RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3003
(106 letters)
>gnl|CDD|189034 cd09864, PIN_Fcf1, PIN domain of rRNA-processing protein, Fcf1
(Utp24, YDR339C), and other eukaryotic homologs.
Fcf1/Utp24 (FAF1-copurifying factor 1/U three-associated
protein 24) is an essential protein involved in pre-rRNA
processing and 40S ribosomal subunit assembly. Component
of the small subunit (SSU) processome, Fcf1 is an
essential nucleolar protein that is required for
processing of the 18S pre-rRNA at sites A0-A2. The Fcf1
protein was reported to interact with Pmc1p (vacuolar
Ca2+ ATPase) and Cor1p (core subunit of the
ubiquinol-cytochrome c reductase complex). The PIN (PilT
N terminus) domain of this protein is a homolog of flap
endonuclease-1 (FEN1)-like PIN domains, but apparently
lack the H3TH domain or extensive arch/clamp region seen
in the latter. PIN domains typically contain three or
four conserved acidic residues (putative metal-binding,
active site residues). The Fcf1 PIN domain subfamily has
four of these putative active site residues and the
Fcf1-Utp23 homolog PIN domain subfamily has three of
them. Point mutation studies of the conserved acidic
residues in the putative active site of Saccharomyces
cerevisiae Fcf1 determined they were essential for
pre-rRNA processing at sites A1 and A2, whereas the
presence of the Fcf1 protein itself is also required for
cleavage at site A0.
Length = 143
Score = 194 bits (495), Expect = 8e-66
Identities = 72/91 (79%), Positives = 84/91 (92%)
Query: 8 IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
IP ITDCV+ E+EKLGQKY+VAL+I KDPRFER+PC HKGTYADDC+V RVTQH+CYIVA
Sbjct: 53 IPCITDCVMAELEKLGQKYRVALKIAKDPRFERLPCDHKGTYADDCLVERVTQHRCYIVA 112
Query: 68 TCDKDLKRRIRKVPGVPIMYISQHRYTIERM 98
TCD+DLKRRIRK+PGVPIMYI H+Y+IER+
Sbjct: 113 TCDRDLKRRIRKIPGVPIMYIRNHKYSIERL 143
>gnl|CDD|218319 pfam04900, Fcf1, Fcf1. Fcf1 is a nucleolar protein involved in
pre-rRNA processing. Depletion of yeast Fcf1 and Fcf2
leads to a decrease in synthesis of the 18S rRNA and
results in a deficit in 40S ribosomal subunits.
Length = 101
Score = 143 bits (362), Expect = 5e-46
Identities = 56/93 (60%), Positives = 75/93 (80%), Gaps = 2/93 (2%)
Query: 8 IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGT--YADDCIVNRVTQHKCYI 65
PYITDCV+ E+EKLG K++ AL+I KD RFER+ C HKGT YADDCI++RV +H CYI
Sbjct: 9 KPYITDCVIAELEKLGPKFRGALKIAKDKRFERLKCNHKGTEVYADDCILDRVGKHNCYI 68
Query: 66 VATCDKDLKRRIRKVPGVPIMYISQHRYTIERM 98
VAT D++L+RR+RK+PGVPI+YI+++ +E
Sbjct: 69 VATQDRELRRRLRKIPGVPIIYINRNVMVLEPP 101
>gnl|CDD|189021 cd08553, PIN_Fcf1-like, PIN domain of rRNA-processing proteins,
Fcf1 (Utp24, YDR339C), Utp23 (YOR004W), and other
eukaryotic homologs. Fcf1 (FAF1-copurifying factor 1,
also known as Utp24) and Utp23 (U three-associated
protein 23) are essential proteins involved in pre-rRNA
processing and 40S ribosomal subunit assembly.
Components of the small subunit (SSU) processome, Fcf1
and Utp23 are essential nucleolar proteins that are
required for processing of the 18S pre-rRNA at sites
A0-A2. The Fcf1 protein was reported to interact with
Pmc1p (vacuolar Ca2+ ATPase) and Cor1p (core subunit of
the ubiquinol-cytochrome c reductase complex). The PIN
(PilT N terminus) domains of these proteins are homologs
of flap endonuclease-1 (FEN1)-like PIN domains, but
apparently lack the H3TH domain or extensive arch/clamp
region seen in the latter. PIN domains typically contain
three or four conserved acidic residues (putative
metal-binding, active site residues). The Fcf1 PIN
domain subfamily has four of these putative active site
residues. Point mutation studies showed that the
conserved acidic residues in the putative active site of
Saccharomyces cerevisiae Fcf1 are essential for pre-rRNA
processing at sites A1 and A2, whereas the presence of
the Fcf1 protein itself is also required for cleavage at
site A0. S. cerevisiae Utp23 lacks several of these key
residues and mutation of the conserved acidic residues
seen in Utp23 did not interfere with rRNA maturation and
cell viability. The subfamily of Fcf1- and Utp23-like
homologs found in eukaryotes (except fungi) posses three
of the four conserved residues seen in S. cerevisiae
Fcf1.
Length = 120
Score = 105 bits (265), Expect = 4e-31
Identities = 42/92 (45%), Positives = 61/92 (66%), Gaps = 5/92 (5%)
Query: 8 IPYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGT-YADDCIVNRVTQH--KCY 64
P IT CVL E+E LG+K K A +I K ER+ C HK AD+C+++ V +H Y
Sbjct: 31 WPCITPCVLAELESLGKKLKDAFKIAKTL--ERLNCNHKEGASADECLLDIVKKHNNHRY 88
Query: 65 IVATCDKDLKRRIRKVPGVPIMYISQHRYTIE 96
VAT D+DL+ ++RK+PGVP++YI Q++ +E
Sbjct: 89 FVATQDQDLRVKLRKIPGVPLVYILQNKMILE 120
>gnl|CDD|224330 COG1412, COG1412, Uncharacterized proteins of PilT N-term./Vapc
superfamily [General function prediction only].
Length = 136
Score = 105 bits (265), Expect = 6e-31
Identities = 42/94 (44%), Positives = 61/94 (64%), Gaps = 3/94 (3%)
Query: 9 PYITDCVLGEIEKLGQKYKVALRI-IKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVA 67
P I CV+ E+EKL +K++ RI I ER+ C+HKG YAD+C++ +H YIVA
Sbjct: 44 PAIPSCVIRELEKLKRKHRGKARIAIALKYAERLECIHKGRYADECLLEAALKHGRYIVA 103
Query: 68 TCDKDLKRRIRKVPGVPIMYISQ-HRYTIERMPD 100
T DK+LKRR+R+ G+P++ + Q IER+ D
Sbjct: 104 TNDKELKRRLREN-GIPVITLRQRKLLIIERLSD 136
>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 = 86.2 bits (213), Expect = 3e-23
Identities = 41/96 (42%), Positives = 49/96 (51%), Gaps = 16/96 (16%)
Query: 8 IPYITDCVLGEIEKLGQKYKVALRIIKDPRF-ERIPCMHKGT---------------YAD 51
YI+D V EI G K+KVALRI KD R +R C HK AD
Sbjct: 30 DVYISDIVAAEIRNKGSKFKVALRIRKDCRDHKRFICFHKEFSEHTFVERLPNETINDAD 89
Query: 52 DCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMY 87
DC +N+ H+ +IVATCD DL+ RK PGV I
Sbjct: 90 DCAINKTCMHRMFIVATCDADLREAARKEPGVIIKS 125
>gnl|CDD|189036 cd09866, PIN_Fcf1-Utp23-H, PIN domain of rRNA-processing protein
Fcf1- and Utp23-like homologs found in eukaryotes except
fungi. PIN domain homologs of Fcf1/Utp24
(FAF1-copurifying factor 1/U three-associated protein
24) and Utp23, essential proteins involved in pre-rRNA
processing and 40S ribosomal subunit assembly, are
included in this subfamily. Fcf1 is a component of the
small subunit (SSU) processome and an essential
nucleolar protein required for processing of the 18S
pre-rRNA at sites A0-A2. These PIN (PilT N terminus)
domains are homologs of flap endonuclease-1 (FEN1)-like
PIN domains, but apparently lack the H3TH domain or
extensive arch/clamp region seen in the latter. PIN
domains typically contain three or four conserved acidic
residues (putative metal-binding, active site residues).
The Fcf1-Utp23 homolog PIN domain subfamily has three of
these conserved acidic residues rather than the four
seen in the Fcf1 PIN domain subfamily.
Length = 147
Score = 72.2 bits (178), Expect = 2e-17
Identities = 32/84 (38%), Positives = 49/84 (58%), Gaps = 6/84 (7%)
Query: 9 PYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKG--TYADDCIVN--RVTQHKCY 64
+ T CV+ E+EKLG AL I K RF+ C H+ A +C+ + + Y
Sbjct: 58 LFTTRCVIAELEKLGPDLYGALLIAK--RFQVAKCGHEKSPVSASECLKSMIGDNNPEHY 115
Query: 65 IVATCDKDLKRRIRKVPGVPIMYI 88
VAT DK+L+ ++RK+PGVP++Y+
Sbjct: 116 FVATQDKELREKLRKIPGVPLLYL 139
>gnl|CDD|189049 cd09879, PIN_AF0591, PIN domain of Archaeoglobus fulgidus AF0591
protein and other similar archaeal homologs. PIN (PilT
N terminus) domain of Archaeoglobus fulgidus AF0591
protein and other similar uncharacterized archaeal
homologs are included in this family. 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.
Length = 117
Score = 57.2 bits (139), Expect = 6e-12
Identities = 24/93 (25%), Positives = 42/93 (45%), Gaps = 14/93 (15%)
Query: 9 PYITDCVLGEIEKLGQKY--------KVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQ 60
+ VL E+EKL +K +VAL++ + ADD I+ +
Sbjct: 30 FVVPSAVLEELEKLSRKGKGKDKRAARVALQLAERCEVVESEGG----PADDAILELAKE 85
Query: 61 HKCYIVATCDKDLKRRIRKVPGVPIMYISQHRY 93
V T D++LK+R+ G+P++Y+ Q +
Sbjct: 86 LGA-AVVTNDRELKKRLLDA-GIPVIYLRQKKK 116
>gnl|CDD|189022 cd09852, PIN_SF, PIN (PilT N terminus) domain: Superfamily. PIN_SF
The PIN (PilT N terminus) domain belongs to a large
nuclease superfamily with representatives from
eukaryota, eubacteria, and archaea. PIN domains were
originally named for their sequence similarity to the
N-terminal domain of an annotated pili biogenesis
protein, PilT, a domain fusion between a PIN-domain and
a PilT ATPase domain. The structural properties of the
PIN domain indicate its putative active center,
consisting of invariant acidic amino acid residues
(putative metal-binding residues) is geometrically
similar in the active center of structure-specific 5'
nucleases (also known as Flap endonuclease-1-like),
PIN-domain ribonucleases of eukaryotic rRNA editing
proteins, and bacterial toxins of toxin-antitoxin (TA)
operons. Seen here, are two major divisions in the PIN
domain superfamily. The first major division, the
structure-specific 5' nuclease family, is represented by
FEN1, the 5'-3' exonuclease of DNA polymerase I, and T4
RNase H nuclease PIN domains. These 5' nucleases are
involved in DNA replication, repair, and recombination.
They are capable of both 5'-3' exonucleolytic activity
and cleaving bifurcated DNA, in an endonucleolytic,
structure-specific manner. Unique to FEN1-like
nucleases, the PIN domain has a helical arch/clamp
region (I domain) of variable length (approximately 16
to 800 residues) and, inserted within the C-terminal
region of the PIN domain, a H3TH (helix-3-turn-helix)
domain, an atypical helix-hairpin-helix-2-like region.
Both the H3TH domain (not included here) and the helical
arch/clamp region are involved in DNA binding. With the
exception of Mkt1, these nucleases have a carboxylate
rich active site that is involved in binding essential
divalent metal ion cofactors (Mg2+, Mn2+, Zn2+, or
Co2+). The second major division of the PIN domain
superfamily, the VapC-Smg6 family, includes such
eukaryotic ribonucleases as, Smg6, an essential factor
in nonsense-mediated mRNA decay; Rrp44, the catalytic
subunit of the exosome; and Nob1, a ribosome assembly
factor critical in pre-rRNA processing. A large
percentage of members in this family are bacterial
ribonuclease toxins of TA operons such as Mycobacterium
tuberculosis VapC and Neisseria gonorrhoeae FitB, as
well as, archaeal homologs, Pyrobaculum aerophilum
Pea0151 and P. aerophilum Pae2754. Also included are the
eukaryotic Fcf1/ Utp24 (FAF1-copurifying factor 1/U
three-associated protein 24) and Utp23-like proteins.
Components of the small subunit processome, Fcf1/Utp24
and Utp23 are essential proteins involved in pre-rRNA
processing and 40S ribosomal subunit assembly.
Length = 120
Score = 47.5 bits (113), Expect = 3e-08
Identities = 20/93 (21%), Positives = 37/93 (39%), Gaps = 15/93 (16%)
Query: 8 IPYITDCVLGEIEKL----------GQKYKVALRIIKDPRFERIPCMHKGT--YADDCIV 55
I V+ E+ KL G+ ++ LR ++ IP +H Y D +
Sbjct: 30 TVIIVFDVVAELLKLEAQKGLRRKKGRVAELLLRDLELLDLMGIPVVHAPGDLYEADAQI 89
Query: 56 NRVTQH-KCYIVATCDKDLKRRIRKVPGVPIMY 87
+ + + T D DL+++ + PGV +
Sbjct: 90 AALAKKGHVVALITNDSDLRQKAK--PGVKVFS 120
>gnl|CDD|189035 cd09865, PIN_Utp23, PIN domain of rRNA-processing protein, Utp23
(YOR004W), and other fungal homologs. Saccharomyces
cerevisiae Utp23 (U three-associated protein 23),
component of the small subunit (SSU) processome, is an
essential protein involved in pre-rRNA processing and
40S ribosomal subunit assembly. The PIN (PilT N
terminus) domain of this protein is a homolog of flap
endonuclease-1 (FEN1)-like PIN domains, but apparently
lack the H3TH domain or extensive arch/clamp region seen
in the latter. PIN domains typically contain three or
four conserved acidic residues (putative metal-binding,
active site residues. S. cerevisiae Utp23 lacks several
of these key residues and mutation of the conserved
acidic residues seen in Utp23 did not interfere with
rRNA maturation and cell viability.
Length = 148
Score = 43.5 bits (103), Expect = 2e-06
Identities = 31/90 (34%), Positives = 51/90 (56%), Gaps = 11/90 (12%)
Query: 9 PYITDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYA---DDCIVNRV-----TQ 60
P IT C + + LG+ + A+ + K FER C H+ A D+C+ + V +
Sbjct: 56 PMITQCCIRALYALGKTVQRAIDLAK--TFERRRCNHRDADALSPDECLKSVVDPKGKNK 113
Query: 61 HKCYIVATCDKDLKRRIRKVPGVPIMYISQ 90
H+ YIVAT D L+ +R +PGVP+++I++
Sbjct: 114 HR-YIVATQDPPLRTDLRSIPGVPLIHINR 142
>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 = 40.9 bits (96), Expect = 8e-06
Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 16/85 (18%)
Query: 7 GIPYITDCVLGEIE-----------KLGQKYKVALRIIKDPRFERIPCMHKGTYA----D 51
G YI VL E+E +L + K+ L+++K+ R E +
Sbjct: 27 GEVYIPQTVLEELEYLALRSLKKLEELALEGKIILKVLKEERIEEEILERLSLKLELLPN 86
Query: 52 DCIVNRVTQH-KCYIVATCDKDLKR 75
D ++ + ++ T D+DL+R
Sbjct: 87 DALILATAKELGNVVLVTNDRDLRR 111
>gnl|CDD|178752 PLN03213, PLN03213, repressor of silencing 3; Provisional.
Length = 759
Score = 31.7 bits (71), Expect = 0.052
Identities = 11/31 (35%), Positives = 20/31 (64%)
Query: 76 RIRKVPGVPIMYISQHRYTIERMPDAYGAPK 106
R+RKV +P+ +H+Y+ +R+P + PK
Sbjct: 126 RLRKVKAMPLSGTGKHKYSFQRVPLSSSLPK 156
>gnl|CDD|189031 cd09861, PIN_VapC-like, PIN domain of ribonucleases (toxins), VapC,
FitB, and PAE0151 of bacterial and archaeal
toxin/antitoxin-like operons, and other similar
homologs. PIN (PilT N terminus) domain of ribonucleases
(toxins) of prokaryotic toxin/antitoxin (TA) operons,
involved in growth inhibition by regulating translation,
are included in this family. They include the
Mycobacterium tuberculosis VapC of the VapBC (virulence
associated proteins) TA operon, and Neisseria
gonorrhoeae FitB of the FitAB (fast intracellular
trafficking) TA operon. Also included in this family are
the uncharacterized Mycobacterium bovis UPF0110 and
Synechocystis sp. PCC 6803 Sll0205 proteins, as well as,
the archaeal Pyrobaculum aerophilum PAE0151 protein. PIN
domain-containing toxins, such as, VapC, are nearly
always co-expressed with an antitoxin, a cognate protein
inhibitor (VapB) forming an inert protein complex.
Disassociation of the protein complex activates the
ribonuclease activity of the toxin by an, as yet
undefined mechanism. VapC-like 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 group typically
contain three or four highly conserved acidic residues
that cluster at the C-terminal end of the beta-sheet and
form a negatively charged pocket near the center of the
molecule. These putative active site residues are
thought to bind Mg2+ and/or Mn2+ ions and are essential
for single-stranded ribonuclease activity. VapC-like PIN
domains are single domain proteins that form dimers.
Length = 123
Score = 26.2 bits (58), Expect = 2.6
Identities = 17/93 (18%), Positives = 33/93 (35%), Gaps = 18/93 (19%)
Query: 1 MEQLQMGIPYITDCVLGE-----IEKLGQKYKVALRIIKDPRFERIPCMHKGTYA----- 50
+E L+ +I+ VL E K G+ + ++K E +P +
Sbjct: 23 LEALEGEELFISAIVLAEVLYVLRRKYGEAEEELELLLKLLGLEVVPLDEEALALALALL 82
Query: 51 --------DDCIVNRVTQHKCYIVATCDKDLKR 75
D ++ + +AT D+D K+
Sbjct: 83 AERYGLSLADALILATAKRLIAPLATFDRDFKK 115
>gnl|CDD|217833 pfam03997, VPS28, VPS28 protein.
Length = 187
Score = 26.3 bits (58), Expect = 2.7
Identities = 21/58 (36%), Positives = 26/58 (44%), Gaps = 8/58 (13%)
Query: 1 MEQLQMGIPYITDCV-----LGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDC 53
+EQL+ YI DCV KL +YKVA R ++ F I K Y DC
Sbjct: 11 LEQLEKA--YIKDCVSPSEYTSTCSKLIVQYKVAFRSVQGTEFPSIEDFCK-KYRLDC 65
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 26.6 bits (60), Expect = 3.1
Identities = 9/32 (28%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 71 KDLKRRIRKVPGVPIMYIS-QHRYTIERMPDA 101
K+L+RR+ + PI++IS ++++ +A
Sbjct: 307 KELRRRLPFLDYAPIVFISALTGQGVDKLLEA 338
>gnl|CDD|177953 PLN02319, PLN02319, aminomethyltransferase.
Length = 404
Score = 26.2 bits (58), Expect = 3.3
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 3/32 (9%)
Query: 46 KGTYADDCIVNRVTQHKCYIV--ATC-DKDLK 74
KG DD ++ +VT Y+V A C DKDL
Sbjct: 122 KGGIIDDTVITKVTDDHIYLVVNAGCRDKDLA 153
>gnl|CDD|199884 cd02854, E_set_GBE_euk_N, N-terminal Early set domain associated
with the catalytic domain of eukaryotic glycogen
branching enzyme (also called 1,4 alpha glucan
branching enzyme). This subfamily is composed of
predominantly eukaryotic 1,4 alpha glucan branching
enzymes, also called glycogen branching enzymes or
starch binding enzymes in plants. E or "early" set
domains are associated with the catalytic domain of the
1,4 alpha glucan branching enzymes at the N-terminal
end. These enzymes catalyze the formation of alpha-1,6
branch points in either glycogen or starch by cleavage
of the alpha-1,4 glucosidic linkage, yielding a
non-reducing end oligosaccharide chain, as well as the
subsequent attachment of short glucosyl chains to the
alpha-1,6 position. Starch is composed of two types of
glucan polymer: amylose and amylopectin. Amylose is
mainly composed of linear chains of alpha-1,4 linked
glucose residues and amylopectin consists of shorter
alpha-1,4 linked chains connected by alpha-1,6
linkages. Amylopectin is synthesized from linear chains
by starch branching enzyme. The N-terminal domains of
the branching enzyme proteins may be related to the
immunoglobulin and/or fibronectin type III
superfamilies. These domains are associated with
different types of catalytic domains at either the
N-terminal or C-terminal end and may be involved in
homodimeric/tetrameric/dodecameric interactions.
Members of this family include members of the alpha
amylase family, sialidase, galactose oxidase,
cellulase, cellulose, hyaluronate lyase, chitobiase,
and chitinase, among others.
Length = 95
Score = 25.6 bits (57), Expect = 3.4
Identities = 11/38 (28%), Positives = 15/38 (39%), Gaps = 10/38 (26%)
Query: 23 GQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQ 60
G K K+ + R +RIP +A RV Q
Sbjct: 56 GSKVKLHVETWDGGRLDRIP-----AWA-----KRVVQ 83
>gnl|CDD|216016 pfam00602, Flu_PB1, Influenza RNA-dependent RNA polymerase subunit
PB1. Two GTP binding sites exist in this protein.
Length = 740
Score = 26.4 bits (58), Expect = 3.5
Identities = 12/51 (23%), Positives = 18/51 (35%), Gaps = 5/51 (9%)
Query: 12 TDCVLGEIEKLGQKYKVALRIIKDPRFERIPCMH-----KGTYADDCIVNR 57
D VL I L +++ + + E + M KG D NR
Sbjct: 87 LDSVLELINNLEEEHPGSFEKSMEEAMEELMNMEFDKLTKGRQTYDWTSNR 137
>gnl|CDD|234274 TIGR03594, GTPase_EngA, ribosome-associated GTPase EngA. EngA
(YfgK, Der) is a ribosome-associated essential GTPase
with a duplication of its GTP-binding domain. It is
broadly to universally distributed among bacteria. It
appears to function in ribosome biogenesis or stability
[Protein synthesis, Other].
Length = 429
Score = 25.9 bits (58), Expect = 4.5
Identities = 7/19 (36%), Positives = 14/19 (73%)
Query: 71 KDLKRRIRKVPGVPIMYIS 89
K+L+R++ + PI++IS
Sbjct: 307 KELRRKLPFLDFAPIVFIS 325
>gnl|CDD|234876 PRK00960, PRK00960, seryl-tRNA synthetase; Provisional.
Length = 517
Score = 26.1 bits (58), Expect = 4.7
Identities = 15/75 (20%), Positives = 26/75 (34%), Gaps = 24/75 (32%)
Query: 20 EKLGQKYKVALRIIKDPRFE-----------------RIPCMHKGTYADDCIVNRVTQHK 62
EKLG+KY++ +R I+ + PC+ + I+
Sbjct: 85 EKLGRKYRIGIRGIEIDNYVITIPADGEKVIELEGLKVPPCVVEIEGEKGTIILIFKD-- 142
Query: 63 CYIVATCDKDLKRRI 77
+ +LKR I
Sbjct: 143 -----VGESELKRNI 152
>gnl|CDD|223824 COG0753, KatE, Catalase [Inorganic ion transport and metabolism].
Length = 496
Score = 25.8 bits (57), Expect = 4.9
Identities = 10/39 (25%), Positives = 15/39 (38%), Gaps = 4/39 (10%)
Query: 51 DDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVPIMYIS 89
D I RV H D DL + + K G+ + +
Sbjct: 462 DPEIKERVLDH----FYKIDPDLGKGVAKALGLALEPEA 496
>gnl|CDD|223481 COG0404, GcvT, Glycine cleavage system T protein
(aminomethyltransferase) [Amino acid transport and
metabolism].
Length = 379
Score = 25.7 bits (57), Expect = 5.4
Identities = 10/34 (29%), Positives = 16/34 (47%), Gaps = 3/34 (8%)
Query: 43 CMHKGTYADDCIVNRVTQHKCYIVATC---DKDL 73
G DD IV R+ + + ++V +KDL
Sbjct: 92 LNEDGGIIDDLIVYRLGEDRFFLVTNAATAEKDL 125
>gnl|CDD|173850 cd01161, VLCAD, Very long chain acyl-CoA dehydrogenase. VLCAD is
an acyl-CoA dehydrogenase (ACAD), which is found in the
mitochondria of eukaryotes and in some bacteria. It
catalyzes the alpha,beta dehydrogenation of the
corresponding trans-enoyl-CoA by FAD, which becomes
reduced. The reduced form of ACAD is reoxidized in the
oxidative half-reaction by electron-transferring
flavoprotein (ETF), from which the electrons are
transferred to the mitochondrial respiratory chain
coupled with ATP synthesis. VLCAD acts as a homodimer.
Length = 409
Score = 25.9 bits (57), Expect = 5.6
Identities = 11/26 (42%), Positives = 17/26 (65%), Gaps = 3/26 (11%)
Query: 13 DCVLGEIEKLGQKYKVALRIIKDPRF 38
+ VLGE+ G +KVA+ I+ + RF
Sbjct: 247 ENVLGEV---GDGFKVAMNILNNGRF 269
>gnl|CDD|226858 COG4451, RbcS, Ribulose bisphosphate carboxylase small subunit
[Energy production and conversion].
Length = 127
Score = 25.2 bits (55), Expect = 6.1
Identities = 9/49 (18%), Positives = 15/49 (30%), Gaps = 10/49 (20%)
Query: 1 MEQLQMGIP-----YITDCVLGEIEK-----LGQKYKVALRIIKDPRFE 39
M L + +I + L Q YK+ + + D R
Sbjct: 1 MIILPKNSRYKTLSSLPPLTDEQIAEQVRYLLSQGYKIGVEYVDDRRPR 49
>gnl|CDD|165912 PLN02270, PLN02270, phospholipase D alpha.
Length = 808
Score = 25.7 bits (56), Expect = 6.7
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 64 YIVATCDKDLKRRIR--KVPGVPIMYISQHR------YTIERMPDAY 102
Y T D++ R IR K PGVP + SQ + Y +PD +
Sbjct: 147 YFEVTKDRNWGRGIRSAKFPGVPYTFFSQRQGCKVSLYQDAHIPDNF 193
>gnl|CDD|227453 COG5124, COG5124, Protein predicted to be involved in meiotic
recombination [Cell division and chromosome
partitioning / General function prediction only].
Length = 209
Score = 24.9 bits (54), Expect = 8.5
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 16 LGEIEKLGQKYKVALRIIKD 35
L E+EKLG K ++ L +KD
Sbjct: 28 LKEVEKLGSKKQIVLMTVKD 47
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 0.447
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: 5,560,069
Number of extensions: 466180
Number of successful extensions: 602
Number of sequences better than 10.0: 1
Number of HSP's gapped: 590
Number of HSP's successfully gapped: 46
Length of query: 106
Length of database: 10,937,602
Length adjustment: 71
Effective length of query: 35
Effective length of database: 7,788,468
Effective search space: 272596380
Effective search space used: 272596380
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: 53 (24.3 bits)