RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12253
(149 letters)
>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 = 174 bits (443), Expect = 2e-55
Identities = 79/163 (48%), Positives = 97/163 (59%), Gaps = 31/163 (19%)
Query: 13 QVAVLLVLRNKKTQEEICIATTHLKARNGALLSTLRNEQ--------------------- 51
QVA+ LR K+T EIC+A THLKAR G LR+EQ
Sbjct: 121 QVAIACTLRCKETGREICLAVTHLKARTG--WERLRSEQGKDLLQNLQSFIEGAKIPLII 178
Query: 52 ------EPTEPIYNTVMNHETLGLTSAYRHRTANNQ-EPQYTTWKIREEGEVCHTIDYVF 104
EPTEP+Y T N +L L SAY+ +A+ Q EP YTTWKIR GE HT+DY+F
Sbjct: 179 CGDFNAEPTEPVYKTFSNS-SLNLNSAYKLLSADGQSEPPYTTWKIRTSGECRHTLDYIF 237
Query: 105 YSQDKFDVEAVLDMPSGEQIGRDRIPSLRYPSDHFSLVCDLTL 147
YS+D VE +LD+P+ EQIG +R+PS YPSDH SLVCD +L
Sbjct: 238 YSKDALSVEQLLDLPTEEQIGPNRLPSFNYPSDHLSLVCDFSL 280
>gnl|CDD|197316 cd09082, Deadenylase, C-terminal deadenylase domain of CCR4,
nocturnin, and related domains. This family contains
the C-terminal catalytic domains of the deadenylases,
CCR4 and 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
the 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. Saccharomyces cerevisiae 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. The deadenylase
activities of Ccr4p and nocturnin differ: nocturnin
degrades poly(A), Ccr4p degrades both poly(A) and
single-stranded DNA, and in contrast to Ccr4p, nocturnin
appears to function in a highly processive manner. 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 = 348
Score = 90.1 bits (222), Expect = 3e-22
Identities = 25/194 (12%), Positives = 47/194 (24%), Gaps = 68/194 (35%)
Query: 21 RNKKTQEEICIATTHLKARNG----------ALLSTLRN--------------------- 49
+ ++ + +A H+ +S ++N
Sbjct: 156 IHAADKQLLIVANAHMHWDPEYSDVKLIQTMMFVSEVKNILEKASSRPGSPTADPNSIPL 215
Query: 50 ------EQEPTEPIYNTVMNHETLGLTSAYR---------------------HRTANNQE 82
P + + N + +
Sbjct: 216 VLCADLNSLPDSGVVEYLSN-GGVADNHKDFKELRYNECLMNFSCNGKNGSSEGRITHGF 274
Query: 83 PQYTTW------KIREEGEVCHTIDYVFYSQDKFDVEAVLDMPSGE---QIGRDRIPSLR 133
+ + + IDY+FYS+ +V VL + + P
Sbjct: 275 QLKSAYENNLMPYTNYTFDFKGVIDYIFYSKTHMNVLGVLGPLDPQWLVENNITGCPHPH 334
Query: 134 YPSDHFSLVCDLTL 147
PSDHFSL+ L L
Sbjct: 335 IPSDHFSLLTQLEL 348
>gnl|CDD|197317 cd09083, EEP-1, Exonuclease-Endonuclease-Phosphatase domain;
uncharacterized family 1. 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 = 252
Score = 51.1 bits (123), Expect = 2e-08
Identities = 43/158 (27%), Positives = 60/158 (37%), Gaps = 39/158 (24%)
Query: 11 PRQVAVLLVLRNKKTQEEICIATTHL-----KAR-NGALL-----STLRNEQ-------- 51
PR + ++KKT +E + THL +AR A L + +
Sbjct: 111 PR-ICTWARFKDKKTGKEFYVFNTHLDHVGEEAREESAKLILERIKEIAGDLPVILTGDF 169
Query: 52 --EPTEPIYNTVMNHETLGLTSAYRHRTANNQEPQYT--TWKIREEGEVCHTIDYVFYSQ 107
EP Y T+ + GL A + P+ T +K G IDY+F S
Sbjct: 170 NAEPDSEPYKTLTSG---GLKDARDTAATTDGGPEGTFHGFKGPPGGS---RIDYIFVSP 223
Query: 108 DKFDVEAVLDMPSGEQIGRDRIPSLRYPSDHFSLVCDL 145
V + +I DR RYPSDHF +V DL
Sbjct: 224 G-VKVLSY-------EILTDRY-DGRYPSDHFPVVADL 252
>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 = 48.8 bits (117), Expect = 2e-07
Identities = 26/86 (30%), Positives = 41/86 (47%), Gaps = 13/86 (15%)
Query: 59 NTVMNHETLGLTSAYRHRTANNQEPQYTTWKIREEGEVCHTIDYVFYSQDKFDVEAVLDM 118
+ + H + L SAY AN E +T + +G IDY+FYS D V +L
Sbjct: 248 ASGLTH-SFKLKSAY----ANLGELPFTNYTPDFKG----VIDYIFYSADTLSVLGLLGP 298
Query: 119 PSGEQIGRDRI---PSLRYPSDHFSL 141
P + +++ P+ +PSDH +L
Sbjct: 299 PDEDWY-LNKVVGLPNPHFPSDHIAL 323
>gnl|CDD|178689 PLN03144, PLN03144, Carbon catabolite repressor protein 4 homolog;
Provisional.
Length = 606
Score = 41.6 bits (98), Expect = 5e-05
Identities = 23/83 (27%), Positives = 38/83 (45%), Gaps = 9/83 (10%)
Query: 64 HETLGLTSA-YRHRT---ANNQEPQYTTWKIREEGEVCHTIDYVFYSQDKFDVEAVLDMP 119
G S + R EP +T + T+DY+FY+ D VE++L++
Sbjct: 516 ARMPGSGSGLEQQRRRMDPATNEPLFTNCT----RDFIGTLDYIFYTADSLTVESLLELL 571
Query: 120 SGEQIGRDR-IPSLRYPSDHFSL 141
E + +D +PS + SDH +L
Sbjct: 572 DEESLRKDTALPSPEWSSDHIAL 594
>gnl|CDD|197339 cd10312, Deadenylase_CCR4b, C-terminal deadenylase domain of CCR4b,
also known as CCR4-NOT transcription complex subunit
6-like. This subfamily contains the C-terminal
catalytic domain of the deadenylase, CCR4b, also known
as CCR4-NOT transcription complex subunit 6-like
(CNOT6L). 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, is a DEDD-type
protein and does not belong in this superfamily. There
are two vertebrate CCR4 proteins, CCR4a (also called
CCR4-NOT transcription complex subunit 6 or CNOT6) and
CCR4b. CCR4b associates with other components, such as
CNOT1-3 and Caf1, to form a CCR4-NOT multisubunit
complex, which regulates transcription and mRNA
degradation. The nuclease domain of CCR4b exhibits
Mg2+-dependent deadenylase activity with strict
specificity for poly (A) RNA as substrate. CCR4b is
mainly localized in the cytoplasm. It regulates cell
growth and influences cell cycle progression by
regulating p27/Kip1 mRNA levels. It contributes to the
prevention of cell death by regulating insulin-like
growth factor-binding protein 5.
Length = 348
Score = 38.1 bits (88), Expect = 8e-04
Identities = 30/82 (36%), Positives = 39/82 (47%), Gaps = 12/82 (14%)
Query: 69 LTSAYRHRTANNQEPQYTTWKIREEGEVCHTIDYVFYSQDKFDVEAVLDMPSGEQIGRDR 128
L SAY NN P YT + +G IDY+FYS+ +V VL + + +
Sbjct: 276 LKSAYE----NNLMP-YTNYTFDFKG----VIDYIFYSKTHMNVLGVLGPLDPQWLVENN 326
Query: 129 I---PSLRYPSDHFSLVCDLTL 147
I P PSDHFSL+ L L
Sbjct: 327 ITGCPHPHIPSDHFSLLTQLEL 348
>gnl|CDD|197340 cd10313, Deadenylase_CCR4a, C-terminal deadenylase domain of CCR4a,
also known as CCR4-NOT transcription complex subunit 6.
This subfamily contains the C-terminal catalytic domain
of the deadenylase, CCR4a, also known as CCR4-NOT
transcription complex subunit 6 (CNOT6). 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, is a DEDD-type protein and does not belong in this
superfamily. There are two vertebrate CCR4 proteins,
CCR4a and CCR4b (also called CNOT6-like or CNOT6L).
CCR4a associates with other components, such as CNOT1-3
and Caf1, to form a CCR4-NOT multisubunit complex, which
regulates transcription and mRNA degradation. The
nuclease domain of CCR4a 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 of various P-body
components. It also plays a role in cellular responses
to DNA damage, by regulating Chk2 activity.
Length = 350
Score = 32.7 bits (74), Expect = 0.051
Identities = 18/51 (35%), Positives = 25/51 (49%), Gaps = 3/51 (5%)
Query: 100 IDYVFYSQDKFDVEAVLDMPSGEQIGRDRI---PSLRYPSDHFSLVCDLTL 147
IDY+FYS+ + + +L + + I P PSDHFSL L L
Sbjct: 300 IDYIFYSKPQLNTLGILGPLDHHWLVENNISGCPHPLIPSDHFSLFAQLEL 350
>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 = 30.8 bits (70), Expect = 0.21
Identities = 30/151 (19%), Positives = 51/151 (33%), Gaps = 39/151 (25%)
Query: 25 TQEEICIATTHLKA-RNGAL-----LSTLRNEQEPTEPIYNTV----MN---------HE 65
+ E + +ATTHL++ ++ + L + + + N + N
Sbjct: 107 SGEPLRLATTHLESLKSHSSERTAQLEEIAKKLKKPPGAANVILGGDFNLRDKEDDTGGL 166
Query: 66 TLGLTSAYR--HRTANNQEPQYT------TWKIREEGEVCHTIDYVFYSQDKFDVEAVLD 117
G A+ EP YT + E D V +++
Sbjct: 167 PNGFVDAWEELG---PPGEPGYTWDTQKNPMLRKGEAGPRKRFDRVLLRGSDLKPKSI-- 221
Query: 118 MPSGEQIGRDRIPSL---RYPSDHFSLVCDL 145
E IG + IP +PSDHF L+ +L
Sbjct: 222 ----ELIGTEPIPGDEEGLFPSDHFGLLAEL 248
>gnl|CDD|223009 PHA03211, PHA03211, serine/threonine kinase US3; Provisional.
Length = 461
Score = 29.9 bits (67), Expect = 0.45
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 69 LTSAYRHRTANNQEPQYT 86
L S YRHR A N+ P YT
Sbjct: 400 LVSQYRHRAARNRRPAYT 417
>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 = 0.49
Identities = 27/156 (17%), Positives = 52/156 (33%), Gaps = 39/156 (25%)
Query: 17 LLVLRNKKTQEEICIATTHLKARNG----------ALLSTLRNEQE-------------- 52
+V++ +E+C+ HL+A +L L+ ++
Sbjct: 98 AVVVKFDVHDKELCVVNAHLQAGGTRADVRDAQLKEVLEFLKRLRQPNSAPVVICGDFNV 157
Query: 53 -PTEPIYNTVMNHETLGLTSAYR--HRTANNQEPQYTTWKIREEGEVCHTIDYVFYSQDK 109
P+E + L + T + YT + +DY+F S
Sbjct: 158 RPSEVDSENPSSMLRLFVALNLVDSFETLPHA---YTFDTYMHNVKS--RLDYIFVS--- 209
Query: 110 FDVEAVLDMPSGEQIGRDRIPSLRYPSDHFSLVCDL 145
+++L +I D + R PSDH+ + L
Sbjct: 210 ---KSLLPSVKSSKILSDAARA-RIPSDHYPIEVTL 241
>gnl|CDD|227564 COG5239, CCR4, mRNA deadenylase, exonuclease subunit and related
nucleases [RNA processing and modification].
Length = 378
Score = 29.7 bits (67), Expect = 0.51
Identities = 20/82 (24%), Positives = 30/82 (36%), Gaps = 19/82 (23%)
Query: 80 NQEPQYTTWKIREEGEVCHTIDYVFYSQ-------------DKFDVEAVLDMPSGEQIGR 126
E +T W IDY+FY + V+ +P+
Sbjct: 300 KGELGFTNWT----PGFKGVIDYIFYHGGLLTRQTGLLGVVEGEYASKVIGLPN-MPFPS 354
Query: 127 DRIPSL-RYPSDHFSLVCDLTL 147
D IP L + SDH +L+C+ L
Sbjct: 355 DHIPLLAEFASDHKNLMCNAFL 376
>gnl|CDD|220002 pfam08751, TrwC, TrwC relaxase. Relaxases are DNA strand
transferases which function during the conjugative cell
to cell DNA transfer. TrwC binds to the origin of
transfer (oriT) and melts the double helix.
Length = 288
Score = 29.2 bits (66), Expect = 0.67
Identities = 27/83 (32%), Positives = 39/83 (46%), Gaps = 17/83 (20%)
Query: 10 APRQVAVLLVLRNKKTQEEICIATTHLKARNGAL-------LSTLRNEQEPTEPIYNTVM 62
AP+ V++L ++ +T+E I A H +A AL T R E TE
Sbjct: 83 APKSVSLLALVGGDETKERIIEA--HDQAVAAALEYLEKHAAYTRRGENGKTEF------ 134
Query: 63 NHETLGLTSA-YRHRTANNQEPQ 84
T GL +A +RHRT+ +PQ
Sbjct: 135 -VNTGGLVAAKFRHRTSRAGDPQ 156
>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 = 28.5 bits (64), Expect = 1.3
Identities = 27/157 (17%), Positives = 46/157 (29%), Gaps = 48/157 (30%)
Query: 31 IATTHLKARNGALLS-TLRNEQ-------------EPTEPI----------------YNT 60
+ THL+A +G+ L +R +Q EP+ Y+
Sbjct: 130 VFGTHLQASDGSCLDRAVRQKQLDELRAFIEEKNIPDNEPVIIAGDFNVDKRSSRDEYDD 189
Query: 61 VMNHETLGLTSAYRHRTANNQEPQYTTWKIREEGEVCHT--------IDYVFYSQDKFDV 112
++ E L +A + P TW + +DY+ YS D
Sbjct: 190 ML--EQLHDYNA-PEPITAGETPL--TWDPGTNLLAKYNYPGGGGERLDYILYSNDHLQP 244
Query: 113 EA----VLDMPSGEQIGRDRIPSLRYPSDHFSLVCDL 145
+ V S + SDH+ +
Sbjct: 245 SSWSNEVEVPKSPTWSVTNGYTFADL-SDHYPVSATF 280
>gnl|CDD|240229 PTZ00014, PTZ00014, myosin-A; Provisional.
Length = 821
Score = 27.3 bits (61), Expect = 4.2
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 4/45 (8%)
Query: 68 GLTSAYRHRTANNQEPQYTTWKIREEGE--VCHTIDYVFYSQDKF 110
S+ NN P+Y K+ + HTI + Y F
Sbjct: 554 KFVSSCNTNLKNN--PKYKPAKVDSNKNFVIKHTIGDIQYCASGF 596
>gnl|CDD|212123 cd10812, GH38N_AMII_ScAms1_like, N-terminal catalytic domain of
yeast vacuolar alpha-mannosidases and similar proteins;
glycoside hydrolase family 38 (GH38). The family is
represented by Saccharomyces cerevisiae
alpha-mannosidase (Ams1) and its eukaryotic homologs.
Ams1 functions as a second resident vacuolar hydrolase
in S. cerevisiae. It aids in recycling macromolecular
components of the cell through hydrolysis of terminal,
non-reducing alpha-d-mannose residues. Ams1 forms an
oligomer in the cytoplasm and retains its oligomeric
form during the import process. It utilizes both the Cvt
(nutrient-rich conditions) and autophagic (starvation
conditions) pathways for biosynthetic delivery to the
vacuole. Mutants in either pathway are defective in Ams1
import. Members in this family show high sequence
similarity with rat ER/cytosolic alpha-mannosidase
Man2C1.
Length = 258
Score = 26.6 bits (59), Expect = 5.7
Identities = 13/33 (39%), Positives = 16/33 (48%)
Query: 112 VEAVLDMPSGEQIGRDRIPSLRYPSDHFSLVCD 144
VE +MPSGE + R + RY F CD
Sbjct: 83 VENDTNMPSGESLARQFLYGQRYFESRFGKRCD 115
>gnl|CDD|227245 COG4908, COG4908, Uncharacterized protein containing a NRPS
condensation (elongation) domain [General function
prediction only].
Length = 439
Score = 26.7 bits (59), Expect = 5.7
Identities = 7/19 (36%), Positives = 11/19 (57%)
Query: 96 VCHTIDYVFYSQDKFDVEA 114
HT+ YV DKF+++
Sbjct: 23 NDHTLHYVITFGDKFNIDR 41
>gnl|CDD|140318 PTZ00297, PTZ00297, pantothenate kinase; Provisional.
Length = 1452
Score = 26.4 bits (58), Expect = 8.1
Identities = 14/43 (32%), Positives = 17/43 (39%), Gaps = 2/43 (4%)
Query: 107 QDKFDVEAVLD--MPSGEQIGRDRIPSLRYPSDHFSLVCDLTL 147
QD F V + P E+ Y SDHF + LTL
Sbjct: 272 QDYFFVTPCVQVEKPRIEKFVVSSRRPYTYLSDHFGVSARLTL 314
>gnl|CDD|233738 TIGR02124, hypE, hydrogenase expression/formation protein HypE.
This family contains HypE (or HupE), a protein required
for expression of catalytically active hydrogenase in
many systems. It appears to be an accessory protein
involved in maturation rather than a regulatory protein
involved in expression. HypE shows considerable homology
to the thiamine-monophosphate kinase ThiL (TIGR01379)
and other enzymes.
Length = 320
Score = 25.7 bits (57), Expect = 9.8
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 94 GEVCHTIDYVFYSQDKFDVEAVLDMPSGEQIGR 126
GEV + + + + +LDMPSGE + R
Sbjct: 286 GEVVERKEGRVVLKTAYGGKRILDMPSGELLPR 318
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
0.319 0.134 0.392
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,434,879
Number of extensions: 637874
Number of successful extensions: 440
Number of sequences better than 10.0: 1
Number of HSP's gapped: 430
Number of HSP's successfully gapped: 23
Length of query: 149
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 61
Effective length of database: 7,034,450
Effective search space: 429101450
Effective search space used: 429101450
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: 54 (24.6 bits)