG+T
Sbjct: 5 RQIVLDTETTGLNQREGHRIIEIGAVELINRRLTGRNFHVYIKPDRLVDPEALAVHGITD 64
Query: 63 KFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLG--YSNFTKYIYRITD 120
+FL +K F+E+ D FL+++ +E+IIHNA FD+GF+D E +LLG + ++TD
Sbjct: 65 EFLADKPTFAEVADEFLDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFC-KVTD 123
Query: 121 TLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNLNF-- 178
TL MAR++ GKRNSLDALC RY I HRTLHG LLDAE+LAEVYLAMT GQ++L F
Sbjct: 124 TLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALLDAEILAEVYLAMTGGQTSLGFAM 183
Query: 179 KPKINNSNNIETKIKIP---NNIPIKLANSNELVQHNMILSKIDKHSNGRCIWKK 230
+ + ET +I + +P+ A EL H L +DK G C+W+K
Sbjct: 184 EGETQQQQGEETIQRIVRQRSRLPVVRATDEELAAHEARLDLLDK-KGGSCLWRK 237
>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 = 273 bits (701), Expect = 1e-94
Identities = 100/166 (60%), Positives = 123/166 (74%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKF 64
IVLD ETTGL+ +GHRIIEIGCVE+ NR++TGN H YINP RD + A +HG+T +F
Sbjct: 2 IVLDTETTGLDPREGHRIIEIGCVELINRRLTGNTFHVYINPERDIPEEAFKVHGITDEF 61
Query: 65 LKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLM 124
L +K KF+EI D FL+++ +E++IHNA+FDVGFL+ ELSLLG R+ DTL +
Sbjct: 62 LADKPKFAEIADEFLDFIRGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLAL 121
Query: 125 ARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMT 170
ARK GK NSLDALC R+ I HRTLHG LLDAELLAEVYL +T
Sbjct: 122 ARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAELLAEVYLELT 167
>gnl|CDD|130473 TIGR01406, dnaQ_proteo, DNA polymerase III, epsilon subunit,
Proteobacterial. This model represents DnaQ, the DNA
polymerase III epsilon subunit, as found in most
Proteobacteria. It consists largely of an exonuclease
domain as described in Pfam model pfam00929. In
Gram-positive bacteria, closely related regions are
found both in the Gram-positive type DNA polymerase III
alpha subunit and as an additional N-terminal domain of
a DinG-family helicase. Both are excluded from this
model, as are smaller proteins, also outside the
Proteobacteria, that are similar in size to the epsilon
subunit but as different in sequence as are the
epsilon-like regions found in Gram-positive bacteria
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 225
Score = 253 bits (648), Expect = 8e-86
Identities = 107/226 (47%), Positives = 140/226 (61%), Gaps = 7/226 (3%)
Query: 3 RHIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTT 62
R I+LD ETTGL+ GHRI+EIG VE+ NR +TG+N H Y+NP RD A +HG+T
Sbjct: 1 RQIILDTETTGLDPKGGHRIVEIGAVELVNRMLTGDNFHVYVNPERDMPAEAAKVHGITD 60
Query: 63 KFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLG--YSNFTKYIYRITD 120
+FL +K KF EI D FL+++ SE++IHNAAFDVGFL+ EL LG ++ R+ D
Sbjct: 61 EFLADKPKFKEIADEFLDFIGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFC-RVID 119
Query: 121 TLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNLNFKP 180
TL MAR+ G+RNSLDALC R+ + HRTLHG LLDA LLAEVYLA+T GQ +L
Sbjct: 120 TLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAHLLAEVYLALTGGQESLLELA 179
Query: 181 ----KINNSNNIETKIKIPNNIPIKLANSNELVQHNMILSKIDKHS 222
+ ++K+ + + EL H L K+ K S
Sbjct: 180 ESNSGEAAKPSKSAEMKLGATLRVLAPREAELQAHEAYLDKLLKKS 225
>gnl|CDD|129663 TIGR00573, dnaq, exonuclease, DNA polymerase III, epsilon subunit
family. All proteins in this family for which functions
are known are components of the DNA polymerase III
complex (epsilon subunit). There is, however, an
outgroup that includes paralogs in some
gamma-proteobacteria and the n-terminal region of DinG
from some low GC gram positive bacteria. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University) [DNA metabolism,
Degradation of DNA].
Length = 217
Score = 173 bits (440), Expect = 2e-54
Identities = 98/217 (45%), Positives = 124/217 (57%), Gaps = 7/217 (3%)
Query: 2 HRHIVLDIETTGLNIIDG----HRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAI 57
R +VLD ETTG N G H IIEIG VEI NR+ITGN H YI P R + A+ I
Sbjct: 1 ERQLVLDTETTGDNETTGLYAGHDIIEIGAVEIINRRITGNKFHTYIKPDRPIDPDAIKI 60
Query: 58 HGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELS-LLGYSNFTKYIY 116
HG+T LK+K F EI ++F +Y+ +E++IHNA+FDVGFL+ E S L T +
Sbjct: 61 HGITDDMLKDKPDFKEIAEDFADYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVI 120
Query: 117 RITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNL 176
TDTL AR GKRN+LDALC RY I+ HR LHG L DA +LA++YL MT Q+
Sbjct: 121 DTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGALADAFILAKLYLVMTGKQTKY 180
Query: 177 NFKPKINNSNNIETK--IKIPNNIPIKLANSNELVQH 211
+ K +K + + A S EL H
Sbjct: 181 GENEGQQSRPYHAIKSIVKKDMLLKLIKAVSTELQAH 217
>gnl|CDD|223916 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related
3'-5' exonucleases [DNA replication, recombination, and
repair].
Length = 243
Score = 158 bits (401), Expect = 3e-48
Identities = 76/235 (32%), Positives = 117/235 (49%), Gaps = 9/235 (3%)
Query: 1 MHRHIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGL 60
R +V+D+ETTGLN RIIEIG V +++ +I + H +NP R IHG+
Sbjct: 12 PTRFVVIDLETTGLNPK-KDRIIEIGAVTLEDGRIVERSFHTLVNPERPIPPEIFKIHGI 70
Query: 61 TTKFLKNKLKFSEIVDNFLNYV-SNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRIT 119
T + L + KF+E++ FL+++ ++ HNAAFDVGFL +E LG +
Sbjct: 71 TDEMLADAPKFAEVLPEFLDFIGGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVL--- 127
Query: 120 DTLLMARKIHTG-KRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRG---QSN 175
DTL +AR+ G R+SLDAL +R I + H L DA LAE++L + G ++
Sbjct: 128 DTLALARRHFPGFDRSSLDALAERLGIDRNPFHPHRALFDALALAELFLLLQTGLLLKAP 187
Query: 176 LNFKPKINNSNNIETKIKIPNNIPIKLANSNELVQHNMILSKIDKHSNGRCIWKK 230
L ++ + + + NEL H L + K + +WK+
Sbjct: 188 LTAILDLDKLAHKALYDTLKTAARLFCGIENELKAHGSWLDALAKELLEKKLWKE 242
>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 = 129 bits (327), Expect = 4e-38
Identities = 58/165 (35%), Positives = 81/165 (49%), Gaps = 8/165 (4%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKF 64
+V D ETTGL+ RIIEIG V++ +NPGR A AIHG+T +
Sbjct: 1 VVFDTETTGLDP-KKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITDEM 59
Query: 65 LKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLM 124
L + F E++ FL ++ ++ HNA+FD+ FL+ EL LG DTL +
Sbjct: 60 LADAPPFEEVLPEFLEFLGGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWI---DTLRL 116
Query: 125 ARKIHTGKRNSL--DALCDRYNISKIHRTLHGGLLDAELLAEVYL 167
AR++ G R+ L +RY I H L DA AE+ L
Sbjct: 117 ARRLLPGLRSHRLGLLLAERYGIPLEGA--HRALADALATAELLL 159
>gnl|CDD|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and
epsilon chain, ribonuclease T and other exonucleases.
Length = 169
Score = 120 bits (302), Expect = 3e-34
Identities = 52/169 (30%), Positives = 80/169 (47%), Gaps = 7/169 (4%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKF 64
+V+D ETTGL+ IIEI V++ +I Y+ P R A IHG+T +
Sbjct: 3 VVIDCETTGLDP-GKDEIIEIAAVDVDGGEI-IEVFDTYVKPDRPITDYATEIHGITPEM 60
Query: 65 LKNKLKFSEIVDNFLNYVSNSEIIIHN-AAFDVGFLDMELSLLGYSNFTKYIYRITDTLL 123
L + F E+++ L ++ ++ N A FD+ FL +E LG K + DTL
Sbjct: 61 LDDAPTFEEVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRLGIKQPPKLP--VIDTLK 118
Query: 124 MARKIHTG-KRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTR 171
+AR + G + SL L R + I R H L DA A+++ +
Sbjct: 119 LARATNPGLPKYSLKKLAKRLLLEVIQRA-HRALDDARATAKLFKKLLE 166
>gnl|CDD|216200 pfam00929, RNase_T, Exonuclease. This family includes a variety of
exonuclease proteins, such as ribonuclease T and the
epsilon subunit of DNA polymerase III.;.
Length = 161
Score = 110 bits (277), Expect = 1e-30
Identities = 58/164 (35%), Positives = 85/164 (51%), Gaps = 5/164 (3%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKF 64
+V+D ETTGL+ + IIEI V I + G Y+ P R A HG+T +
Sbjct: 1 VVIDCETTGLDP-EKDEIIEIAAVSIVGGENIGPVFDTYVKPERLITDEATEFHGITPEM 59
Query: 65 LKNKLKFSEIVDNFLNYVS-NSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLL 123
L+N F E+++ FL ++ ++ HNA+FDVGFL + K I DTL+
Sbjct: 60 LRNAPSFEEVLEAFLEFLKKLKILVGHNASFDVGFLLYDDLRFLKLPMPKLNDVI-DTLI 118
Query: 124 MARKIHTG-KRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVY 166
+ + + G KR SLDAL ++ + KI R H L DA AE++
Sbjct: 119 LDKATYKGFKRRSLDALAEKLGLEKIQRA-HRALDDARATAELF 161
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 89.9 bits (224), Expect = 1e-20
Identities = 55/204 (26%), Positives = 92/204 (45%), Gaps = 16/204 (7%)
Query: 6 VLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKFL 65
V D+ETTGL+ + IIEIG V+IKN +I + ++I PG + G+T +
Sbjct: 423 VFDVETTGLSAVY-DEIIEIGAVKIKNGEII-DKFEFFIKPGHPLSAFTTELTGITDDMV 480
Query: 66 KNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTK-YIYRITDTLLM 124
K+ E++ F + +S ++ HNA+FDVGF++ LG I DTL +
Sbjct: 481 KDAPSIEEVLPKFKEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVI----DTLEL 536
Query: 125 ARKIHTG-KRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNLNFKPKIN 183
+R ++ K + L+ L ++ + H H DAE A + + + I
Sbjct: 537 SRFLYPELKSHRLNTLAKKFGVELEHH--HRADYDAEATAYLLIKFL----KDLKEKGIT 590
Query: 184 NSNNIETKIKIPNNIPIKLANSNE 207
N + + K+ + K A
Sbjct: 591 NLDELNKKLG--SEDAYKKARPKH 612
>gnl|CDD|233397 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
Gram-positive type. This model describes a polypeptide
chain of DNA polymerase III. Full-length homologs of
this protein are restricted to the Gram-positive
lineages, including the Mycoplasmas. This protein is
designated alpha chain and given the gene symbol polC,
but is not a full-length homolog of other polC genes.
The N-terminal region of about 200 amino acids is rich
in low-complexity sequence, poorly alignable, and not
included n this model [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1213
Score = 84.4 bits (209), Expect = 9e-19
Identities = 51/168 (30%), Positives = 82/168 (48%), Gaps = 12/168 (7%)
Query: 5 IVLDIETTGL-NIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTK 63
+V DIETTGL D IIE G V++KN +I + ++I P + G+T
Sbjct: 193 VVFDIETTGLSPQYD--EIIEFGAVKVKNGRI-IDKFQFFIKPHEPLSAFVTELTGITQD 249
Query: 64 FLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTK-YIYRITDTL 122
L+N + E+++ F + +S ++ HNA+FD+GFL+ +G I DTL
Sbjct: 250 MLENAPEIEEVLEKFKEFFKDSILVAHNASFDIGFLNTNFEKVGLEPLENPVI----DTL 305
Query: 123 LMARKIHTG-KRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAM 169
+AR ++ K + L +C + + H DAE A+V+ M
Sbjct: 306 ELARALNPEYKSHRLGNICKKLGVDLDD--HHRADYDAEATAKVFKVM 351
>gnl|CDD|225087 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive
type) [DNA replication, recombination, and repair].
Length = 1444
Score = 84.3 bits (209), Expect = 1e-18
Identities = 55/171 (32%), Positives = 91/171 (53%), Gaps = 18/171 (10%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKF 64
+V DIETTGL+ + IIEI V+IKN +I + ++I PGR + + G+T +
Sbjct: 424 VVFDIETTGLSPVY-DEIIEIAAVKIKNGRII-DKFQFFIKPGRPLSATITELTGITDEM 481
Query: 65 LKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKY-IYRIT---- 119
L+N + E+++ F ++ +S ++ HNA+FD+GFL+ N+ KY + +T
Sbjct: 482 LENAPEIEEVLEKFREFIGDSILVAHNASFDMGFLNT--------NYEKYGLEPLTNPVI 533
Query: 120 DTLLMARKIHTG-KRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAM 169
DTL +AR ++ K + L LC + + H DAE A+V+
Sbjct: 534 DTLELARALNPEFKSHRLGTLCKKLGVELER--HHRADYDAEATAKVFFVF 582
>gnl|CDD|180525 PRK06310, PRK06310, DNA polymerase III subunit epsilon; Validated.
Length = 250
Score = 78.7 bits (194), Expect = 1e-17
Identities = 46/173 (26%), Positives = 85/173 (49%), Gaps = 6/173 (3%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKF 64
+ LD ETTGL++ RIIE + ++ +++ + INP R + IH ++
Sbjct: 10 VCLDCETTGLDV-KKDRIIEFAAIRFTFDEVI-DSVEFLINPERVVSAESQRIHHISDAM 67
Query: 65 LKNKLKFSEIVDNFLNYVSNSEIII-HNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLL 123
L++K K +E+ + + I+ H+ FD+ L E +G + +K+ Y I DTL
Sbjct: 68 LRDKPKIAEVFPQIKGFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKH-YYIIDTLR 126
Query: 124 MARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNL 176
+A++ NSL+AL +N+ + H + D E+ +V+ + + L
Sbjct: 127 LAKEYGDSPNNSLEALAVHFNVP--YDGNHRAMKDVEINIKVFKHLCKRFRTL 177
>gnl|CDD|236085 PRK07740, PRK07740, hypothetical protein; Provisional.
Length = 244
Score = 77.8 bits (192), Expect = 2e-17
Identities = 41/163 (25%), Positives = 75/163 (46%), Gaps = 6/163 (3%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKF 64
+V D+ETTG + G I+ IG V+ K ++ + + + P R + L + G+T +
Sbjct: 62 VVFDLETTGFSPQQGDEILSIGAVKTKGGEVETDTFYSLVKPKRPIPEHILELTGITAED 121
Query: 65 LKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLM 124
+ +E++ F ++ ++ H+A D FL L FT +R+ DT+ +
Sbjct: 122 VAFAPPLAEVLHRFYAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFT---HRLIDTMFL 178
Query: 125 ARKI-HTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVY 166
+ + H +LD Y I R H L DA + A+++
Sbjct: 179 TKLLAHERDFPTLDDALAYYGIPIPRR--HHALGDALMTAKLW 219
>gnl|CDD|236148 PRK08074, PRK08074, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 928
Score = 75.8 bits (187), Expect = 8e-16
Identities = 44/170 (25%), Positives = 80/170 (47%), Gaps = 7/170 (4%)
Query: 1 MHRHIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGL 60
R +V+D+ETTG + G +II+I V +++ +I ++NP R + G+
Sbjct: 2 SKRFVVVDLETTGNSPKKGDKIIQIAAVVVEDGEIL-ERFSSFVNPERPIPPFITELTGI 60
Query: 61 TTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITD 120
+ + +K F ++ + + + + HN FD+ FL+ EL GY+ D
Sbjct: 61 SEEMVKQAPLFEDVAPEIVELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHC---PKLD 117
Query: 121 TLLMARKIH-TGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYLAM 169
T+ +AR + T + L L + + H H DAE+ AE++L +
Sbjct: 118 TVELARILLPTAESYKLRDLSEELGLE--HDQPHRADSDAEVTAELFLQL 165
>gnl|CDD|236123 PRK07883, PRK07883, hypothetical protein; Validated.
Length = 557
Score = 73.4 bits (181), Expect = 4e-15
Identities = 45/168 (26%), Positives = 73/168 (43%), Gaps = 14/168 (8%)
Query: 6 VLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKFL 65
V+D+ETTG + G I EIG V+++ ++ G +NPGR + G+TT +
Sbjct: 19 VVDLETTGGSP-AGDAITEIGAVKVRGGEVLGE-FATLVNPGRPIPPFITVLTGITTAMV 76
Query: 66 KNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMA 125
E++ FL + + ++ HNA FD+GFL + GY + T+ +A
Sbjct: 77 AGAPPIEEVLPAFLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPG---PPVLCTVRLA 133
Query: 126 RKIHT--GKRN-SLDALCDRYNISKI--HRTLHGGLLDAELLAEVYLA 168
R++ N L L + + HR L DA +V
Sbjct: 134 RRVLPRDEAPNVRLSTLARLFGATTTPTHRALD----DARATVDVLHG 177
>gnl|CDD|233398 TIGR01407, dinG_rel, DnaQ family exonuclease/DinG family helicase,
putative. This model represents a family of proteins in
Gram-positive bacteria. The N-terminal region of about
200 amino acids resembles the epsilon subunit of E. coli
DNA polymerase III and the homologous region of the
Gram-positive type DNA polymerase III alpha subunit. The
epsilon subunit contains an exonuclease domain. The
remainder of this protein family resembles a predicted
ATP-dependent helicase, the DNA damage-inducible protein
DinG of E. coli [DNA metabolism, DNA replication,
recombination, and repair].
Length = 850
Score = 71.8 bits (176), Expect = 1e-14
Identities = 43/166 (25%), Positives = 75/166 (45%), Gaps = 8/166 (4%)
Query: 3 RHIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTT 62
R+ V+D+ETTG + +II+IG V +++ +I + H +NP + G++
Sbjct: 1 RYAVVDLETTG-TQLSFDKIIQIGIVVVEDGEIV-DTFHTDVNPNEPIPPFIQELTGISD 58
Query: 63 KFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTL 122
L+ FS++ + + + + HN FD+ FL L GY K DT+
Sbjct: 59 NMLQQAPYFSQVAQEIYDLLEDGIFVAHNVHFDLNFLAKALKDCGYEPLPK---PRIDTV 115
Query: 123 LMARKIH-TGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYL 167
+A+ T + L L + ++ H H DA+ AE+ L
Sbjct: 116 ELAQIFFPTEESYQLSELSEALGLT--HENPHRADSDAQATAELLL 159
>gnl|CDD|236391 PRK09145, PRK09145, DNA polymerase III subunit epsilon; Validated.
Length = 202
Score = 66.1 bits (162), Expect = 2e-13
Identities = 42/185 (22%), Positives = 75/185 (40%), Gaps = 31/185 (16%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIK-NRQITGNNLHYYINPGRDSEKSALAIHGLTTK 63
+ LD ETTGL+ I+ I V+I+ NR +T L + P + ++ IH L +
Sbjct: 32 VALDCETTGLDP-RRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQ 90
Query: 64 FLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLL 123
L++ L E + L ++ N ++ + FDV L+ +Y+ + L
Sbjct: 91 DLEDGLSEEEALRQLLAFIGNRPLVGYYLEFDVAMLN------------RYVRPLLGIPL 138
Query: 124 MARKI------HTGKRN---------SLDALCDRYNISKIHRTLHGGLLDAELLAEVYLA 168
I + K DA+ ++ + R H L DA + A ++L
Sbjct: 139 PNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVLGR--HDALNDAIMAALIFLR 196
Query: 169 MTRGQ 173
+ +G
Sbjct: 197 LRKGD 201
>gnl|CDD|235864 PRK06807, PRK06807, DNA polymerase III subunit epsilon; Validated.
Length = 313
Score = 67.1 bits (164), Expect = 3e-13
Identities = 43/165 (26%), Positives = 79/165 (47%), Gaps = 9/165 (5%)
Query: 4 HIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTK 63
++V+D ETTG N + +II++ V+ +N ++ + Y+NP R ++ G+T
Sbjct: 10 YVVIDFETTGFNPYN-DKIIQVAAVKYRNHELV-DQFVSYVNPERPIPDRITSLTGITNY 67
Query: 64 FLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLL 123
+ + E++ FL ++ + I+ HNA+FD+ FL +++LG ++ DT+
Sbjct: 68 RVSDAPTIEEVLPLFLAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKN---KVIDTVF 124
Query: 124 MARKIHTGKRN-SLDALCDRYNISKIHRTLHGGLLDAELLAEVYL 167
+A+K N L+ L I + H D A VY
Sbjct: 125 LAKKYMKHAPNHKLETLKRMLGIRL---SSHNAFDDCITCAAVYQ 166
>gnl|CDD|180524 PRK06309, PRK06309, DNA polymerase III subunit epsilon; Validated.
Length = 232
Score = 64.1 bits (156), Expect = 2e-12
Identities = 51/174 (29%), Positives = 70/174 (40%), Gaps = 17/174 (9%)
Query: 1 MHRHIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGL 60
M I D ETTG I D RIIEI +T + +NP A IHG+
Sbjct: 1 MPALIFYDTETTGTQI-DKDRIIEIAAYN----GVTSESFQTLVNPEIPIPAEASKIHGI 55
Query: 61 TTKFLKNKLKFSEIVDNFLNYVSNSEIII--HNAAFDVGFLDMELSLLGYSNFTKYIYRI 118
TT + + KF E F+ + I++ +N AFD L E G T R
Sbjct: 56 TTDEVADAPKFPEAYQKFIEFCGTDNILVAHNNDAFDFPLLRKECRRHGLEPPT---LRT 112
Query: 119 TDTLLMARKIHTG-KRNSLDALCDRYNIS--KIHRTLHGGLLDAELLAEVYLAM 169
D+L A+K +++L L Y + HR L D L V+ A+
Sbjct: 113 IDSLKWAQKYRPDLPKHNLQYLRQVYGFEENQAHRALD----DVITLHRVFSAL 162
>gnl|CDD|180377 PRK06063, PRK06063, DNA polymerase III subunit epsilon;
Provisional.
Length = 313
Score = 64.0 bits (156), Expect = 4e-12
Identities = 42/161 (26%), Positives = 74/161 (45%), Gaps = 9/161 (5%)
Query: 6 VLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKFL 65
V+D+ET+G RII + + + ++ +NPG D +HGLT + L
Sbjct: 19 VVDVETSGFRP-GQARIISLAVLGLDADGNVEQSVVTLLNPGVDP--GPTHVHGLTAEML 75
Query: 66 KNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMA 125
+ + +F++I + ++ HN AFD FL E G + ++ T+ +A
Sbjct: 76 EGQPQFADIAGEVAELLRGRTLVAHNVAFDYSFLAAEAERAG---AELPVDQVMCTVELA 132
Query: 126 RKIHTGKRN-SLDALCDRYNISKIHRTLHGGLLDAELLAEV 165
R++ G N L+ L + + + R H L DA +LA +
Sbjct: 133 RRLGLGLPNLRLETLAAHWGVPQ-QRP-HDALDDARVLAGI 171
>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 = 58.7 bits (143), Expect = 5e-11
Identities = 43/169 (25%), Positives = 73/169 (43%), Gaps = 19/169 (11%)
Query: 5 IVLDIETTGLNIIDGHR--IIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTT 62
+ +D ET + R IG V++++ QI + I P + +AIHG+T
Sbjct: 2 VAIDFETA-----NADRASACSIGLVKVRDGQIVDT-FYTLIRPPTRFDPFNIAIHGITP 55
Query: 63 KFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLD--MELSLLGYSNFTKYIYRITD 120
+ + + F E+ ++ S ++ HNA+FD L +E L Y+
Sbjct: 56 EDVADAPTFPEVWPEIKPFLGGSLVVAHNASFDRSVLRAALEAYGLPPPP-----YQYLC 110
Query: 121 TLLMARKIHTGKRN-SLDALCDRYNISKIHRTLHGGLLDAELLAEVYLA 168
T+ +AR++ N L+ + + I H H L DA AE+ LA
Sbjct: 111 TVRLARRVWPLLPNHKLNTVAEHLGIELNH---HDALEDARACAEILLA 156
>gnl|CDD|181176 PRK07942, PRK07942, DNA polymerase III subunit epsilon;
Provisional.
Length = 232
Score = 52.7 bits (127), Expect = 2e-08
Identities = 39/161 (24%), Positives = 69/161 (42%), Gaps = 23/161 (14%)
Query: 1 MHRH----IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLH---YYINPGRDSEKS 53
M H D+ETTG++ RI+ V + G + + +PG + +
Sbjct: 1 MSWHPGPLAAFDLETTGVDPETA-RIVTAALVVVDA---DGEVVESREWLADPGVEIPEE 56
Query: 54 ALAIHGLTTKFLKNKLK-----FSEIVDNFLNY-VSNSEIIIHNAAFDVGFLDMELSLLG 107
A A+HG+TT++ + + +EI D +++ NA +D+ LD EL G
Sbjct: 57 ASAVHGITTEYARAHGRPAAEVLAEIADALREAWARGVPVVVFNAPYDLTVLDRELRRHG 116
Query: 108 YSNFTKYIYRITDTLLMARKIHT---GKRNSLDALCDRYNI 145
+ + D ++ + + GKR L ALC+ Y +
Sbjct: 117 LPSLVP--GPVIDPYVIDKAVDRYRKGKRT-LTALCEHYGV 154
>gnl|CDD|236281 PRK08517, PRK08517, DNA polymerase III subunit epsilon;
Provisional.
Length = 257
Score = 48.5 bits (116), Expect = 6e-07
Identities = 42/167 (25%), Positives = 69/167 (41%), Gaps = 24/167 (14%)
Query: 6 VLDIETTGLNIIDGHRIIEIGCVEIKNRQITG--------NNLHYYINPGRDSEKSALAI 57
+DIET G + H+IIEIG V++KN +I + YI +
Sbjct: 72 FVDIETNG-SKPKKHQIIEIGAVKVKNGEIIDRFESFVKAKEVPEYIT----------EL 120
Query: 58 HGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYR 117
G+T + L+N E+++ F ++ +S + HN FD F+ L +G + R
Sbjct: 121 TGITYEDLENAPSLKEVLEEFRLFLGDSVFVAHNVNFDYNFISRSLEEIG---LGPLLNR 177
Query: 118 ITDTLLMARKIHTGKRNSLDALCDRYNIS--KIHRTLHGGLLDAELL 162
T+ +A++ R L L + I HR L E+
Sbjct: 178 KLCTIDLAKRTIESPRYGLSFLKELLGIEIEVHHRAYADALAAYEIF 224
>gnl|CDD|181186 PRK07983, PRK07983, exodeoxyribonuclease X; Provisional.
Length = 219
Score = 47.4 bits (113), Expect = 1e-06
Identities = 28/97 (28%), Positives = 48/97 (49%), Gaps = 14/97 (14%)
Query: 6 VLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKFL 65
V+D ET GL I+EI V++ + +I N + + + P R A+AIH +T +
Sbjct: 4 VIDTETCGLQ----GGIVEIASVDVIDGKIV-NPMSHLVRPDRPISPQAMAIHRITEAMV 58
Query: 66 KNKLKFSEIVDNFLN---YVSNSEIIIHNAAFDVGFL 99
+K +++ ++ YV+ HNA+FD L
Sbjct: 59 ADKPWIEDVIPHYYGSEWYVA------HNASFDRRVL 89
>gnl|CDD|236392 PRK09146, PRK09146, DNA polymerase III subunit epsilon; Validated.
Length = 239
Score = 47.2 bits (113), Expect = 2e-06
Identities = 34/132 (25%), Positives = 62/132 (46%), Gaps = 7/132 (5%)
Query: 7 LDIETTGLNIIDGHRIIEIGCVEIKNRQI-TGNNLHYYINPGRDSEKSALAIHGLTTKFL 65
LD ETTGL+ + I+ IG V ++I H+ + P R E+ ++ IHG+T L
Sbjct: 52 LDFETTGLDA-EQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSEL 110
Query: 66 KNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMEL-SLLGYSNFTKYIYRITDTLLM 124
++ I+D L ++ +++H + FLD L + +G + + DT+ +
Sbjct: 111 QDAPDLERILDELLEALAGKVVVVHYRRIERDFLDQALRNRIGEG----IEFPVIDTMEI 166
Query: 125 ARKIHTGKRNSL 136
+I + L
Sbjct: 167 EARIQRKQAGGL 178
>gnl|CDD|236397 PRK09182, PRK09182, DNA polymerase III subunit epsilon; Validated.
Length = 294
Score = 45.0 bits (107), Expect = 1e-05
Identities = 30/112 (26%), Positives = 44/112 (39%), Gaps = 22/112 (19%)
Query: 2 HRHIVLDIETTGLNIIDGHR---IIEIGCV--------EIKNRQITGNNLHYYINPGRDS 50
++LD ETTGL+ R IIEIG V I + P R
Sbjct: 37 RLGVILDTETTGLD----PRKDEIIEIGMVAFEYDDDGRIG--DVLD-TFGGLQQPSRPI 89
Query: 51 EKSALAIHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIII-HNAAFDVGFLDM 101
+ G+T + + + VD + +++II HNA FD FL+
Sbjct: 90 PPEITRLTGITDEMVAGQTIDPAAVDALIA---PADLIIAHNAGFDRPFLER 138
>gnl|CDD|188129 TIGR01298, RNaseT, ribonuclease T. This model describes
ribonuclease T, an enzyme found so far only in
gamma-subdivision Proteobacteria such as Escherichia
coli and Xylella fastidiosa. Ribonuclease T is
homologous to the DNA polymerase III alpha chain. It can
liberate AMP from the common C-C-A terminus of uncharged
tRNA. It appears also to be involved in RNA maturation.
It also acts as a 3' to 5' single-strand DNA-specific
exonuclease; it is distinctive for its ability to remove
residues near a double-stranded stem. Ribonuclease T is
a high copy suppressor in E. coli of a uv-repair defect
caused by deletion of three other single-stranded DNA
exonucleases [Transcription, RNA processing].
Length = 200
Score = 44.1 bits (104), Expect = 1e-05
Identities = 42/185 (22%), Positives = 74/185 (40%), Gaps = 25/185 (13%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIK----NRQITGNNLHYYINP--GRDSEKSALAIH 58
+V+D+ET G N ++EI + +K + H++I P G + E AL
Sbjct: 11 VVVDVETGGFNA-ATDALLEIAAITLKMDEQGFLFPDHTYHFHIEPFEGANIEPEALEFT 69
Query: 59 GLTTKFLKNKLK------------FSEIVDNFLNYVSNSEIII-HNAAFDVGFLDMELSL 105
G+ L + L+ F + I++ HNA+FD+GFL+ ++
Sbjct: 70 GID---LDHPLRGAVQEEAALTEIFRGVRKAMKANGCQRAILVGHNASFDLGFLNAAVAR 126
Query: 106 LGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEV 165
G + + DT +A + + L C + +R H L D E AE+
Sbjct: 127 TGIKRNPFHPFSSFDTATLAGLAY--GQTVLAKACQAAGMDFDNRQAHSALYDTEKTAEL 184
Query: 166 YLAMT 170
+ +
Sbjct: 185 FCGIV 189
>gnl|CDD|235735 PRK06195, PRK06195, DNA polymerase III subunit epsilon; Validated.
Length = 309
Score = 40.1 bits (94), Expect = 4e-04
Identities = 26/82 (31%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 25 IGCVEIKNRQITGNNLHYYINPGRDSEKSA-LAIHGLTTKFLKNKLKFSEIVDNFLNYVS 83
IG V +K+ +I +HY I P + IHG+ ++++L+F +I + +Y +
Sbjct: 21 IGIVVVKDGEIV-EKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIKHYFN 79
Query: 84 NSEIIIHNAAFDVGFLDMELSL 105
N+ +I HNA+FD+ L L L
Sbjct: 80 NNLVIAHNASFDISVLRKTLEL 101
>gnl|CDD|180905 PRK07246, PRK07246, bifunctional ATP-dependent DNA helicase/DNA
polymerase III subunit epsilon; Validated.
Length = 820
Score = 40.1 bits (94), Expect = 7e-04
Identities = 45/170 (26%), Positives = 75/170 (44%), Gaps = 18/170 (10%)
Query: 3 RHIVLDIETTGLNIIDGHR--IIEIGCVEIKNRQITGNNLHYY--INPGRDSEKSALAIH 58
++ V+D+E TG G II++G V I+ +I Y +NP ++ +
Sbjct: 8 KYAVVDLEATGA----GPNASIIQVGIVIIEGGEIID---SYTTDVNPHEPLDEHIKHLT 60
Query: 59 GLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRI 118
G+T + L FS++ + + + + + HN FD L L L GY T +
Sbjct: 61 GITDQQLAQAPDFSQVARHIYDLIEDCIFVAHNVKFDANLLAEALFLEGYELRTPRV--- 117
Query: 119 TDTLLMARKIH-TGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVYL 167
DT+ +A+ T ++ SL L NI H + DA AE++L
Sbjct: 118 -DTVELAQVFFPTLEKYSLSHLSRELNIDLADA--HTAIADARATAELFL 164
>gnl|CDD|235529 PRK05601, PRK05601, DNA polymerase III subunit epsilon; Validated.
Length = 377
Score = 37.1 bits (86), Expect = 0.005
Identities = 26/98 (26%), Positives = 45/98 (45%), Gaps = 3/98 (3%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTKF 64
+ + I+T+G++ R+I I V + + H +NPG D L HGL+ +
Sbjct: 49 VAVSIQTSGIHPSTS-RLITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHL--HGLSAEE 105
Query: 65 LKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDME 102
+FS+I+ + +I+HNA GF+ E
Sbjct: 106 FAQGKRFSQILKPLDRLIDGRTLILHNAPRTWGFIVSE 143
>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 = 36.1 bits (84), Expect = 0.007
Identities = 27/114 (23%), Positives = 52/114 (45%), Gaps = 23/114 (20%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIK-NRQ---ITGNNLHYYINP--GRDSEKSALAIH 58
+V+D+ET G N ++EI V ++ + Q H++I P G + + +AL +
Sbjct: 8 VVVDVETGGFN-PQTDALLEIAAVTLEMDEQGNLYPDETFHFHILPFEGANLDPAALEFN 66
Query: 59 GLTTKFLKNKLKFS----EIVDNFLNYV---------SNSEIIIHNAAFDVGFL 99
G+ + +F+ E + + + + ++ HNA FD+GFL
Sbjct: 67 GID---PFHPFRFAVDEKEALKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFL 117
>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 = 35.7 bits (83), Expect = 0.008
Identities = 40/183 (21%), Positives = 66/183 (36%), Gaps = 27/183 (14%)
Query: 5 IVLDIETT----GLNIIDGHRIIEIGCVEI--KNRQITGNNLHYYINP---GRDSEKSAL 55
+V+D E T + IIEIG V + K ++I Y+ P + S+
Sbjct: 2 LVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIID-TFSSYVKPVINPKLSDFCT- 59
Query: 56 AIHGLTTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLGYSNFTKYI 115
+ G+T + + N F E++ FL + + + V + D +L L N KY
Sbjct: 60 ELTGITQEDVDNAPSFPEVLKEFLEW-----LGKNGKYAFVTWGDWDLKDLL-QNQCKYK 113
Query: 116 YRITDTLLM---------ARKIHTGKRNSLDALCDRYNISKIHRTLHGGLLDAELLAEVY 166
A+ KR L + + R H GL DA +A +
Sbjct: 114 IINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRH-HRGLDDARNIARIL 172
Query: 167 LAM 169
+
Sbjct: 173 KRL 175
>gnl|CDD|223426 COG0349, Rnd, Ribonuclease D [Translation, ribosomal structure and
biogenesis].
Length = 361
Score = 35.7 bits (83), Expect = 0.013
Identities = 20/98 (20%), Positives = 31/98 (31%), Gaps = 23/98 (23%)
Query: 88 IIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRY---N 144
I H A FD+ L + F + DT + A+ G + L L +
Sbjct: 74 IFHAARFDLEVL--------LNLFGLLPTPLFDTQIAAKLAGFGTSHGLADLVEELLGVE 125
Query: 145 ISKIHRT------------LHGGLLDAELLAEVYLAMT 170
+ K + L D E L +Y +T
Sbjct: 126 LDKSEQRSDWLARPLSEAQLEYAAADVEYLLPLYDKLT 163
>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 = 35.0 bits (81), Expect = 0.014
Identities = 38/148 (25%), Positives = 57/148 (38%), Gaps = 20/148 (13%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCV-----EIKNRQITG-------NNLHYYINPGRDSEK 52
+ LD+ETTGL + I E+ V + N + L NPGR
Sbjct: 2 VFLDLETTGLPKHNRPEITELCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGRAISP 61
Query: 53 SALAIHGLTTKFLKNKLKFSE----IVDNFLNYV-SNSEIIIHNA-AFDVGFLDMELSLL 106
A I GL+ L++K F ++ FL ++ HN FD L EL L
Sbjct: 62 GASEITGLSNDLLEHKAPFDSDTANLIKLFLRRQPKPICLVAHNGNRFDFPILRSELERL 121
Query: 107 GYSNFTKYIYRITDTLLMARKIHTGKRN 134
G + I + D+L R++ +
Sbjct: 122 G-TKLPDDILCV-DSLPAFRELDQSLGS 147
>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 = 34.1 bits (79), Expect = 0.031
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 13/52 (25%)
Query: 7 LDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIH 58
+D+E TGL+ + RI+EI C+ IT +L N +E L IH
Sbjct: 4 IDLEMTGLDP-EKDRILEIACI------ITDGDL----NI--IAEGPELVIH 42
>gnl|CDD|180670 PRK06722, PRK06722, exonuclease; Provisional.
Length = 281
Score = 34.3 bits (78), Expect = 0.038
Identities = 27/107 (25%), Positives = 44/107 (41%), Gaps = 5/107 (4%)
Query: 5 IVLDIETT--GLNIIDGHRIIEIGCV--EIKNRQITGNNLHYYINPGRDSEKSALAIHGL 60
IV DIE D I++IG V E ++ G + PG + + G+
Sbjct: 8 IVFDIERNFRPYKSEDPSEIVDIGAVKIEASTMKVIGE-FSELVKPGARLTRHTTKLTGI 66
Query: 61 TTKFLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFLDMELSLLG 107
T K L KF +I++ F+ ++ I + D FL + +L
Sbjct: 67 TKKDLIGVEKFPQIIEKFIQFIGEDSIFVTWGKEDYRFLSHDCTLHS 113
>gnl|CDD|235429 PRK05359, PRK05359, oligoribonuclease; Provisional.
Length = 181
Score = 33.6 bits (78), Expect = 0.041
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 7/36 (19%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNL 40
I +D+E TGL+ + RIIEI + +T +L
Sbjct: 6 IWIDLEMTGLDP-ERDRIIEIATI------VTDADL 34
>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 = 33.7 bits (78), Expect = 0.042
Identities = 14/69 (20%), Positives = 23/69 (33%), Gaps = 11/69 (15%)
Query: 86 EIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRY-- 143
+ H A D+ L +F + DT + AR + G L AL +
Sbjct: 66 VKVFHAAREDLELL--------KRDFGILPQNLFDTQIAARLLGLGDSVGLAALVEELLG 117
Query: 144 -NISKIHRT 151
+ K +
Sbjct: 118 VELDKGEQR 126
>gnl|CDD|179951 PRK05168, PRK05168, ribonuclease T; Provisional.
Length = 211
Score = 33.6 bits (78), Expect = 0.047
Identities = 31/114 (27%), Positives = 52/114 (45%), Gaps = 23/114 (20%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIK----NRQITGNNLHYYINP--GRDSEKSALAIH 58
+V+D+ET G N ++EI V +K LH+++ P G + E ALA +
Sbjct: 20 VVIDVETAGFN-AKTDALLEIAAVTLKMDEQGWLYPDETLHFHVEPFEGANLEPEALAFN 78
Query: 59 GLTTKFLKNKLKF--SE---IVDNF--------LNYVSNSEIIIHNAAFDVGFL 99
G+ N L+ SE + + F + + + ++ HNA FD+ FL
Sbjct: 79 GID---PDNPLRGAVSEKEALHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFL 129
>gnl|CDD|216604 pfam01612, DNA_pol_A_exo1, 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 catalyzes 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 = 31.9 bits (73), Expect = 0.14
Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 8/61 (13%)
Query: 84 NSEIIIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRY 143
N + HNA FD+ L +F + + DT+L A + + +SLD L ++Y
Sbjct: 75 NITKVGHNAKFDLEVL--------ARDFGIKLENLFDTMLAAYLLGYPRSHSLDDLAEKY 126
Query: 144 N 144
Sbjct: 127 L 127
>gnl|CDD|235591 PRK05755, PRK05755, DNA polymerase I; Provisional.
Length = 880
Score = 32.4 bits (75), Expect = 0.18
Identities = 29/143 (20%), Positives = 51/143 (35%), Gaps = 41/143 (28%)
Query: 4 HIVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTK 63
D ETT L+ + ++ + YI P ++ LA
Sbjct: 317 LFAFDTETTSLDPMQA-ELVGLSFA-------VEPGEAAYI-PLDQLDREVLAA------ 361
Query: 64 FLKNKLKFSEIVDNFLNYVSNSEIIIHNAAFDVGFL---DMELSLLGYSNFTKYIYRITD 120
LK L+ I + + N +D+ L +EL + + D
Sbjct: 362 -LKPLLEDPAI-----------KKVGQNLKYDLHVLARYGIELRGIAF-----------D 398
Query: 121 TLLMARKIHTGKRNSLDALCDRY 143
T+L + + G+R+ LD+L +RY
Sbjct: 399 TMLASYLLDPGRRHGLDSLAERY 421
>gnl|CDD|239826 cd04334, ProRS-INS, INS is an amino acid-editing domain inserted
(INS) into the bacterial class II prolyl-tRNA synthetase
(ProRS) however, this CD is not exclusively bacterial.
It is also found at the N-terminus of the
eukaryotic/archaea-like ProRS's of yeasts and
single-celled parasites. ProRS catalyzes the attachment
of proline to tRNA(Pro); proline is first activated by
ATP, and then transferred to the acceptor end of
tRNA(Pro). ProRS can inadvertently process noncognate
amino acids such as alanine and cysteine, and to avoid
such errors, in post-transfer editing, the INS domain
deacylates mischarged Ala-tRNA(Pro), thus ensuring the
fidelity of translation. Misacylated Cys-tRNA(Pro) is
not edited by ProRS. In addition to the INS editing
domain, the prokaryote-like ProRS protein contains
catalytic and anticodon-binding domains which form a
dimeric interface.
Length = 160
Score = 30.2 bits (69), Expect = 0.46
Identities = 19/87 (21%), Positives = 38/87 (43%), Gaps = 17/87 (19%)
Query: 127 KIHTGKRNSLDALCDRYNI--SKIHRTLHGGLLDAELLAEVYLAMTRGQSNLNFKPKINN 184
K+ T + +++ L + + S+ +TL L+ A+ E+ + RG LN
Sbjct: 29 KVATPGQKTIEELAEFLGVPPSQTVKTL---LVKADGEEELVAVLLRGDHELN------- 78
Query: 185 SNNIETKI-KIPNNIPIKLANSNELVQ 210
E K+ + P++LA+ E+
Sbjct: 79 ----EVKLENLLGAAPLELASEEEIEA 101
>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 = 29.0 bits (66), Expect = 1.5
Identities = 32/146 (21%), Positives = 51/146 (34%), Gaps = 41/146 (28%)
Query: 5 IVLDIETTGLNIIDGHRIIEIG-CVEIKNRQITGNNLHYYINPGRDSEKSALAIHGLTTK 63
D ETT L+ + ++ I VE YYI P L
Sbjct: 8 FAFDTETTSLDPMQA-ELVGISFAVEPGEA--------YYI-P-------------LGHD 44
Query: 64 FLKNKLKFSEIVDNFLNYVSNSEIII--HNAAFDVGFL---DMELSLLGYSNFTKYIYRI 118
+ +L E++ + + I N FD+ L +EL +
Sbjct: 45 YGGEQLPREEVLAALKPLLEDPSIKKVGQNLKFDLHVLANHGIELRGPAF---------- 94
Query: 119 TDTLLMARKIHTGKRN-SLDALCDRY 143
DT+L + ++ G+R LD L +RY
Sbjct: 95 -DTMLASYLLNPGRRRHGLDDLAERY 119
>gnl|CDD|185083 PRK15129, PRK15129, L-Ala-D/L-Glu epimerase; Provisional.
Length = 321
Score = 28.6 bits (64), Expect = 2.6
Identities = 19/39 (48%), Positives = 23/39 (58%), Gaps = 8/39 (20%)
Query: 129 HTGKRNSLDALCDRY---NISKIHRTLHGGLLDAELLAE 164
HT R+SL AL RY NI K+ +T GGL +A LA
Sbjct: 229 HT--RSSLKALKGRYEMVNI-KLDKT--GGLTEALALAT 262
>gnl|CDD|224860 COG1949, Orn, Oligoribonuclease (3'->5' exoribonuclease) [RNA
processing and modification].
Length = 184
Score = 27.3 bits (61), Expect = 5.0
Identities = 14/36 (38%), Positives = 20/36 (55%), Gaps = 7/36 (19%)
Query: 5 IVLDIETTGLNIIDGHRIIEIGCVEIKNRQITGNNL 40
I +D+E TGL+ + RIIEI + +T NL
Sbjct: 9 IWIDLEMTGLDP-ERDRIIEIATI------VTDANL 37
>gnl|CDD|239640 cd03585, NTR_TIMP, NTR domain, TIMP subfamily; TIMPs, or tissue
inibitors of metalloproteases, are essential regulators
of extracellular matrix turnover and remodeling. They
form complexes with matrix metalloproteases (MMPs) and
inactivate them irreversibly by non-covalently binding
their active zinc-binding sites. The levels of activated
membrane-type MMPs, MMPs, and free TIMPs determine the
balance between matrix degradation and matrix formation
or stabilization. Consequently, TIMPs play roles in
processes that require the remodeling and degradation of
connective tissue, such as development, morphogenesis,
wound healing, as well as in various diseases and
pathological states such as tumor cell metastasis,
arthritis, and artherosclerosis. Most TIMPs bind to a
variety of MMPs. TIMP-1 and TIMP-2 appear to be
multifunctional proteins with diverse biological action.
They may exhibit growth factor-like activity and can
inhibit angiogenesis. TIMP-3 has been implicated in
apoptosis.
Length = 183
Score = 27.0 bits (60), Expect = 6.8
Identities = 13/51 (25%), Positives = 20/51 (39%), Gaps = 11/51 (21%)
Query: 189 ETKIKIPNNIPIKLANSNELVQHNMILSKID-----------KHSNGRCIW 228
E KI IP +++ NE + + + K K S+G C W
Sbjct: 127 ECKITPCYTIPCFVSSPNECLWTDWLSEKSINGHQAKHYACIKRSDGSCSW 177
>gnl|CDD|233038 TIGR00593, pola, DNA polymerase I. All proteins in this family for
which functions are known are DNA polymerases Many also
have an exonuclease motif. 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 = 887
Score = 27.3 bits (61), Expect = 7.7
Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 4/57 (7%)
Query: 88 IIHNAAFDVGFLDMELSLLGYSNFTKYIYRITDTLLMARKIHTGKRNSLDALCDRYN 144
I D FL L G + I DT+L A + + ++LD L RY
Sbjct: 378 QIKKIGHDAKFLMHLLKREG----IELGGVIFDTMLAAYLLDPAQVSTLDTLARRYL 430
>gnl|CDD|183118 PRK11402, PRK11402, DNA-binding transcriptional regulator FrlR;
Provisional.
Length = 241
Score = 27.1 bits (60), Expect = 8.0
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 4/46 (8%)
Query: 139 LCDRYNISKIHRTLHGGLLDAELLAEVYLAMTRGQSNLNFKPKINN 184
LC +YN+S+I T+ + D L+A+ L +G+ K+ N
Sbjct: 39 LCTQYNVSRI--TIRKAISD--LVADGVLIRWQGKGTFVQSQKVEN 80
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
0.321 0.138 0.399
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,599,425
Number of extensions: 1093623
Number of successful extensions: 1027
Number of sequences better than 10.0: 1
Number of HSP's gapped: 976
Number of HSP's successfully gapped: 68
Length of query: 230
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 136
Effective length of database: 6,768,326
Effective search space: 920492336
Effective search space used: 920492336
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: 57 (25.7 bits)