RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14558
(136 letters)
>gnl|CDD|197313 cd09079, RgfB-like, Streptococcus agalactiae RgfB, part of a
putative two component signal transduction system, and
related proteins. This family includes Streptococcus
agalactiae RgfB (for regulator of fibrinogen binding)
and related proteins. The function of RgfB is unknown.
It is part of a putative two component signal
transduction system designated rgfBDAC (the rgf locus
was identified in a screen for mutants of Streptococcus
agalactiae with altered binding to fibrinogen).
RgfA,-C,and -D do not belong to this superfamily: rgfA
encodes a putative response regulator, and rgfC, a
putative histidine kinase. All four genes are
co-transcribed, and may be involved in regulating
expression of bacterial cell surface components. This
family belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 259
Score = 64.6 bits (158), Expect = 2e-13
Identities = 28/132 (21%), Positives = 51/132 (38%), Gaps = 17/132 (12%)
Query: 7 KDRDIRIRAIAAELACNKYDIVCLQEVWKNDDFEL----IKSVVFEALPYAHYFYSGVMG 62
+++ ++ +A +A YD++ LQEV ++ D + IK F L Y G
Sbjct: 12 ENQKEKLERLAKIIAEEDYDVIALQEVNQSIDAPVSQVPIKEDNFALLLYEKLRELGATY 71
Query: 63 SGVCILSRYEITEVLFHQWQLNGYIHKIFHADWFGGKGV-----GLCQVL-----VNGFR 112
ILS + L+ D++ K ++L +NG
Sbjct: 72 YWTWILSHIGYDKYDEGLAILSKRPIAEVE-DFYVSKSQDYTDYKSRKILGATIEINGQP 130
Query: 113 LNVYTTHVSISW 124
++VY+ H + W
Sbjct: 131 IDVYSCH--LGW 140
>gnl|CDD|197312 cd09078, nSMase, Neutral sphingomyelinases (nSMase) catalyze the
hydrolysis of sphingomyelin in biological membranes to
ceramide and phosphorylcholine. Sphingomyelinases
(SMase) are phosphodiesterases that catalyze the
hydrolysis of sphingomyelin to ceramide and
phosphorylcholine. Eukaryotic SMases have been
classified according to their pH optima and are known as
acid SMase, alkaline SMase, and neutral SMase (nSMase).
Eukaryotic proteins in this family are nSMases, and are
activated by a variety of stress-inducing agents such as
cytokines or UV radiation. Ceramides and other metabolic
derivatives, including sphingosine, are lipid "second
messenger" molecules that participate in the regulation
of stress-induced cellular responses, including cell
death, adhesion, differentiation, and proliferation.
Bacterial neutral SMases, which also belong to this
domain family, are secreted proteins that act as
membrane-damaging virulence factors. They promote
colonization of the host tissue. This family belongs to
the large EEP (exonuclease/endonuclease/phosphatase)
superfamily that contains functionally diverse enzymes
that share a common catalytic mechanism of cleaving
phosphodiester bonds.
Length = 280
Score = 57.4 bits (139), Expect = 8e-11
Identities = 35/132 (26%), Positives = 50/132 (37%), Gaps = 31/132 (23%)
Query: 4 KVSKDRDIRIRAIAAELACNKYDIVCLQEVWKNDDFELIKSVVFEALPYAHYFY------ 57
+D R+ I L +YD+V LQEV+ D K ++ Y
Sbjct: 18 NGDDGQDERLDLIPKALL--QYDVVVLQEVF---DARARKRLLNGLKKEYPYQTDVVGRS 72
Query: 58 -----SGVMGSGVCILSRYEITEVLFHQWQLNGYIHKIFH----ADWFGGKGVGLCQVLV 108
S ++ GV ILSRY I E + IF AD KGV ++
Sbjct: 73 PSGWSSKLVDGGVVILSRYPIVEKDQY----------IFPNGCGADCLAAKGVLYAKINK 122
Query: 109 NGFR-LNVYTTH 119
G + +V+ TH
Sbjct: 123 GGTKVYHVFGTH 134
>gnl|CDD|223780 COG0708, XthA, Exonuclease III [DNA replication, recombination,
and repair].
Length = 261
Score = 48.0 bits (115), Expect = 2e-07
Identities = 25/69 (36%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 12 RIRAIAAELACNKYDIVCLQEVWKNDDFELIKSVVFEALPYAHYFYSGVMG-SGVCILSR 70
R++ + L + D++CLQE K D E EAL Y H F G G SGV ILS+
Sbjct: 14 RLKKLLDWLEEEQPDVLCLQET-KAQD-EQFPREELEALGYHHVFNHGQKGYSGVAILSK 71
Query: 71 YEITEVLFH 79
+V
Sbjct: 72 KPPDDVRRG 80
>gnl|CDD|197318 cd09084, EEP-2, Exonuclease-Endonuclease-Phosphatase (EEP) domain
superfamily; uncharacterized family 2. This family of
uncharacterized proteins belongs to a superfamily that
includes the catalytic domain
(exonuclease/endonuclease/phosphatase, EEP, domain) of
a diverse set of proteins including the ExoIII family
of apurinic/apyrimidinic (AP) endonucleases, inositol
polyphosphate 5-phosphatases (INPP5), neutral
sphingomyelinases (nSMases), deadenylases (such as the
vertebrate circadian-clock regulated nocturnin),
bacterial cytolethal distending toxin B (CdtB),
deoxyribonuclease 1 (DNase1), the endonuclease domain
of the non-LTR retrotransposon LINE-1, and related
domains. These diverse enzymes share a common catalytic
mechanism of cleaving phosphodiester bonds; their
substrates range from nucleic acids to phospholipids
and perhaps, proteins.
Length = 246
Score = 41.5 bits (98), Expect = 4e-05
Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 2/63 (3%)
Query: 13 IRAIAAELACNKYDIVCLQEVWKNDDFELIKS-VVFEALPYAHYFYSGVM-GSGVCILSR 70
I + DI+CLQE + ++ + ++ + PY + Y G+G+ I S+
Sbjct: 18 PDKILDFIKKQDPDILCLQEYYGSEGDKDDDLRLLLKGYPYYYVVYKSDSGGTGLAIFSK 77
Query: 71 YEI 73
Y I
Sbjct: 78 YPI 80
>gnl|CDD|197320 cd09086, ExoIII-like_AP-endo, Escherichia coli exonuclease III
(ExoIII) and Neisseria meningitides NExo-like subfamily
of the ExoIII family purinic/apyrimidinic (AP)
endonucleases. This subfamily includes Escherichia
coli ExoIII, Neisseria meningitides NExo,and related
proteins. These are ExoIII family AP endonucleases and
they belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different
AP endonuclease enzymes catalyze the different
reactions with different efficiencies. Many organisms
have two AP endonucleases, usually one is the dominant
AP endonuclease, the other has weak AP endonuclease
activity. For example, Neisseria meningitides Nape and
NExo, and exonuclease III (ExoIII) and endonuclease IV
(EndoIV) in Escherichia coli. NExo and ExoIII are
found in this subfamily. NExo is the non-dominant AP
endonuclease. It exhibits strong 3'-5' exonuclease and
3'-deoxyribose phosphodiesterase activities.
Escherichia coli ExoIII is an active AP endonuclease,
and in addition, it exhibits double strand
(ds)-specific 3'-5' exonuclease, exonucleolytic RNase
H, 3'-phosphomonoesterase and 3'-phosphodiesterase
activities, all catalyzed by a single active site.
Class II AP endonucleases have been classified into two
families, designated ExoIII and EndoIV, based on their
homology to the Escherichia coli enzymes ExoIII and
endonuclease IV (EndoIV). This subfamily belongs to the
ExoIII family; the EndoIV family belongs to a different
superfamily.
Length = 254
Score = 40.6 bits (96), Expect = 6e-05
Identities = 26/72 (36%), Positives = 33/72 (45%), Gaps = 12/72 (16%)
Query: 11 IRIRA--IAAELACNKYDIVCLQEVWK--NDDFELIKSVVFEALPYAHYFYSGVMGS--G 64
IR R + L D++CLQE K +D F FEAL Y H G + G
Sbjct: 11 IRARLEQVLDWLKEEDPDVLCLQET-KVEDDQFPA---DAFEALGY-HVAVHG-QKAYNG 64
Query: 65 VCILSRYEITEV 76
V ILSR + +V
Sbjct: 65 VAILSRLPLEDV 76
>gnl|CDD|233064 TIGR00633, xth, exodeoxyribonuclease III (xth). All proteins in
this family for which functions are known are 5' AP
endonucleases that funciton in base excision repair and
the repair of abasic sites in DNA.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 = 255
Score = 33.0 bits (76), Expect = 0.030
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 23 NKYDIVCLQEVWKNDDFELIKSVVFEALPYAHYFYSGVMG-SGVCILSRYEITEVLF 78
+ D++CLQE K D + + E + + + G SGV ILS+ E +V +
Sbjct: 26 EQPDVLCLQET-KVADEQFPAELFEELGYHVFFHGAKSKGYSGVAILSKVEPLDVRY 81
>gnl|CDD|197336 cd10281, Nape_like_AP-endo, Neisseria meningitides Nape-like
subfamily of the ExoIII family purinic/apyrimidinic
(AP) endonucleases. This subfamily includes Neisseria
meningitides Nape and related proteins. These are
Escherichia coli exonuclease III (ExoIII)-like AP
endonucleases and belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different
AP endonuclease enzymes catalyze the different
reactions with different efficiences. Many organisms
have two AP endonucleases, usually one is the dominant
AP endonuclease, the other has weak AP endonuclease
activity; for example, Neisseria meningitides Nape and
NExo. Nape, found in this subfamily, is the dominant AP
endonuclease. It exhibits strong AP endonuclease
activity, and also exhibits 3'-5'exonuclease and
3'-deoxyribose phosphodiesterase activities.
Length = 253
Score = 32.6 bits (75), Expect = 0.035
Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 26 DIVCLQEVWKNDDFELIKSVVFEALPY-AHYFYSGVMG-SGVCILSRYEITEV 76
D+VCLQEV + + +L FE Y A++F + G +GV I SR + V
Sbjct: 29 DVVCLQEV-RAQEEQLDDD-FFEPEGYNAYFFDAEKKGYAGVAIYSRTQPKAV 79
>gnl|CDD|217520 pfam03372, Exo_endo_phos, Endonuclease/Exonuclease/phosphatase
family. This large family of proteins includes
magnesium dependent endonucleases and a large number of
phosphatases involved in intracellular signalling. This
family includes: AP endonuclease proteins EC:4.2.99.18,
DNase I proteins EC:3.1.21.1, Synaptojanin an
inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56,
Sphingomyelinase EC:3.1.4.12 and Nocturnin.
Length = 143
Score = 32.3 bits (73), Expect = 0.038
Identities = 20/110 (18%), Positives = 31/110 (28%), Gaps = 38/110 (34%)
Query: 12 RIRAIAAELACNKYDIVCLQEVWKNDDFELIKSVVFEALPYAHYFYSGVMGSGVCILSRY 71
+ A+A L D++ LQ ILSRY
Sbjct: 11 GLAALADLLRAQDPDVLALQ----------------------------------AILSRY 36
Query: 72 EITEVLFHQWQLNGYIHKIFHADWFGGKGVGLCQVLVNGFRLNVYTTHVS 121
+ E + + G G G+ V V+G L + H+
Sbjct: 37 PLEEKIVLDFTELGAGGIAVLRLSSGAHGI----VKVSGQTLTLVNVHLP 82
>gnl|CDD|188032 TIGR00195, exoDNase_III, exodeoxyribonuclease III. The model
brings in reverse transcriptases at scores below 50,
model also contains eukaryotic apurinic/apyrimidinic
endonucleases which group in the same family [DNA
metabolism, DNA replication, recombination, and
repair].
Length = 254
Score = 32.4 bits (74), Expect = 0.050
Identities = 25/75 (33%), Positives = 30/75 (40%), Gaps = 18/75 (24%)
Query: 12 RIRAIAAELACNKYDIVCLQEVWKNDDFELIKSVVFEALPYA-------HYFYSGVMG-S 63
R A L N+ D++CLQE K V E P H F+SG G S
Sbjct: 14 RPHKGLAWLKENQPDVLCLQE---------TK-VQDEQFPLEPFHKEGYHVFFSGQKGYS 63
Query: 64 GVCILSRYEITEVLF 78
GV I S+ E V
Sbjct: 64 GVAIFSKEEPISVRR 78
>gnl|CDD|197307 cd09073, ExoIII_AP-endo, Escherichia coli exonuclease III
(ExoIII)-like apurinic/apyrimidinic (AP) endonucleases.
The ExoIII family AP endonucleases belong to the large
EEP (exonuclease/endonuclease/phosphatase) superfamily
that contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, which is
then followed by the coordinated actions of DNA
polymerase, deoxyribose phosphatase, and DNA ligase. If
left unrepaired, AP sites block DNA replication, which
have both mutagenic and cytotoxic effects. AP
endonucleases can carry out a wide range of excision
and incision reactions on DNA, including 3'-5'
exonuclease, 3'-deoxyribose phosphodiesterase,
3'-phosphatase, and occasionally, nonspecific DNase
activities. Different AP endonuclease enzymes catalyze
the different reactions with different efficiences.
Many organisms have two functional AP endonucleases,
for example, APE1/Ref-1 and Ape2 in humans, Apn1 and
Apn2 in bakers yeast, Nape and NExo in Neisseria
meningitides, and exonuclease III (ExoIII) and
endonuclease IV (EndoIV) in Escherichia coli. Usually,
one of the two is the dominant AP endonuclease, the
other has weak AP endonuclease activity, but exhibits
strong 3'-5' exonuclease, 3'-deoxyribose
phosphodiesterase, and 3'-phosphatase activities. Class
II AP endonucleases have been classified into two
families, designated ExoIII and EndoIV, based on their
homology to the Escherichia coli enzymes. This family
contains the ExoIII family; the EndoIV family belongs
to a different superfamily.
Length = 251
Score = 31.5 bits (72), Expect = 0.10
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 20 LACNKYDIVCLQEVWKNDDFELIKSVVFEALPYAHYFYSGVMG---SGVCILSR 70
L K DI+CLQE K D+ +L + + + H ++S SGV LS+
Sbjct: 22 LKEEKPDILCLQET-KADEDKLPEELQ--HVEGYHSYWSPARKKGYSGVATLSK 72
>gnl|CDD|226098 COG3568, ElsH, Metal-dependent hydrolase [General function
prediction only].
Length = 259
Score = 31.2 bits (71), Expect = 0.12
Identities = 31/128 (24%), Positives = 45/128 (35%), Gaps = 31/128 (24%)
Query: 12 RIRAIAAELACNKYDIVCLQEVWKNDDFELIKSVVFEALPY-------AHYFYSGVMG-- 62
RI + E+ DIV LQEV D LP+ A Y++SG
Sbjct: 32 RIAEVIREVG---ADIVALQEV---DGAFGRHRDGLLDLPHLLGRLGLAPYWWSGAAFGA 85
Query: 63 ------SGVCILSRYEITEVLFHQWQLNGYIHKIFHADWFGGKGVGLCQVLVNGFR-LNV 115
G ILSR I +V + +G L ++ + G + L V
Sbjct: 86 VYGEGQHGNAILSRLPIRDVENLALPDPTGLE---------PRGALLAEIELPGGKPLRV 136
Query: 116 YTTHVSIS 123
H+ +S
Sbjct: 137 INAHLGLS 144
>gnl|CDD|224133 COG1212, KdsB, CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell
envelope biogenesis, outer membrane].
Length = 247
Score = 29.9 bits (68), Expect = 0.29
Identities = 16/49 (32%), Positives = 21/49 (42%), Gaps = 7/49 (14%)
Query: 13 IRAIAAELACNKYDIVCLQEVWKNDDFELIKS-----VVFEALPYAHYF 56
IRA+A L + D+ L K D E + VV + YA YF
Sbjct: 110 IRAVAENLENSNADMATL--AVKITDEEEAFNPNVVKVVLDKEGYALYF 156
>gnl|CDD|197306 cd08372, EEP, Exonuclease-Endonuclease-Phosphatase (EEP) domain
superfamily. This large superfamily includes the
catalytic domain (exonuclease/endonuclease/phosphatase
or EEP domain) of a diverse set of proteins including
the ExoIII family of apurinic/apyrimidinic (AP)
endonucleases, inositol polyphosphate 5-phosphatases
(INPP5), neutral sphingomyelinases (nSMases),
deadenylases (such as the vertebrate circadian-clock
regulated nocturnin), bacterial cytolethal distending
toxin B (CdtB), deoxyribonuclease 1 (DNase1), the
endonuclease domain of the non-LTR retrotransposon
LINE-1, and related domains. These diverse enzymes
share a common catalytic mechanism of cleaving
phosphodiester bonds; their substrates range from
nucleic acids to phospholipids and perhaps proteins.
Length = 241
Score = 29.8 bits (67), Expect = 0.41
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 6/51 (11%)
Query: 24 KYDIVCLQEVWKNDDFELIKSVVFEALPYAHYFYSGV----MGSGVCILSR 70
DIVCLQEV + + + H + SG GV ILS+
Sbjct: 26 DPDIVCLQEVKDSQYSAVALN--QLLPEGYHQYQSGPSRKEGYEGVAILSK 74
>gnl|CDD|132436 TIGR03395, sphingomy, sphingomyelin phosphodiesterase. Members of
this family are bacterial proteins that act as
sphingomyelin phosphodiesterase (EC 3.1.4.12), also
called sphingomyelinase. Some members of this family
have been shown to act as hemolysins [Cellular
processes, Pathogenesis].
Length = 283
Score = 29.4 bits (66), Expect = 0.49
Identities = 27/125 (21%), Positives = 46/125 (36%), Gaps = 22/125 (17%)
Query: 12 RIRAIAAELACNKYDIVCLQEVWKNDDFELIKSVVFEALPY----------------AHY 55
R IA+ D+V L E + + + + E PY +Y
Sbjct: 24 RADLIASADYIKNQDVVILNEAFDTSASKRLLDNLREEYPYQTDVIGRSKKGWDKTLGNY 83
Query: 56 FYSGVMGSGVCILSRYEITEVLFHQWQLNGYIHKIFHADWFGGKGVGLCQVLVNGFRLNV 115
S + GV I+S++ I E + + + AD KG ++ NG + +V
Sbjct: 84 SSSALEDGGVAIVSKWPIEEKIQYIFNKGC------GADNLSNKGFAYVKINKNGKKFHV 137
Query: 116 YTTHV 120
TH+
Sbjct: 138 IGTHL 142
>gnl|CDD|197314 cd09080, TDP2, Phosphodiesterase domain of human TDP2, a
5'-tyrosyl DNA phosphodiesterase, and related domains.
Human TDP2, also known as TTRAP (TRAF/TNFR-associated
factors, and tumor necrosis factor
receptor/TNFR-associated protein), is a 5'-tyrosyl DNA
phosphodiesterase. It is required for the efficient
repair of topoisomerase II-induced DNA double strand
breaks. The topoisomerase is covalently linked by a
phosphotyrosyl bond to the 5'-terminus of the break.
TDP2 cleaves the DNA 5'-phosphodiester bond and
restores 5'-phosphate termini, needed for subsequent
DNA ligation, and hence repair of the break. TDP2 and
3'-tyrosyl DNA phosphodiesterase (TDP1) are
complementary activities; together, they allow cells to
remove trapped topoisomerase from both 3'- and 5'-DNA
termini. TTRAP has been reported as being involved in
apoptosis, embryonic development, and transcriptional
regulation, and it may inhibit the activation of
nuclear factor-kB. This family belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 248
Score = 29.2 bits (66), Expect = 0.55
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 10 DIRIRAIAAELACNKYDIVCLQEV 33
R+RAI L D++ LQEV
Sbjct: 17 AERMRAILKLLEELDPDVIFLQEV 40
>gnl|CDD|197330 cd09096, Deadenylase_nocturnin, C-terminal deadenylase domain of
nocturnin and related domains. This subfamily contains
the C-terminal catalytic domain of the deadenylase,
nocturnin, and related domains. Nocturnin is a
poly(A)-specific 3' exonuclease that specifically
degrades the 3' poly(A) tail of RNA in a process known
as deadenylation. This nuclease activity is manganese
dependent. Nocturnin is expressed in the cytoplasm of
Xenopus laevis retinal photoreceptor cells in a
rhythmic fashion, and it has been proposed that it
participates in posttranscriptional regulation of the
circadian clock or its outputs, and that the mRNA
target(s) of this deadenylase are circadian
clock-related. In mouse, the nocturnin gene, mNoc, is
expressed in a circadian pattern in a range of tissues
including retina, spleen, heart, kidney, and liver. It
is highly expressed in bone-marrow stromal cells,
adipocytes and hepatocytes. In mammals, nocturnin plays
a role in regulating mesenchymal stem-cell lineage
allocation, perhaps through regulating PPAR-gamma
(peroxisome proliferator-activated receptor-gamma)
nuclear translocation. This subfamily belongs to the
large EEP (exonuclease/endonuclease/phosphatase)
superfamily that contains functionally diverse enzymes
that share a common catalytic mechanism of cleaving
phosphodiester bonds.
Length = 280
Score = 28.5 bits (64), Expect = 0.85
Identities = 14/48 (29%), Positives = 21/48 (43%), Gaps = 3/48 (6%)
Query: 10 DIRIRAIAAELACNKYDIVCLQEVWKNDDFELIKSVVFEALPYAHYFY 57
+ R I E+ DI+CLQEV D ++ + L Y F+
Sbjct: 30 EERKYLILEEILTYDPDILCLQEV---DHYKDTLQPLLSRLGYQGTFF 74
>gnl|CDD|197321 cd09087, Ape1-like_AP-endo, Human Ape1-like subfamily of the
ExoIII family purinic/apyrimidinic (AP) endonucleases.
This subfamily includes human Ape1 (also known as Apex,
Hap1, or Ref-1) and related proteins. These are
Escherichia coli exonuclease III (ExoIII)-like AP
endonucleases and they belong to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. AP endonucleases participate in the DNA base
excision repair (BER) pathway. AP sites are one of the
most common lesions in cellular DNA. During BER, the
damaged DNA is first recognized by DNA glycosylase. AP
endonucleases then catalyze the hydrolytic cleavage of
the phosphodiester bond 5' to the AP site, and this is
followed by the coordinated actions of DNA polymerase,
deoxyribose phosphatase, and DNA ligase. If left
unrepaired, AP sites block DNA replication, and have
both mutagenic and cytotoxic effects. AP endonucleases
can carry out a variety of excision and incision
reactions on DNA, including 3'-5' exonuclease,
3'-deoxyribose phosphodiesterase, 3'-phosphatase, and
occasionally, nonspecific DNase activities. Different
AP endonuclease enzymes catalyze the different
reactions with different efficiences. Many organisms
have two AP endonucleases, usually one is the dominant
AP endonuclease, the other has weak AP endonuclease
activity; for example, Ape1 and Ape2 in humans. Ape1 is
found in this subfamily, it exhibits strong
AP-endonuclease activity but shows weak 3'-5'
exonuclease and 3'-phosphodiesterase activities. Class
II AP endonucleases have been classified into two
families, designated ExoIII and EndoIV, based on their
homology to the Escherichia coli enzymes exonuclease
III (ExoIII) and endonuclease IV (EndoIV). This
subfamily belongs to the ExoIII family; the EndoIV
family belongs to a different superfamily.
Length = 253
Score = 27.9 bits (63), Expect = 1.7
Identities = 14/55 (25%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 26 DIVCLQEVW-KNDDFELIKSVVFEALPYAHYFYSGVMG-SGVCILSRYEITEVLF 78
DI+CLQE + D + + + ++ + G SG ILS+ + V +
Sbjct: 29 DILCLQETKLQEGDVPKELKELLKG-YHQYWNAAEKKGYSGTAILSKKKPLSVTY 82
>gnl|CDD|178689 PLN03144, PLN03144, Carbon catabolite repressor protein 4 homolog;
Provisional.
Length = 606
Score = 27.8 bits (62), Expect = 2.2
Identities = 10/15 (66%), Positives = 13/15 (86%), Gaps = 1/15 (6%)
Query: 26 DIVCLQEVWKNDDFE 40
DI+CLQEV ++D FE
Sbjct: 300 DILCLQEV-QSDHFE 313
>gnl|CDD|132487 TIGR03446, mycothiol_Mca, mycothiol conjugate amidase Mca.
Mycobacterium tuberculosis, Corynebacterium glutamicum,
and related species use the thiol mycothiol in place of
glutathione. This enzyme, homologous to the
(dispensible) MshB enzyme of mycothiol biosynthesis, is
described as an amidase that acts on conjugates to
mycothiol. It is a detoxification enzyme [Cellular
processes, Detoxification].
Length = 283
Score = 27.4 bits (61), Expect = 2.7
Identities = 8/21 (38%), Positives = 14/21 (66%)
Query: 31 QEVWKNDDFELIKSVVFEALP 51
+ +W ++FEL +S V +LP
Sbjct: 255 RRLWPTEEFELARSRVPTSLP 275
>gnl|CDD|216204 pfam00933, Glyco_hydro_3, Glycosyl hydrolase family 3 N terminal
domain.
Length = 296
Score = 27.3 bits (61), Expect = 2.8
Identities = 14/48 (29%), Positives = 24/48 (50%), Gaps = 5/48 (10%)
Query: 57 YSGVMGSGVCILSRYEITEVLFHQWQLNGYIHKIFHADWFGGKGVGLC 104
Y+ V GS C + Y +T +L +W +G++ +DW G G+
Sbjct: 200 YNKVNGSPAC-GNSYLLTGLLREEWGFDGFV----VSDWLGMNGIADH 242
>gnl|CDD|233680 TIGR02001, gcw_chp, conserved hypothetical protein,
proteobacterial. This model represents a conserved
hypothetical protein about 240 residues in length found
so far in Proteobacteria including Shewanella
oneidensis, Ralstonia solanacearum, and Colwellia
psychrerythraea, usually as part of a paralogous family.
The function is unknown.
Length = 243
Score = 27.0 bits (60), Expect = 2.9
Identities = 19/79 (24%), Positives = 26/79 (32%), Gaps = 13/79 (16%)
Query: 52 YAHYFYSGVMGSGVCILSRYEITEVLFHQWQLNGYIHKIFHADWFGGKGVGLCQV----- 106
+Y Y G GS Y ++ + GY + + D FGG G
Sbjct: 110 LLYYSYPGASGSDYSYTELY--GKISY-LGSRLGYSLAVNYDDDFGGSGADGGYYAFDAD 166
Query: 107 --LVNGFRLNVYTTHVSIS 123
L G L+ HV S
Sbjct: 167 FTLKEGHTLS---LHVGYS 182
>gnl|CDD|225261 COG2388, COG2388, Predicted acetyltransferase [General function
prediction only].
Length = 99
Score = 26.2 bits (58), Expect = 3.6
Identities = 10/40 (25%), Positives = 14/40 (35%), Gaps = 10/40 (25%)
Query: 94 DWFGGKGVG--LCQVLVNGFRLNVYTTHVSISWVIIPLCP 131
D G+G+ L + + R IIPLC
Sbjct: 49 DELRGQGIAQKLVEKALEEAREAGLK--------IIPLCS 80
>gnl|CDD|235473 PRK05450, PRK05450, 3-deoxy-manno-octulosonate
cytidylyltransferase; Provisional.
Length = 245
Score = 26.6 bits (60), Expect = 4.2
Identities = 14/49 (28%), Positives = 19/49 (38%), Gaps = 7/49 (14%)
Query: 13 IRAIAAELACNKYDIVCLQEVWKNDDFELIKS-----VVFEALPYAHYF 56
I +A LA + D+ L D E + VV +A A YF
Sbjct: 109 IDQVAEPLANPEADMATL--AVPIHDAEEAFNPNVVKVVLDADGRALYF 155
>gnl|CDD|222860 PHA02536, Q, portal vertex protein; Provisional.
Length = 346
Score = 26.6 bits (59), Expect = 4.5
Identities = 10/36 (27%), Positives = 19/36 (52%)
Query: 27 IVCLQEVWKNDDFELIKSVVFEALPYAHYFYSGVMG 62
++ + EV D+F IK++ + + AH +MG
Sbjct: 254 LIPVSEVATKDEFFNIKNISADDVLAAHRVPPQLMG 289
>gnl|CDD|217238 pfam02811, PHP, PHP domain. The PHP (Polymerase and Histidinol
Phosphatase) domain is a putative phosphoesterase
domain.
Length = 174
Score = 26.4 bits (58), Expect = 4.7
Identities = 16/93 (17%), Positives = 24/93 (25%), Gaps = 6/93 (6%)
Query: 8 DRDIRIRAIAAELACNKY----DIVCLQEVWKNDDFELIKSVVFEALPYAHYFYSGVMG- 62
D D A A K + E+ DD + + V G
Sbjct: 37 DHDNLFGAPEFYEAAKKKRAGLKPIIGVEINIVDDEDEKDLDEDDLNKSLDLVLLSVHGY 96
Query: 63 SGVCIL-SRYEITEVLFHQWQLNGYIHKIFHAD 94
+ L S + L G I + H +
Sbjct: 97 RNLPELSSAAYTEDELLEAVLEEGLIIILAHPE 129
>gnl|CDD|233186 TIGR00920, 2A060605, 3-hydroxy-3-methylglutaryl-coenzyme A
reductase. [Transport and binding proteins,
Carbohydrates, organic alcohols, and acids].
Length = 889
Score = 26.4 bits (58), Expect = 6.3
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 48 EALPYAHYFYSGVMGS 63
+ LPY +Y YS VMG+
Sbjct: 510 QNLPYKNYDYSLVMGA 525
>gnl|CDD|227564 COG5239, CCR4, mRNA deadenylase, exonuclease subunit and related
nucleases [RNA processing and modification].
Length = 378
Score = 26.3 bits (58), Expect = 6.3
Identities = 16/48 (33%), Positives = 19/48 (39%), Gaps = 1/48 (2%)
Query: 12 RIRAIAAELACNKYDIVCLQEVWKNDDFELIKSVVFEALPYAHYFYSG 59
R R + EL DI+CLQEV D + K L Y F
Sbjct: 61 RSRLLLQELLYYNADILCLQEVDAEDFEDFWKD-QLGKLGYDGIFIPK 107
>gnl|CDD|197331 cd09097, Deadenylase_CCR4, C-terminal deadenylase domain of CCR4
and related domains. This subfamily contains the
C-terminal catalytic domain of the deadenylases,
Saccharomyces cerevisiae Ccr4p and two vertebrate
homologs (CCR4a and CCR4b), and related domains. CCR4
belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds. CCR4 is the major deadenylase subunit of the
CCR4-NOT transcription complex, which contains two
deadenylase subunits and several noncatalytic subunits.
The other deadenylase subunit, Caf1 (called Pop2 in
yeast), is a DEDD-type protein and does not belong in
this superfamily. Saccharomyces cerevisiae CCR4 (or
Ccr4p) is a 3'-5' poly(A) RNA and ssDNA exonuclease. It
is the catalytic subunit of the yeast mRNA deadenylase
(Ccr4p/Pop2p/Not complex). This complex participates in
various ways in mRNA metabolism, including
transcription initiation and elongation, and mRNA
degradation. Ccr4p degrades both poly(A) and
single-stranded DNA. There are two vertebrate homologs
of Ccr4p, CCR4a (also called CCR4-NOT transcription
complex subunit 6 or CNOT6) and CCR4b (also called
CNOT6-like or CNOT6L), which independently associate
with other components to form distinct CCR4-NOT
multisubunit complexes. The nuclease domain of CNOT6
and CNOT6L exhibits Mg2+-dependent deadenylase
activity, with specificity for poly (A) RNA as
substrate. CCR4a is a component of P-bodies and is
necessary for foci formation. CCR4b regulates p27/Kip1
mRNA levels, thereby influencing cell cycle
progression. They both contribute to the prevention of
cell death by regulating insulin-like growth
factor-binding protein 5.
Length = 329
Score = 26.1 bits (58), Expect = 6.5
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 10 DIRIRAIAAELACNKYDIVCLQEVWKNDDFE 40
D R + I E+ DI+CLQEV + D +E
Sbjct: 28 DYRKQNILKEILSYNADILCLQEV-ETDQYE 57
>gnl|CDD|234948 PRK01372, ddl, D-alanine--D-alanine ligase; Reviewed.
Length = 304
Score = 25.8 bits (58), Expect = 7.5
Identities = 17/78 (21%), Positives = 23/78 (29%), Gaps = 30/78 (38%)
Query: 14 RAIAAELACNKYDIVCLQEV-WKNDDFELIKS----VVFEAL------------------ 50
A+ A L YD + D +K VF AL
Sbjct: 26 AAVLAALREAGYDAH---PIDPGEDIAAQLKELGFDRVFNALHGRGGEDGTIQGLLELLG 82
Query: 51 -PYAHYFYSGVMGSGVCI 67
PY SGV+ S + +
Sbjct: 83 IPYTG---SGVLASALAM 97
>gnl|CDD|197338 cd10283, MnuA_DNase1-like, Mycoplasma pulmonis MnuA
nuclease-like. This subfamily includes Mycoplasma
pulmonis MnuA, a membrane-associated nuclease related
to Deoxyribonuclease 1 (DNase1 or DNase I, EC
3.1.21.1). The in vivo role of MnuA is as yet
undetermined. This subfamily belongs to the large EEP
(exonuclease/endonuclease/phosphatase) superfamily that
contains functionally diverse enzymes that share a
common catalytic mechanism of cleaving phosphodiester
bonds.
Length = 266
Score = 25.8 bits (57), Expect = 8.6
Identities = 8/28 (28%), Positives = 13/28 (46%)
Query: 7 KDRDIRIRAIAAELACNKYDIVCLQEVW 34
+ AIA ++ D++ LQEV
Sbjct: 14 SKGKEKNPAIAEIISAFDLDLIALQEVM 41
>gnl|CDD|233654 TIGR01953, NusA, transcription termination factor NusA. This model
describes NusA, or N utilization substance protein A, a
bacterial transcription termination factor. It binds to
RNA polymerase alpha subunit and promotes termination at
certain RNA hairpin structures. It is named for the
interaction in E. coli of phage lambda antitermination
protein N with the N-utilization substance, consisting
of NusA, NusB, NusE (ribosomal protein S10), and nusG.
This model represents a region of NusA shared in all
bacterial forms, and including an S1 (pfam00575) and a
KH (pfam00013) RNA binding domains. Proteobacterial
forms have an additional C-terminal region, not included
in this model, with two repeats of 50-residue domain
rich in acidic amino acids [Transcription, Transcription
factors].
Length = 341
Score = 25.7 bits (57), Expect = 8.9
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 4/36 (11%)
Query: 9 RDIRIRAIAAELACNKYDIVCLQEVWKNDDFELIKS 44
+ RI+AI+ EL K DI+ + +D E I +
Sbjct: 252 KGSRIQAISKELNGEKIDII----EYSDDPAEFIAN 283
>gnl|CDD|205365 pfam13184, KH_5, NusA-like KH domain.
Length = 67
Score = 24.5 bits (54), Expect = 9.4
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 4/38 (10%)
Query: 12 RIRAIAAELACNKYDIVCLQEVWKNDDFELIKSVVFEA 49
RIRAI+ EL K D+V + D E I + + A
Sbjct: 27 RIRAISDELNGEKIDVV----EYSEDIKEFIANALSPA 60
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
0.326 0.143 0.467
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,144,531
Number of extensions: 636779
Number of successful extensions: 665
Number of sequences better than 10.0: 1
Number of HSP's gapped: 652
Number of HSP's successfully gapped: 47
Length of query: 136
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 49
Effective length of database: 7,078,804
Effective search space: 346861396
Effective search space used: 346861396
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.6 bits)