RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 043054
(90 letters)
>gnl|CDD|185498 PTZ00173, PTZ00173, 60S ribosomal protein L10; Provisional.
Length = 213
Score = 95.1 bits (237), Expect = 5e-26
Identities = 32/62 (51%), Positives = 44/62 (70%)
Query: 20 EALRRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWNSENRIVPDGMNAKLFGCHGPLADR 79
EALRRAK+KFP RQKI+VS KWGFT ++R +Y + +E +++ DG++ KL GPL
Sbjct: 150 EALRRAKYKFPGRQKIVVSNKWGFTNYTREEYQKLRAEGKLIQDGVHVKLISPKGPLTKV 209
Query: 80 QP 81
P
Sbjct: 210 NP 211
>gnl|CDD|129380 TIGR00279, L10e, ribosomal protein L10.e. This model finds the
archaeal and eukaryotic forms of ribosomal protein L10.
The protein is encoded by multiple loci in some
eukaryotes and has been assigned a number of
extra-ribosomal functions, some of which will require
re-evaluation in the context of identification as a
ribosomal protein. L10.e is distantly related to
eubacterial ribosomal protein L16 [Protein synthesis,
Ribosomal proteins: synthesis and modification].
Length = 172
Score = 38.7 bits (90), Expect = 8e-05
Identities = 14/27 (51%), Positives = 18/27 (66%)
Query: 19 QEALRRAKFKFPVRQKIIVSRKWGFTK 45
+EALRRA KFPV KI++ + W K
Sbjct: 146 KEALRRAAMKFPVPCKIVIEKGWELLK 172
>gnl|CDD|238714 cd01433, Ribosomal_L16_L10e, Ribosomal_L16_L10e: L16 is an
essential protein in the large ribosomal subunit of
bacteria, mitochondria, and chloroplasts. Large subunits
that lack L16 are defective in peptidyl transferase
activity, peptidyl-tRNA hydrolysis activity, association
with the 30S subunit, binding of aminoacyl-tRNA and
interaction with antibiotics. L16 is required for the
function of elongation factor P (EF-P), a protein
involved in peptide bond synthesis through the
stimulation of peptidyl transferase activity by the
ribosome. Mutations in L16 and the adjoining bases of
23S rRNA confer antibiotic resistance in bacteria,
suggesting a role for L16 in the formation of the
antibiotic binding site. The GTPase RbgA (YlqF) is
essential for the assembly of the large subunit, and it
is believed to regulate the incorporation of L16. L10e
is the archaeal and eukaryotic cytosolic homolog of
bacterial L16. L16 and L10e exhibit structural
differences at the N-terminus.
Length = 112
Score = 34.4 bits (80), Expect = 0.001
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 9 IPSRPIANPTQEALRRAKFKFPVRQKII 36
+ P +EALRRA K P++ KI+
Sbjct: 85 VRGVPEEEVAKEALRRAAKKLPIKTKIV 112
>gnl|CDD|223275 COG0197, RplP, Ribosomal protein L16/L10E [Translation, ribosomal
structure and biogenesis].
Length = 146
Score = 30.2 bits (69), Expect = 0.065
Identities = 13/28 (46%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 19 QEALRRAKFKFPVRQKI-IVSRKWGFTK 45
+EALRRA K PV+ K I K T+
Sbjct: 118 REALRRAAAKLPVKTKFVIRIEKREGTE 145
>gnl|CDD|235252 PRK04199, rpl10e, 50S ribosomal protein L10e; Reviewed.
Length = 172
Score = 29.4 bits (67), Expect = 0.16
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 20 EALRRAKFKFPVRQKIIVSRKWGFTK 45
EALRRA K P +I+V + K
Sbjct: 147 EALRRAAMKLPTPCRIVVEKGKELLK 172
>gnl|CDD|215820 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.
Length = 129
Score = 29.0 bits (66), Expect = 0.19
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 19 QEALRRAKFKFPVRQKI 35
+EALRRA K P++ KI
Sbjct: 113 KEALRRAASKLPIKTKI 129
>gnl|CDD|239743 cd03774, MATH_SPOP, Speckle-type POZ protein (SPOP) family, MATH
domain; composed of proteins with similarity to human
SPOP. SPOP was isolated as a novel antigen recognized by
serum from a scleroderma patient, whose overexpression
in COS cells results in a discrete speckled pattern in
the nuclei. It contains an N-terminal MATH domain and a
C-terminal BTB (also called POZ) domain. Together with
Cul3, SPOP constitutes an ubiquitin E3 ligase which is
able to ubiquitinate the PcG protein BMI1, the variant
histone macroH2A1 and the death domain-associated
protein Daxx. Therefore, SPOP may be involved in the
regulation of these proteins and may play a role in
transcriptional regulation, apoptosis and X-chromosome
inactivation. Cul3 binds to the BTB domain of SPOP
whereas Daxx and the macroH2A1 nonhistone region have
been shown to bind to the MATH domain. Both MATH and BTB
domains are necessary for the nuclear speckled
accumulation of SPOP. There are many proteins, mostly
uncharacterized, containing both MATH and BTB domains
from C. elegans and plants which are excluded from this
family.
Length = 139
Score = 27.5 bits (61), Expect = 0.73
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 16/55 (29%)
Query: 24 RAKFKF---------------PVRQKIIVSRKWGFTKFSRADYLRWNSENRIVPD 63
RAKFKF + + + WGF KF R D+L + N ++PD
Sbjct: 72 RAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFL-LDEANGLLPD 125
>gnl|CDD|200457 cd11318, AmyAc_bac_fung_AmyA, Alpha amylase catalytic domain found
in bacterial and fungal Alpha amylases (also called
1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC
3.2.1.1) catalyzes the hydrolysis of alpha-(1,4)
glycosidic linkages of glycogen, starch, related
polysaccharides, and some oligosaccharides. This group
includes bacterial and fungal proteins. The
Alpha-amylase family comprises the largest family of
glycoside hydrolases (GH), with the majority of enzymes
acting on starch, glycogen, and related oligo- and
polysaccharides. These proteins catalyze the
transformation of alpha-1,4 and alpha-1,6 glucosidic
linkages with retention of the anomeric center. The
protein is described as having 3 domains: A, B, C. A is
a (beta/alpha) 8-barrel; B is a loop between the beta 3
strand and alpha 3 helix of A; C is the C-terminal
extension characterized by a Greek key. The majority of
the enzymes have an active site cleft found between
domains A and B where a triad of catalytic residues
(Asp, Glu and Asp) performs catalysis. Other members of
this family have lost the catalytic activity as in the
case of the human 4F2hc, or only have 2 residues that
serve as the catalytic nucleophile and the acid/base,
such as Thermus A4 beta-galactosidase with 2 Glu
residues (GH42) and human alpha-galactosidase with 2 Asp
residues (GH31). The family members are quite extensive
and include: alpha amylase, maltosyltransferase,
cyclodextrin glycotransferase, maltogenic amylase,
neopullulanase, isoamylase, 1,4-alpha-D-glucan
maltotetrahydrolase, 4-alpha-glucotransferase,
oligo-1,6-glucosidase, amylosucrase, sucrose
phosphorylase, and amylomaltase.
Length = 391
Score = 27.1 bits (61), Expect = 1.2
Identities = 12/35 (34%), Positives = 15/35 (42%)
Query: 26 KFKFPVRQKIIVSRKWGFTKFSRADYLRWNSENRI 60
KF FP R KW + FS DY + + I
Sbjct: 138 KFTFPGRGGKYSDFKWNWQHFSGVDYDQKTKKKGI 172
>gnl|CDD|236411 PRK09203, rplP, 50S ribosomal protein L16; Reviewed.
Length = 138
Score = 26.6 bits (60), Expect = 1.2
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 19 QEALRRAKFKFPVRQKIIV 37
+EALR A K P++ K +
Sbjct: 115 REALRLAAAKLPIKTKFVK 133
>gnl|CDD|197206 cd09107, PLDc_vPLD3_4_5_like_2, Putative catalytic domain, repeat
2, of vertebrate phospholipases, PLD3, PLD4 and PLD5,
viral envelope proteins K4 and p37, and similar
proteins. Putative catalytic domain, repeat 2, of
vertebrate phospholipases D, PLD3, PLD4, and PLD5 (EC
3.1.4.4), viral envelope proteins (vaccinia virus
proteins K4 and p37), and similar proteins. Most family
members contain two copies of the HKD motifs
(H-x-K-x(4)-D, where x represents any amino acid
residue), and have been classified into the
phospholipase D (PLD) superfamily. Proteins in this
subfamily are associated with Golgi membranes, altering
their lipid content by the conversion of phospholipids
into phosphatidic acid, which is thought to be involved
in the regulation of lipid movement. ADP ribosylation
factor (ARF), a small guanosine triphosphate binding
protein, might be required activity. The vaccinia virus
p37 protein, encoded by the F13L gene, is also
associated with Golgi membranes and is required for the
envelopment and spread of the extracellular enveloped
virus (EEV). The vaccinia virus protein K4, encoded by
the HindIII K4L gene, remains to be characterized.
Sequence analysis indicates that the vaccinia virus
proteins K4 and p37 might have evolved from one or more
captured eukaryotic genes involved in cellular lipid
metabolism. Up to date, no catalytic activity of PLD3
has been shown. Furthermore, due to the lack of
functional important histidine and lysine residues in
the HKD motif, mammalian PLD5 has been characterized as
an inactive PLD. The poxvirus p37 proteins may also
lack PLD enzymatic activity, since they contain only
one partially conserved HKD motif (N-x-K-x(4)-D).
Length = 175
Score = 26.4 bits (59), Expect = 1.9
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 21 ALRRAKFKFPVRQKIIVSRKWGFTKFSRADYLRWNS 56
ALRRA V+ +++VS W T S +L+
Sbjct: 58 ALRRAAVDRGVKVRLLVS-NWKHTDPSMDAFLKSLQ 92
>gnl|CDD|197267 cd09170, PLDc_Nuc, Catalytic domain of EDTA-resistant nuclease
Nuc from Salmonella typhimurium and similar proteins.
Catalytic domain of an EDTA-resistant nuclease Nuc from
Salmonella typhimurium and similar proteins. Nuc is an
endonuclease cleaving both single- and double-stranded
DNA. It is the smallest known member of the
phospholipase D (PLD, EC 3.1.4.4) superfamily that
includes a diverse group of proteins with various
catalytic functions. Most members of this superfamily
have two copies of the conserved HKD motif
(H-x-K-x(4)-D, where x represents any amino acid
residue) in a single polypeptide chain and both are
required for catalytic activity. However, Nuc only has
one copy of the HKD motif per subunit but form a
functionally active homodimer (it is most likely also
active in solution as a multimeric protein), which has
a single active site at the dimer interface containing
the HKD motifs from both subunits. Due to the lack of a
distinct domain for DNA binding, Nuc cuts DNA
non-specifically. It utilizes a two-step mechanism to
cleave phosphodiester bonds: Upon substrate binding,
the bond is first attacked by a histidine residue from
one HKD motif to form a covalent phosphohistidine
intermediate, which is then hydrolyzed by water with
the aid of a second histidine residue from the other
HKD motif in the opposite subunit.
Length = 142
Score = 25.9 bits (58), Expect = 2.0
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 11 SRPIANPTQEALRRAKFKFPVRQKIIVSRKWGFTKFSRADYLR 53
S PIA AL AK K V ++++ + K+S +YL
Sbjct: 36 SPPIA----RALIAAK-KRGVDVRVVLDKSQAGGKYSALNYLA 73
>gnl|CDD|239650 cd03678, MM_CoA_mutase_1, Coenzyme B12-dependent-methylmalonyl
coenzyme A (CoA) mutase (MCM) family, unknown subfamily
1; composed of uncharacterized bacterial proteins
containing a C-terminal MCM domain. MCM catalyzes the
isomerization of methylmalonyl-CoA to succinyl-CoA. The
reaction proceeds via radical intermediates beginning
with a substrate-induced homolytic cleavage of the Co-C
bond of coenzyme B12 to produce cob(II)alamin and the
deoxyadenosyl radical. MCM plays an important role in
the conversion of propionyl-CoA to succinyl-CoA during
the degradation of propionate for the Krebs cycle. In
some bacteria, MCM is involved in the reverse metabolic
reaction, the rearrangement of succinyl-CoA to
methylmalonyl-CoA. Members of this subfamily also
contain an N-terminal coenzyme B12 binding domain
followed by a domain similar to the E. coli ArgK
membrane ATPase.
Length = 495
Score = 26.3 bits (58), Expect = 2.2
Identities = 11/32 (34%), Positives = 20/32 (62%), Gaps = 5/32 (15%)
Query: 14 IANPTQEALRRAKFKFPVRQKIIVSRKWGFTK 45
I PT+E++RRA + ++I++R+ G K
Sbjct: 386 ITTPTEESVRRA-----LAIQLIINRELGLAK 412
>gnl|CDD|133011 cd02518, GT2_SpsF, SpsF is a glycosyltrnasferase implicated in the
synthesis of the spore coat. Spore coat polysaccharide
biosynthesis protein F (spsF) is a glycosyltransferase
implicated in the synthesis of the spore coat in a
variety of bacteria challenged by stress as starvation.
The spsF gene is expressed in the late stage of coat
development responsible for a terminal step in coat
formation that involves the glycosylation of the coat.
SpsF gene mutation resulted in spores that appeared
normal. But, the spores tended to aggregate and had
abnormal adsorption properties, indicating a surface
alteration.
Length = 233
Score = 24.5 bits (54), Expect = 9.8
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 43 FTKFSRADYLRWNSENRIVPDGMNAKLF 70
S ADY N+ R PDG++ ++F
Sbjct: 112 LFLKSGADYTS-NTLPRTYPDGLDVEVF 138
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
0.324 0.140 0.446
Gapped
Lambda K H
0.267 0.0739 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,758,115
Number of extensions: 379802
Number of successful extensions: 359
Number of sequences better than 10.0: 1
Number of HSP's gapped: 359
Number of HSP's successfully gapped: 17
Length of query: 90
Length of database: 10,937,602
Length adjustment: 58
Effective length of query: 32
Effective length of database: 8,365,070
Effective search space: 267682240
Effective search space used: 267682240
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 53 (24.2 bits)