RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4844
(254 letters)
>gnl|CDD|189032 cd09862, PIN_Rrp44, PIN domain of yeast exosome subunit Rrp44
endoribonuclease and other eukaryotic homologs. PIN
(PilT N terminus) domain of the Saccharomyces cerevisiae
exosome subunit Rrp44 (Ribosomal RNA-processing protein
44 or Protein Dis3 homolog) and other similar eukaryotic
homologs are included in this family. The eukaryotic
exosome is a conserved macromolecular complex
responsible for many RNA-processing and RNA-degradation
reactions. It is composed of nine core subunits that
directly binds Rrp44. The Rrp44 nuclease is the
catalytic subunit of the exosome and has endonuclease
activity in the PIN domain and an exoribonuclease
activity in its RNase II-like region. Rrp44 binding to
the exosome is mediated mainly by the PIN domain and by
subunits Rrp41-Rrp45, and binding predictions indicate
that the PIN domain active site is positioned on the
outer surface of the exosome. These PIN domains are
structural homologs of flap endonuclease-1 (FEN1)-like
PIN domains, but lack the extensive arch/clamp region
and the H3TH (helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region, seen in FEN1-like PIN
domains. PIN domains within this subgroup contain four
highly conserved acidic residues (putative
metal-binding, active site residues) which cluster at
the C-terminal end of the beta-sheet and form a
negatively charged pocket near the center of the
molecule. Recombinant Rrp44 was shown to possess
manganese-dependent endonuclease activity in vitro that
was abolished by point mutations in the putative metal
binding residues of its PIN domain.
Length = 182
Score = 254 bits (650), Expect = 3e-86
Identities = 94/186 (50%), Positives = 129/186 (69%), Gaps = 12/186 (6%)
Query: 13 VMKIVREHYLRDDLSCGSELCLACDTKEAILDKIPTSSKAILDKIPTSSSKKYMEPHYLL 72
V+K+VREHYLRDD+ CGS+ C CD P S L P SS PHYL+
Sbjct: 8 VLKVVREHYLRDDIPCGSKACTECD---------PDESPLSLGPPPKSSLFT--SPHYLV 56
Query: 73 LDTNIILEQIDILEEPTLCNVILVQTILQEVKHRSSSVYKRLKDLISNPSRKFYVFVNEH 132
DTN++L QID+LE P++ +VI++QT+L+EV+HRS +Y RL+ LI +P ++FYVF NEH
Sbjct: 57 PDTNVVLHQIDLLEHPSITDVIILQTVLEEVRHRSLPIYNRLRALIKDPDKRFYVFSNEH 116
Query: 133 HYETYVEQEPGESVNDRNDRALRRVATWYEEHL-ESAVRVILLSEDVRNRDLATQSGLLT 191
H ETYVE+EPGES+NDRNDRA+R WY EHL + +++V+LL+ D NR+ A + G+
Sbjct: 117 HRETYVEREPGESINDRNDRAIRVATKWYSEHLPKLSIKVVLLTNDRANREKAAEEGITA 176
Query: 192 SSIEGY 197
+I+ Y
Sbjct: 177 KTIKEY 182
>gnl|CDD|214771 smart00670, PINc, Large family of predicted nucleotide-binding
domains. From similarities to 5'-exonucleases, these
domains are predicted to be RNases. PINc domains in
nematode SMG-5 and yeast NMD4p are predicted to be
involved in RNAi.
Length = 111
Score = 67.1 bits (164), Expect = 2e-14
Identities = 26/117 (22%), Positives = 51/117 (43%), Gaps = 11/117 (9%)
Query: 69 HYLLLDTNIILEQI--DILEEP--TLCNVILVQTILQEVKHRSSSVYKRLKDLISNPSRK 124
++LDTN++++ + D LE+ V + QT+L+E+++ + K+L++L
Sbjct: 1 MKVVLDTNVLIDGLIRDALEKLLEKKGEVYIPQTVLEELEYLALRSLKKLEELALEGKII 60
Query: 125 FYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNR 181
V E E +E+ + ND + A V+L++ D R
Sbjct: 61 LKVLKEERIEEEILERLSLKLELLPNDALILATAKELGN-------VVLVTNDRDLR 110
>gnl|CDD|222278 pfam13638, PIN_4, PIN domain. Members of this family of bacterial
domains are predicted to be RNases (from similarities to
5'-exonucleases).
Length = 129
Score = 61.8 bits (151), Expect = 3e-12
Identities = 28/126 (22%), Positives = 51/126 (40%), Gaps = 6/126 (4%)
Query: 73 LDTNIILEQIDILEEPTLCNVILV-QTILQEV-KHRSSSVYKRLKDLISNPSRKFYVFVN 130
LDTN++L D L N +++ T+L+E+ K + S + L R +
Sbjct: 3 LDTNVLLHDPDALFSFAEENDVVIPITVLEELDKLKKRSDLRELGRNAREAIRFLDELLE 62
Query: 131 EHHYETYVE---QEPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRNRDLATQS 187
+ V+ + + D+ND + A +E L V+L++ D+ R A
Sbjct: 63 DGSGRIRVQTLDERLPPEIEDKNDDRILDCALLLQEEL-PDRPVVLVTNDINLRIKAKAL 121
Query: 188 GLLTSS 193
G+
Sbjct: 122 GIPAED 127
>gnl|CDD|189024 cd09854, PIN_VapC-Smg6_family, PIN domains of VapC and Smg6
ribonucleases, ribosome assembly factor NOB1,
rRNA-processing protein Fcf1, Archaeoglobus fulgidus
AF0591 protein, and homologs. PIN (PilT N terminus)
domains of such ribonucleases as the toxins of
prokaryotic toxin/antitoxin operons FitAB and VapBC, as
well as, eukaryotic ribonucleases such as Smg6, ribosome
assembly factor NOB1, exosome subunit Rrp44
endoribonuclease and, rRNA-processing protein Fcf1, are
included in this family. Also included are the PIN
domains of the Pyrobaculum aerophilum Pea0151 and
Archaeoglobus fulgidus AF0591 proteins and other similar
archaeal homologs. These PIN domains are structural
homologs of flap endonuclease-1 (FEN1)-like PIN domains,
but lack the extensive arch/clamp region and the H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region, seen in FEN1-like PIN
domains. PIN domains typically contain three or four
highly conserved acidic residues (putative
metal-binding, active site residues) which cluster at
the C-terminal end of the beta-sheet and form a
negatively charged pocket near the center of the
molecule.
Length = 125
Score = 57.3 bits (138), Expect = 1e-10
Identities = 31/126 (24%), Positives = 57/126 (45%), Gaps = 20/126 (15%)
Query: 72 LLDTNIILEQI--------DILEEP-TLCNVILVQTILQEVKHRSSS--VYKRLKDLISN 120
+LDTN+IL I D+L+ C+V + + E++++ S V R++
Sbjct: 1 ILDTNVILFAISHKLDIIHDLLDCLNAFCDVYISDIVAAEIRNKGSKFKVALRIRKDC-R 59
Query: 121 PSRKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDVRN 180
++F F E T+VE+ P E++ND +D A+ + I+ + D
Sbjct: 60 DHKRFICFHKEFSEHTFVERLPNETINDADDCAINKTCMHRM--------FIVATCDADL 111
Query: 181 RDLATQ 186
R+ A +
Sbjct: 112 REAARK 117
>gnl|CDD|189050 cd09880, PIN_Smg5-Smg6-like, PIN domain. PIN (PilT N terminus)
domain of nonsense-mediated decay (NMD) factors, Smg5
and Smg6, and homologs are included in this family. Smg5
and Smg6 are essential factors in NMD, a
post-transcriptional regulatory pathway that recognizes
and rapidly degrades mRNAs containing premature
translation termination codons. In vivo, the Smg6 PIN
domain elicits degradation of bound mRNAs, as well as,
metal-ion dependent, degradation of single-stranded RNA,
in vitro. These PIN domains are structural homologs of
flap endonuclease-1 (FEN1)-like PIN domains, but lack
the extensive arch/clamp region and the H3TH
(helix-3-turn-helix) domain, an atypical
helix-hairpin-helix-2-like region, seen in FEN1-like PIN
domains. Point mutation studies of the conserved
aspartate residues in the catalytic center of the Smg6
PIN domain revealed that Smg6 is the endonuclease
involved in human NMD. However, Smg5 lacks several of
these key catalytic residues and does not degrade
single-stranded RNA, in vivo. Eukaryotic Smg5 and
Smg6-like PIN domains are present at the C-terminal end
of telomerase activating proteins, Est1. Many of the
bacterial homologs in this group have an N-terminal PIN
domain and a C-terminal PhoH-like ATPase domain.
Length = 139
Score = 33.8 bits (78), Expect = 0.027
Identities = 27/118 (22%), Positives = 46/118 (38%), Gaps = 10/118 (8%)
Query: 70 YLLLDTNIILEQIDILEEPTL---CNVILVQTILQEVKHRSSSVYKRLKDLISNPSRKFY 126
YL+LDTN++L + +L + V++ T+LQE+ S + L L R
Sbjct: 1 YLVLDTNVLLSHLKLLRKLLESGELIVVIPYTVLQELDGLKKSPRRELGHLARRAIRFLE 60
Query: 127 -VFVNEH---HYETYVEQ--EPGESVNDRNDRALRRVATWYEEHLESAVRVILLSEDV 178
+T E ND + A +++E +V+LL+ D
Sbjct: 61 DALKKGDPRLRGQTLTESLLALDGFDKRSNDDRILDCALYFQEQYPGE-KVVLLTNDR 117
>gnl|CDD|189025 cd09855, PIN_VapC-Smg6-like, PIN domains of VapC and Smg6
ribonucleases, ribosome assembly factor NOB1,
Archaeoglobus fulgidus AF0591 protein and homologs. PIN
(PilT N terminus) domains of such ribonucleases as the
toxins of prokaryotic toxin/antitoxin operons FitAB and
VapBC, as well as, eukaryotic ribonucleases such as
Smg6, ribosome assembly factor NOB1, exosome subunit
Rrp44 endoribonuclease are included in this family. Also
included are the PIN domains of the Pyrobaculum
aerophilum Pea0151 and Archaeoglobus fulgidus AF0591
proteins and other similar archaeal homologs. These PIN
domains are structural homologs of flap endonuclease-1
(FEN1)-like PIN domains, but lack the extensive
arch/clamp region and the H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region,
seen in FEN1-like PIN domains. PIN domains typically
contain three or four highly conserved acidic residues
(putative metal-binding, active site residues) which
cluster at the C-terminal end of the beta-sheet and form
a negatively charged pocket near the center of the
molecule.
Length = 128
Score = 30.1 bits (68), Expect = 0.46
Identities = 24/129 (18%), Positives = 43/129 (33%), Gaps = 23/129 (17%)
Query: 72 LLDTNIILEQIDILEEPTLCN------------VILVQTILQEVKHRSSSVYKRLKDLI- 118
LDTN++L +D +E V++ +L E+++ ++ K +D +
Sbjct: 1 FLDTNVVLYALDGRDEKQAKAAEVLELLVKDRDVVISVQVLAELRNVATRKLKLSEDEVG 60
Query: 119 ---SNPSRKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHLESAVRVILLS 175
R V T + D A+ A Y+ +LLS
Sbjct: 61 ERLERVLRACEVLPLTPSVITEANRLARRYQLSYWDAAIIATAKRYQN-------SVLLS 113
Query: 176 EDVRNRDLA 184
ED +
Sbjct: 114 EDFPHGAAL 122
>gnl|CDD|238025 cd00070, GLECT, Galectin/galactose-binding lectin. This domain
exclusively binds beta-galactosides, such as lactose,
and does not require metal ions for activity. GLECT
domains occur as homodimers or tandemly repeated
domains. They are developmentally regulated and may be
involved in differentiation, cell-cell interaction and
cellular regulation.
Length = 127
Score = 28.8 bits (65), Expect = 1.2
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 118 ISNPSRKFYVFVNEHHYETYVEQEPGESVN 147
I KF +FVN H+ ++ + P ES++
Sbjct: 84 ILVEEDKFQIFVNGQHFFSFPHRLPLESID 113
>gnl|CDD|214709 smart00532, LIGANc, Ligase N family.
Length = 441
Score = 29.1 bits (66), Expect = 2.1
Identities = 15/57 (26%), Positives = 23/57 (40%), Gaps = 14/57 (24%)
Query: 111 YKRLKDLISNPSRKFYVFVNEHHYETYVEQEPGESVNDRN-DRALRRVATWYEEHLE 166
L+ L+ N+H Y YV P ++D DR +R + E+H E
Sbjct: 5 ISELRKLL-----------NQHDYRYYVLDAP--IISDAEYDRLMRELKELEEKHPE 48
>gnl|CDD|223999 COG1073, COG1073, Hydrolases of the alpha/beta superfamily [General
function prediction only].
Length = 299
Score = 28.5 bits (63), Expect = 3.4
Identities = 10/55 (18%), Positives = 18/55 (32%), Gaps = 8/55 (14%)
Query: 111 YKRLKDLISNPSRKFYVFVNEHHYETYVEQEPGESVNDRNDRALRRVATWYEEHL 165
+ P +K H + Y ++AL ++A + E HL
Sbjct: 252 EDLYEAARERP-KKLLFVPGGGHIDLY-------DNPPAVEQALDKLAEFLERHL 298
>gnl|CDD|205228 pfam13047, DUF3907, Protein of unknown function (DUF3907). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 160 amino acids in length.
There is a conserved AYTG sequence motif.
Length = 148
Score = 27.3 bits (61), Expect = 5.5
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 107 SSSVYKRLKDLISNPSRKFYVFVNEHHYETYVEQEPGESVNDRNDRA-LRRVATWYEEHL 165
+ + LK +++ ++NE + V +EPG+ + LRR+ + EE L
Sbjct: 2 TEQTGEFLKKVVTEIED----YLNETTLSSLVAEEPGDEAYYEGVLSDLRRLLVFCEEGL 57
Query: 166 ESAVRVILLSEDVRN 180
E A RV+L E R
Sbjct: 58 E-ACRVLLRREPFRK 71
>gnl|CDD|172826 PRK14350, ligA, NAD-dependent DNA ligase LigA; Provisional.
Length = 669
Score = 27.5 bits (61), Expect = 7.7
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 177 DVRNRDLATQSGLLTSSIEGYISTLSNGEPLLDKLSKKEAVVETSVKDSL 226
DV N L + +T S GY ++ L+DKL+KK A+ T V L
Sbjct: 588 DVENSFLFGKKFCITGSFNGYSRSV-----LIDKLTKKGAIFNTCVTKYL 632
>gnl|CDD|176540 cd08598, PI-PLC1c_yeast, Catalytic domain of putative yeast
phosphatidylinositide-specific phospholipases C. This
family corresponds to the catalytic domain present in a
group of putative phosphoinositide-specific
phospholipase C (PI-PLC, EC 3.1.4.11) encoded by PLC1
genes from yeasts, which are homologs of the delta
isoforms of mammalian PI-PLC in terms of overall
sequence similarity and domain organization. Mammalian
PI-PLC is a signaling enzyme that hydrolyzes the
membrane phospholipids
phosphatidylinositol-4,5-bisphosphate (PIP2) to
generate two important second messengers in eukaryotic
signal transduction cascades, inositol
1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG).
InsP3 triggers inflow of calcium from intracellular
stores, while DAG, together with calcium, activates
protein kinase C, which then phosphorylates other
molecules, leading to altered cellular activity. Calcium
is required for the catalysis. The prototype of this CD
is protein Plc1p encoded by PLC1 genes from
Saccharomyces cerevisiae. Plc1p contains both highly
conserved X- and Y- regions of PLC catalytic core
domain, as well as a presumptive EF-hand like calcium
binding motif. Experiments show that Plc1p displays
calcium dependent catalytic properties with high
similarity to those of the mammalian PLCs, and plays
multiple roles in modulating the membrane/protein
interactions in filamentation control. CaPlc1p encoded
by CAPLC1 from the closely related yeast Candida
albicans, an orthologue of S. cerevisiae Plc1p, is also
included in this group. Like Plc1p, CaPlc1p has
conserved presumptive catalytic domain, shows PLC
activity when expressed in E. coli, and is involved in
multiple cellular processes. There are two other gene
copies of CAPLC1 in C. albicans, CAPLC2 (also named as
PIPLC) and CAPLC3. Experiments show CaPlc1p is the only
enzyme in C. albicans which functions as PLC. The
biological functions of CAPLC2 and CAPLC3 gene products
must be clearly different from CaPlc1p, but their exact
roles remain unclear. Moreover, CAPLC2 and CAPLC3 gene
products are more similar to extracellular bacterial
PI-PLC than to the eukaryotic PI-PLC, and they are not
included in this subfamily.
Length = 231
Score = 27.2 bits (61), Expect = 8.7
Identities = 8/14 (57%), Positives = 9/14 (64%)
Query: 191 TSSIEGYISTLSNG 204
SS+EGYI L G
Sbjct: 29 DSSVEGYIRALQRG 42
>gnl|CDD|102354 PRK06392, PRK06392, homoserine dehydrogenase; Provisional.
Length = 326
Score = 27.1 bits (60), Expect = 9.9
Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 188 GLLTSSIEGYISTLSNGEPLLDKLS--KKEAVVETSVKDSLYPLHA 231
G+++S+I I +NG LD + +K + ET+ D L L A
Sbjct: 168 GIVSSTINYVIRQEANGRGFLDVVKIAQKMGIAETNYSDDLMGLDA 213
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
0.316 0.132 0.370
Gapped
Lambda K H
0.267 0.0674 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,588,970
Number of extensions: 1174924
Number of successful extensions: 1005
Number of sequences better than 10.0: 1
Number of HSP's gapped: 998
Number of HSP's successfully gapped: 26
Length of query: 254
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 159
Effective length of database: 6,723,972
Effective search space: 1069111548
Effective search space used: 1069111548
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.2 bits)