RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3897
(240 letters)
>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 = 232 bits (594), Expect = 2e-78
Identities = 79/151 (52%), Positives = 109/151 (72%), Gaps = 3/151 (1%)
Query: 81 YALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPY 140
+ALD EM YT GLE+ RVTVV+ +G+++ + LVKPD EI+DYNT++SGI+ +
Sbjct: 1 FALDCEMCYTTDGLELTRVTVVDENGKVVLDELVKPDGEIVDYNTRFSGITEEMLENVT- 59
Query: 141 KTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGLPYRRSLKS 200
TL+DVQ L+ +S D+I+VGH LENDL+ALKLIH +IDT++LFPH G PY+ SLK+
Sbjct: 60 TTLEDVQKKLLSLISPDTILVGHSLENDLKALKLIHPRVIDTAILFPHPRGPPYKPSLKN 119
Query: 201 IVSQLLHQSIQ--SGTHDSFEDARACIDLIL 229
+ + L + IQ G HDS EDARA ++L+
Sbjct: 120 LAKKYLGRDIQQGEGGHDSVEDARAALELVK 150
>gnl|CDD|99840 cd06137, DEDDh_RNase, DEDDh 3'-5' exonuclease domain of the
eukaryotic exoribonucleases PAN2, RNA exonuclease
(REX)-1,-3, and -4, ISG20, and similar proteins. This
group is composed of eukaryotic exoribonucleases that
include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3
(Rex3p), REX4 (or Rex4p), ISG20, and similar proteins.
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. PAN2 is the catalytic subunit of poly(A)
nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease
which plays an important role in the posttranscriptional
maturation of pre-mRNAs. REX proteins are required for
the processing and maturation of many RNA species, and
ISG20 is an interferon-induced antiviral exonuclease
with a strong preference for single-stranded RNA.
Length = 161
Score = 145 bits (368), Expect = 4e-44
Identities = 54/161 (33%), Positives = 89/161 (55%), Gaps = 12/161 (7%)
Query: 81 YALDTEMVYTVHGL-EVARVTVVNV-DGRLIYNTLVKPDCEIIDYNTKYSGISAKDF--- 135
ALD EMV G EV R++ V+V G ++ ++LV+P + D+ T++SG++ D
Sbjct: 1 VALDCEMVGLADGDSEVVRISAVDVLTGEVLIDSLVRPSVRVTDWRTRFSGVTPADLEEA 60
Query: 136 IRNPYKTLKD--VQNDLMGFVSKDSIIVGHGLENDLRALKLIHSNIIDTSVLFPHSFGLP 193
+ + L F+ D+I+VGH L+NDL AL++IH+ ++DT++L + P
Sbjct: 61 AKAGKTIFGWEAARAALWKFIDPDTILVGHSLQNDLDALRMIHTRVVDTAILTREAVKGP 120
Query: 194 Y---RRSLKSIVSQLLHQSIQSG--THDSFEDARACIDLIL 229
+ SL+++ L IQ G HDS EDA A +++L
Sbjct: 121 LAKRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAAREVVL 161
>gnl|CDD|99847 cd06144, REX4_like, DEDDh 3'-5' exonuclease domain of RNA
exonuclease 4, XPMC2, Interferon Stimulated Gene product
of 20 kDa, and similar proteins. This subfamily is
composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2,
Interferon (IFN) Stimulated Gene product of 20 kDa
(ISG20), and similar proteins. REX4 is involved in
pre-rRNA processing. It controls the ratio between the
two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene
which was identified through its ability to correct a
mitotic defect in fission yeast. The human homolog of
XPMC2 (hPMC2) may be involved in angiotensin II-induced
adrenal cell cycle progression and cell proliferation.
ISG20 is an IFN-induced antiviral exonuclease with a
strong preference for single-stranded RNA and minor
activity towards single-stranded DNA. These proteins 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.
REX proteins function in the processing and maturation
of many RNA species, similar to the function of
Escherchia coli RNase T.
Length = 152
Score = 122 bits (309), Expect = 2e-35
Identities = 62/152 (40%), Positives = 78/152 (51%), Gaps = 9/152 (5%)
Query: 82 ALDTEMVYTVHGLEV---ARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRN 138
ALD EMV ARV++VN DG ++Y+T VKP + DY T SGI +
Sbjct: 2 ALDCEMVGVGPDGSESALARVSIVNEDGNVVYDTYVKPQEPVTDYRTAVSGIRPEHLKDA 61
Query: 139 PYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIH--SNIIDTSVLFP-HSFGLPYR 195
P ++VQ + + K I+VGH L+NDL+ LKL H I DTS P
Sbjct: 62 P--DFEEVQKKVAELL-KGRILVGHALKNDLKVLKLDHPKKLIRDTSKYKPLRKTAKGKS 118
Query: 196 RSLKSIVSQLLHQSIQSGTHDSFEDARACIDL 227
SLK + QLL IQ G H S EDARA + L
Sbjct: 119 PSLKKLAKQLLGLDIQEGEHSSVEDARAAMRL 150
>gnl|CDD|214685 smart00479, EXOIII, exonuclease domain in DNA-polymerase alpha and
epsilon chain, ribonuclease T and other exonucleases.
Length = 169
Score = 120 bits (303), Expect = 3e-34
Identities = 50/167 (29%), Positives = 78/167 (46%), Gaps = 17/167 (10%)
Query: 80 VYALDTEMVYTVHG-LEVARVTVVNVDGRLI---YNTLVKPDCEIIDYNTKYSGISAKDF 135
+ +D E G E+ + V+VDG I ++T VKPD I DY T+ GI+ +
Sbjct: 2 LVVIDCETTGLDPGKDEIIEIAAVDVDGGEIIEVFDTYVKPDRPITDYATEIHGIT-PEM 60
Query: 136 IRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSN----------IIDTSVL 185
+ + T ++V +L+ F+ ++ G+ DLR LKL H +IDT L
Sbjct: 61 LDDA-PTFEEVLEELLEFLRGRILVAGNSAHFDLRFLKLEHPRLGIKQPPKLPVIDTLKL 119
Query: 186 FPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLILWKL 232
+ + SLK + +LL + IQ H + +DARA L L
Sbjct: 120 ARATNPGLPKYSLKKLAKRLLLEVIQR-AHRALDDARATAKLFKKLL 165
>gnl|CDD|99852 cd06149, ISG20, DEDDh 3'-5' exonuclease domain of Interferon
Stimulated Gene product of 20 kDa, and similar proteins.
Interferon (IFN) Stimulated Gene product of 20 kDa
(ISG20) is an IFN-induced antiviral exonuclease with a
strong preference for single-stranded RNA and minor
activity towards single-stranded DNA. It was also
independently identified by its response to estrogen and
was called HEM45 (human estrogen regulated transcript).
ISG20 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. ISG20 may be a major effector of innate
immunity against pathogens including viruses, bacteria,
and parasites. It is located in promyelocytic leukemia
(PML) nuclear bodies, sites for oncogenic DNA viral
transcription and replication. It may carry out its
function by degrading viral RNAs as part of the
IFN-regulated antiviral response.
Length = 157
Score = 97.9 bits (244), Expect = 1e-25
Identities = 56/158 (35%), Positives = 85/158 (53%), Gaps = 16/158 (10%)
Query: 82 ALDTEMVYT---VHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYSGISAKDFIR- 137
A+D EMV T E+AR ++VN G ++Y+ ++P+ + DY T++SGI + +
Sbjct: 2 AIDCEMVGTGPGGRESELARCSIVNYHGDVLYDKYIRPEGPVTDYRTRWSGIRRQHLVNA 61
Query: 138 NPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALKLIHSN--IIDTS--VLFPHSFGLP 193
P+ Q +++ + K ++VGH + ND +ALK H DTS L G P
Sbjct: 62 TPFAV---AQKEILKIL-KGKVVVGHAIHNDFKALKYFHPKHMTRDTSTIPLLNRKAGFP 117
Query: 194 Y--RRSLKSIVSQLLHQSIQSGT--HDSFEDARACIDL 227
R SLK + +LLH+ IQ G H S EDARA ++L
Sbjct: 118 ENCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMEL 155
>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 = 94.0 bits (234), Expect = 4e-24
Identities = 43/163 (26%), Positives = 77/163 (47%), Gaps = 19/163 (11%)
Query: 81 YALDTEMVYT----VHGLEVARVTVVN-VDGRLIYNTLVKPDCEIIDYNTKYSGISAKDF 135
+D E +E+A V++V + +++T VKP+ I D T++ GI+
Sbjct: 1 VVIDCETTGLDPEKDEIIEIAAVSIVGGENIGPVFDTYVKPERLITDEATEFHGIT--PE 58
Query: 136 IRNPYKTLKDVQNDLMGFVSKDSIIVGH--------GLENDLRALKLIHS--NIIDTSVL 185
+ + ++V + F+ K I+VGH L +DLR LKL N + +++
Sbjct: 59 MLRNAPSFEEVLEAFLEFLKKLKILVGHNASFDVGFLLYDDLRFLKLPMPKLNDVIDTLI 118
Query: 186 FPHSFGLPY-RRSLKSIVSQLLHQSIQSGTHDSFEDARACIDL 227
+ + RRSL ++ +L + IQ H + +DARA +L
Sbjct: 119 LDKATYKGFKRRSLDALAEKLGLEKIQRA-HRALDDARATAEL 160
>gnl|CDD|99846 cd06143, PAN2_exo, DEDDh 3'-5' exonuclease domain of the eukaryotic
exoribonuclease PAN2. PAN2 is the catalytic subunit of
poly(A) nuclease (PAN), a Pab1p-dependent 3'-5'
exoribonuclease which plays an important role in the
posttranscriptional maturation of pre-mRNAs. PAN
catalyzes the deadenylation of poly(A) tails, which are
initially synthesized to default lengths of 70 to 90, to
mRNA-specific lengths of 55 to 71. Pab1p and PAN also
play a role in the export and decay of mRNA. PAN2
contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain
with 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.
Length = 174
Score = 86.1 bits (214), Expect = 5e-21
Identities = 51/148 (34%), Positives = 70/148 (47%), Gaps = 18/148 (12%)
Query: 96 VARVTVV----NVDGRLIYNTLVKPDCEIIDYNTKYSGISAKD----FIRNPYKTLKDVQ 147
+ARV+VV ++G + + ++DY T++SGI D TLK
Sbjct: 33 LARVSVVRGEGELEGVPFIDDYISTTEPVVDYLTRFSGIKPGDLDPKTSSKNLTTLKSAY 92
Query: 148 NDLMGFVSKDSIIVGHGLENDLRALKLI--HSNIIDTSVLFPHSFGLPYRR--SLKSIVS 203
L V I VGHGL D R + + +IDT LF LP +R SL+ +
Sbjct: 93 LKLRLLVDLGCIFVGHGLAKDFRVINIQVPKEQVIDTVELF----HLPGQRKLSLRFLAW 148
Query: 204 QLLHQSIQSGTHDSFEDARACIDLILWK 231
LL + IQS THDS EDAR L L++
Sbjct: 149 YLLGEKIQSETHDSIEDARTA--LKLYR 174
>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 = 60.0 bits (146), Expect = 2e-11
Identities = 37/164 (22%), Positives = 61/164 (37%), Gaps = 26/164 (15%)
Query: 82 ALDTEMVYTVHGLEVAR-----VTVVNVDGRLI----YNTLVKPDCEIIDYNTKYSGISA 132
DTE GL+ + + V VDG + + TLV P I T GI+
Sbjct: 2 VFDTET----TGLDPKKDRIIEIGAVKVDGGIEIVERFETLVNPGRPIPPEATAIHGITD 57
Query: 133 KDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRALK---------LIHSNIIDTS 183
+ P ++V + + F+ ++V H DLR L + + IDT
Sbjct: 58 EMLADAP--PFEEVLPEFLEFL-GGRVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTL 114
Query: 184 VLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARACIDL 227
L L ++++ ++ G H + DA A +L
Sbjct: 115 RLARRLLPGLRSHRLGLLLAERYGIPLE-GAHRALADALATAEL 157
>gnl|CDD|176653 cd06141, WRN_exo, DEDDy 3'-5' exonuclease domain of WRN and similar
proteins. WRN is a unique RecQ DNA helicase exhibiting
an exonuclease activity. 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. Mutations in the
WRN gene cause Werner syndrome, an autosomal recessive
disorder associated with premature aging and increased
susceptibility to cancer and type II diabetes. WRN
interacts with key proteins involved in DNA replication,
recombination, and repair. It is believed to maintain
genomic stability and life span by participating in DNA
processes. WRN is stimulated by Ku70/80, an important
regulator of genomic stability.
Length = 170
Score = 43.0 bits (102), Expect = 3e-05
Identities = 16/66 (24%), Positives = 26/66 (39%), Gaps = 5/66 (7%)
Query: 150 LMGFVSKDSII-VGHGLENDLRALKLIH----SNIIDTSVLFPHSFGLPYRRSLKSIVSQ 204
L + SI+ VG G++ D R L ++D S L SL +V +
Sbjct: 65 LKQLLEDPSILKVGVGIKGDARKLARDFGIEVRGVVDLSHLAKRVGPRRKLVSLARLVEE 124
Query: 205 LLHQSI 210
+L +
Sbjct: 125 VLGLPL 130
>gnl|CDD|223916 COG0847, DnaQ, DNA polymerase III, epsilon subunit and related
3'-5' exonucleases [DNA replication, recombination, and
repair].
Length = 243
Score = 42.1 bits (99), Expect = 1e-04
Identities = 34/153 (22%), Positives = 66/153 (43%), Gaps = 26/153 (16%)
Query: 94 LEVARVTVVNVDGRLI---YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDL 150
+E+ VT+ DGR++ ++TLV P+ I K GI+ + P +V +
Sbjct: 33 IEIGAVTLE--DGRIVERSFHTLVNPERPIPPEIFKIHGITDEMLADAP--KFAEVLPEF 88
Query: 151 MGFVSKDSIIVGH---------GLENDLRALKLIHSNIIDT----SVLFPHSFGLPYRRS 197
+ F+ ++V H +E++ +++ ++DT FP R S
Sbjct: 89 LDFIGGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGF----DRSS 144
Query: 198 LKSIVSQL-LHQSIQSGTHDSFEDARACIDLIL 229
L ++ +L + ++ H + DA A +L L
Sbjct: 145 LDALAERLGIDRNPF-HPHRALFDALALAELFL 176
>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 = 36.0 bits (84), Expect = 0.006
Identities = 34/144 (23%), Positives = 58/144 (40%), Gaps = 32/144 (22%)
Query: 99 VTVVNVDGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSK 156
+ V DG+++ + TL++P +N GI+ +D P T +V ++ F+
Sbjct: 21 LVKVR-DGQIVDTFYTLIRPPTRFDPFNIAIHGITPEDVADAP--TFPEVWPEIKPFLG- 76
Query: 157 DSIIVGHGLENDLRALK--LIHSNI-------IDTSVLFPHSFGLPYRRSLK-------S 200
S++V H D L+ L + + T L RR +
Sbjct: 77 GSLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVRL--------ARRVWPLLPNHKLN 128
Query: 201 IVSQLLHQSIQSGTHDSFEDARAC 224
V++ L + HD+ EDARAC
Sbjct: 129 TVAEHLGIELNH--HDALEDARAC 150
>gnl|CDD|180525 PRK06310, PRK06310, DNA polymerase III subunit epsilon; Validated.
Length = 250
Score = 34.8 bits (80), Expect = 0.023
Identities = 26/119 (21%), Positives = 42/119 (35%), Gaps = 25/119 (21%)
Query: 83 LDTEMVYTVHGLEVAR-----VTVVNVDGRLIYN---TLVKPDCEIIDYNTKYSGISAKD 134
LD E GL+V + + + + L+ P+ + + + IS
Sbjct: 12 LDCETT----GLDVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAM 67
Query: 135 FIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRAL-----------KLIHSNIIDT 182
P + +V + GF + IVGH + DL+ L H IIDT
Sbjct: 68 LRDKP--KIAEVFPQIKGFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDT 124
>gnl|CDD|180670 PRK06722, PRK06722, exonuclease; Provisional.
Length = 281
Score = 32.7 bits (74), Expect = 0.12
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 110 YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLEN 167
++ LVKP + + TK +GI+ KD I + + + F+ +DSI V G E+
Sbjct: 46 FSELVKPGARLTRHTTKLTGITKKDLIG--VEKFPQIIEKFIQFIGEDSIFVTWGKED 101
>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 = 32.4 bits (74), Expect = 0.22
Identities = 24/83 (28%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 94 LEVARVTVVNVDGRLI--YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLM 151
+E V V N GR+I + +KP + + T+ +GI+ +D + N +++V
Sbjct: 210 IEFGAVKVKN--GRIIDKFQFFIKPHEPLSAFVTELTGIT-QDMLENAP-EIEEVLEKFK 265
Query: 152 GFVSKDSIIVGHGLENDLRALKL 174
F KDSI+V H D+ L
Sbjct: 266 EFF-KDSILVAHNASFDIGFLNT 287
>gnl|CDD|185160 PRK15248, PRK15248, fimbrial outer membrane usher protein StbC;
Provisional.
Length = 853
Score = 31.4 bits (71), Expect = 0.45
Identities = 20/50 (40%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 91 VHGLEV--ARVTVVNVDGRLIYNTLVKPDCEIID--YNTKYSGISAKDFI 136
V G+ A V VV G++IY T V P ID YNT+Y G + I
Sbjct: 278 VRGVAASSAHV-VVKQLGKVIYETNVPPGPFYIDDLYNTRYQGDLEVEVI 326
>gnl|CDD|235864 PRK06807, PRK06807, DNA polymerase III subunit epsilon; Validated.
Length = 313
Score = 30.2 bits (68), Expect = 0.82
Identities = 29/124 (23%), Positives = 52/124 (41%), Gaps = 15/124 (12%)
Query: 110 YNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDL 169
+ + V P+ I D T +GI+ P T+++V + F+ + +IV H D+
Sbjct: 44 FVSYVNPERPIPDRITSLTGITNYRVSDAP--TIEEVLPLFLAFLHTN-VIVAHNASFDM 100
Query: 170 RALKL---------IHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFED 220
R LK + +IDT L L+++ L I+ +H++F+D
Sbjct: 101 RFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRML---GIRLSSHNAFDD 157
Query: 221 ARAC 224
C
Sbjct: 158 CITC 161
>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 = 29.6 bits (67), Expect = 0.84
Identities = 14/57 (24%), Positives = 20/57 (35%), Gaps = 7/57 (12%)
Query: 159 IIVGHGLENDLRALKLIH----SNIIDTSVLFPHSF-GLPYRRSLKSIVSQLLHQSI 210
VGH + DL L N+ DT + G P SL + + L +
Sbjct: 77 TKVGHNAKFDLEVLARDFGIKLENLFDTMLA--AYLLGYPRSHSLDDLAEKYLGVEL 131
>gnl|CDD|214681 smart00474, 35EXOc, 3'-5' exonuclease. 3\' -5' exonuclease
proofreading domain present in DNA polymerase I, Werner
syndrome helicase, RNase D and other enzymes.
Length = 172
Score = 29.6 bits (67), Expect = 0.84
Identities = 31/148 (20%), Positives = 43/148 (29%), Gaps = 34/148 (22%)
Query: 117 DCEIIDYNTKYSGISA--------KDFIRNPYKTLKDVQNDL-MGFVSKDSIIVGHGLEN 167
D E ++ + FI +P L D L + VGH +
Sbjct: 27 DTETTGLDSYSGKLVLIQISVTGEGAFIIDPLA-LGDDLEILKDLLEDETITKVGHNAKF 85
Query: 168 DLRALK---LIHSNIIDTSVLFPHSFGLPYRR--SLKSIVSQLL-------HQSIQSGTH 215
DL L + NI DT + L L +++ L Q G
Sbjct: 86 DLHVLARFGIELENIFDTMLA--AYLLLGGPSKHGLATLLLGYLGVELDKEEQKSDWGAR 143
Query: 216 DSFE--------DARACIDL--ILWKLL 233
E DA A + L L K L
Sbjct: 144 PLSEEQLEYAAEDADALLRLYEKLEKEL 171
>gnl|CDD|213331 cd05129, RasGAP_RAP6, Ras-GTPase Activating Domain of
Rab5-activating protein 6. Rab5-activating protein 6
(RAP6) is an endosomal protein with a role in the
regulation of receptor-mediated endocytosis. RAP6
contains a Vps9 domain, which is involved in the
activation of Rab5, and a Ras GAP domain (RGD). Rab5 is
a small GTPase required for the control of the endocytic
route, and its activity is regulated by guanine
nucleotide exchange factor, such as Rabex5, and GAPs,
such as RN-tre. Human Rap6 protein is localized on the
plasma membrane and on the endosome. RAP6 binds to Rab5
and Ras through the Vps9 and RGD domains, respectively.
Length = 365
Score = 30.0 bits (68), Expect = 1.1
Identities = 18/66 (27%), Positives = 26/66 (39%), Gaps = 9/66 (13%)
Query: 165 LENDLRAL-KLIHSNIIDTSVLFPHSFGLPYRRSLKSIVSQLLHQSIQSGTHDSFEDARA 223
+ L AL S++ + FP S L+ IV QL +SG + E
Sbjct: 171 FLSRLVALVNKFISSLRQSVYCFPQS--------LRWIVRQLRKILTRSGDDEEAEARAL 222
Query: 224 CIDLIL 229
C DL+
Sbjct: 223 CTDLLF 228
>gnl|CDD|237152 PRK12627, flgB, flagellar basal body rod protein FlgB;
Provisional.
Length = 128
Score = 28.5 bits (64), Expect = 1.7
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 44 SGLRISALDHVGGINGPLEGYVKTKPRKSPPPNGYGVYALDTEMV 88
+G+R + H+ G V T PNG V +L+ EM+
Sbjct: 55 TGMRATRPGHLNGAAAGAADPVVTDAGGPASPNGNSV-SLEEEML 98
>gnl|CDD|218187 pfam04637, Herpes_pp85, Herpesvirus phosphoprotein 85 (HHV6-7
U14/HCMV UL25). This family includes UL25 proteins from
HCMV, as well as U14 proteins from HHV 6 and HHV7. These
85 kD phosphoproteins appear to act as structural
antigens, but their precise function is otherwise
unknown.
Length = 502
Score = 28.9 bits (65), Expect = 3.0
Identities = 22/87 (25%), Positives = 37/87 (42%), Gaps = 8/87 (9%)
Query: 135 FIRNPYKTLKDVQNDLMGFVSKDSIIVGHGLENDLRAL-KLIH---SNIIDTSVLFPHSF 190
KT +DV NDL+ +S ++I H E LRAL K I +++ +
Sbjct: 207 TTIKRSKTPEDVLNDLLFLLSLGNMIYRHRRE--LRALRKWIVLQLNSLCEDLYFA--YT 262
Query: 191 GLPYRRSLKSIVSQLLHQSIQSGTHDS 217
+P R +++ + I S + D
Sbjct: 263 QVPETRETFLDLAREVANMISSNSPDD 289
>gnl|CDD|153138 cd06350, PBP1_GPCR_family_C_like, Ligand-binding domain of
membrane-bound glutamate receptors that mediate
excitatory transmission on the cellular surface through
initial binding of glutamate and are categorized into
ionotropic glutamate receptors (iGluRs) and metabotropic
glutamate receptors (mGluRs). Ligand-binding domain of
membrane-bound glutamate receptors that mediate
excitatory transmission on the cellular surface through
initial binding of glutamate and are categorized into
ionotropic glutamate receptors (iGluRs) and metabotropic
glutamate receptors (mGluRs). The metabotropic glutamate
receptors (mGluR) are key receptors in the modulation of
excitatory synaptic transmission in the central nervous
system. The mGluRs are coupled to G proteins and are
thus distinct from the iGluRs which internally contain
ligand-gated ion channels. The mGluR structure is
divided into three regions: the extracellular region,
the seven-spanning transmembrane region and the
cytoplasmic region. The extracellular region is further
devided into the ligand-binding domain (LBD) and the
cysteine-rich domain. The LBD has sequence similarity to
the LIVBP, which is a bacterial periplasmic protein
(PBP), as well as to the extracellular region of both
iGluR and the gamma-aminobutyric acid (GABA)b receptor.
iGluRs are divided into three main subtypes based on
pharmacological profile: NMDA, AMPA, and kainate
receptors. All family C GPCRs have a large extracellular
N terminus that contain a domain with homology to
bacterial periplasmic amino acid-binding proteins.
Length = 348
Score = 28.1 bits (63), Expect = 4.2
Identities = 26/134 (19%), Positives = 45/134 (33%), Gaps = 18/134 (13%)
Query: 98 RVTVVNVD---GRLIYNTLVKPDCEIIDYNTKYSGISAKDFIRNPYKTLKDVQNDLMGFV 154
V +V D GR + L + E+ I+ + I P T +D++ L
Sbjct: 162 WVGLVYSDDDYGRSGLSDLEE---ELEKNGIC---IAFVEAI-PPSSTEEDIKRILKKLK 214
Query: 155 SKDS-IIVGHGLENDLRAL--KLIHSNIIDTSVLFPHSFGLPYRRSLK-----SIVSQLL 206
S + +IV G E+D L + + + + L V
Sbjct: 215 SSTARVIVVFGDEDDALRLFCEAYKLGMTGKYWIISTDWDTSTCLLLFTLDAFQGVLGFS 274
Query: 207 HQSIQSGTHDSFED 220
+ +SG F+D
Sbjct: 275 GHAPRSGEIPGFKD 288
>gnl|CDD|238214 cd00354, FBPase, Fructose-1,6-bisphosphatase, an enzyme that
catalyzes the hydrolysis of fructose-1,6-biphosphate
into fructose-6-phosphate and is critical in
gluconeogenesis pathway. The alignment model also
includes chloroplastic FBPases and
sedoheptulose-1,7-biphosphatases that play a role in
pentose phosphate pathway (Calvin cycle).
Length = 315
Score = 27.9 bits (63), Expect = 4.2
Identities = 16/52 (30%), Positives = 22/52 (42%), Gaps = 4/52 (7%)
Query: 77 GYGVYALDTEMVYTVHGLEVARVTVVNVDGRLIYNTLVKPDCEIIDYNTKYS 128
GY +Y T +V T+ G V T+ G I L P+ +I YS
Sbjct: 147 GYALYGPSTMLVLTL-GQGVHGFTLDPSLGEFI---LTHPNVKIPKKGKIYS 194
>gnl|CDD|131530 TIGR02477, PFKA_PPi, diphosphate--fructose-6-phosphate
1-phosphotransferase. Diphosphate--fructose-6-phosphate
1-phosphotransferase catalyzes the addition of phosphate
from diphosphate (PPi) to fructose 6-phosphate to give
fructose 1,6-bisphosphate (EC 2.7.1.90). The enzyme is
also known as pyrophosphate-dependent
phosphofructokinase. The usage of PPi-dependent enzymes
in glycolysis presumably frees up ATP for other
processes. TIGR02482 represents the ATP-dependent
6-phosphofructokinase enzyme contained within Pfam
pfam00365: Phosphofructokinase. This model hits
primarily bacterial, plant alpha, and plant beta
sequences [Energy metabolism,
Glycolysis/gluconeogenesis].
Length = 539
Score = 27.7 bits (62), Expect = 6.8
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 185 LFPHSFGLPYRRSLKSIVSQLLHQSIQSG 213
LFP+++GLP S HQ ++ G
Sbjct: 43 LFPNTYGLPIITFEPGEASPDEHQPLKIG 71
>gnl|CDD|216001 pfam00577, Usher, Type VII secretion system (T7SS), usher protein.
The chaperone-usher (CU) pathway or Type VII secretion
system (T7SS) in Gram-negative (diderm) bacteria is
responsible for the secretion and assembly of prepilins
for fimbriae biogenesis, the prototypical Type 1 pili.
Following the prepilins export to the periplasm by the
Sec translocon, the biogenesis of fimbriae requires a
two-component assembly and transport system which is
composed of a periplasmic chaperone and an outer
membrane protein, which has been termed a molecular
'usher'. The usher protein is rather large (from 86 to
100 Kd) and seems to be mainly composed of
membrane-spanning beta-sheets, a structure reminiscent
of porins. Although the degree of sequence similarity of
these proteins is not very high they share a number of
characteristics. One of these is the presence of two
pairs of cysteines, the first one located in the
N-terminal part and the second at the C-terminal
extremity that are probably involved in disulphide
bonds. The best conserved region is located in the
central part of these proteins.
Length = 552
Score = 27.6 bits (62), Expect = 6.8
Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 3/35 (8%)
Query: 97 ARVTVVNVDGRLIYNTLVKPDC-EIID-YNTKYSG 129
ARVTV +G +IY T V P EI D Y + G
Sbjct: 99 ARVTVRQ-NGYVIYQTTVPPGPFEITDLYPSGSGG 132
>gnl|CDD|224520 COG1604, COG1604, CRISPR system related protein, RAMP superfamily
[Defense mechanisms].
Length = 257
Score = 27.0 bits (60), Expect = 8.5
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 2/54 (3%)
Query: 177 SNIIDTSVLFPHSFGLPY--RRSLKSIVSQLLHQSIQSGTHDSFEDARACIDLI 228
+I +T + +GLPY +K IV + + D E + +I
Sbjct: 93 PSIFETGLTLDPIYGLPYIPGSEIKGIVRSYFFEVLGEEDRDKVESGKEYHLVI 146
>gnl|CDD|235668 PRK06007, fliF, flagellar MS-ring protein; Reviewed.
Length = 542
Score = 27.2 bits (61), Expect = 9.1
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 91 VHGLEVARVTVVNVDGRLI 109
V GL+ VT+V+ +GRL+
Sbjct: 202 VPGLKPENVTIVDQNGRLL 220
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.138 0.411
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: 12,287,199
Number of extensions: 1146066
Number of successful extensions: 1040
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1012
Number of HSP's successfully gapped: 43
Length of query: 240
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 146
Effective length of database: 6,768,326
Effective search space: 988175596
Effective search space used: 988175596
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)