RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 043596
(96 letters)
>gnl|CDD|185498 PTZ00173, PTZ00173, 60S ribosomal protein L10; Provisional.
Length = 213
Score = 98.2 bits (245), Expect = 3e-27
Identities = 34/70 (48%), Positives = 47/70 (67%)
Query: 18 DSNSHHAQEALRRAKFKFPVRQKIIVSRKWGFTKFSRANYLRCKSENRIVPDGVNAKLFE 77
++ A EALRRAK+KFP RQKI+VS KWGFT ++R Y + ++E +++ DGV+ KL
Sbjct: 142 EAYVPQAIEALRRAKYKFPGRQKIVVSNKWGFTNYTREEYQKLRAEGKLIQDGVHVKLIS 201
Query: 78 CHGPLANRQP 87
GPL P
Sbjct: 202 PKGPLTKVNP 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 = 42.5 bits (100), Expect = 3e-06
Identities = 17/34 (50%), Positives = 21/34 (61%)
Query: 18 DSNSHHAQEALRRAKFKFPVRQKIIVSRKWGFTK 51
SN A+EALRRA KFPV KI++ + W K
Sbjct: 139 PSNFDVAKEALRRAAMKFPVPCKIVIEKGWELLK 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 = 39.8 bits (94), Expect = 1e-05
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 16 GTDSNSHHAQEALRRAKFKFPVRQKII 42
A+EALRRA K P++ KI+
Sbjct: 86 RGVPEEEVAKEALRRAAKKLPIKTKIV 112
>gnl|CDD|223275 COG0197, RplP, Ribosomal protein L16/L10E [Translation, ribosomal
structure and biogenesis].
Length = 146
Score = 34.9 bits (81), Expect = 0.002
Identities = 14/32 (43%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 21 SHHAQEALRRAKFKFPVRQKI-IVSRKWGFTK 51
A+EALRRA K PV+ K I K T+
Sbjct: 114 EELAREALRRAAAKLPVKTKFVIRIEKREGTE 145
>gnl|CDD|215820 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.
Length = 129
Score = 33.2 bits (77), Expect = 0.005
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 20 NSHHAQEALRRAKFKFPVRQKI 41
+ A+EALRRA K P++ KI
Sbjct: 108 SEEVAKEALRRAASKLPIKTKI 129
>gnl|CDD|235252 PRK04199, rpl10e, 50S ribosomal protein L10e; Reviewed.
Length = 172
Score = 33.3 bits (77), Expect = 0.007
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 23 HAQEALRRAKFKFPVRQKIIVSRKWGFTK 51
A+EALRRA K P +I+V + K
Sbjct: 144 AAKEALRRAAMKLPTPCRIVVEKGKELLK 172
>gnl|CDD|236411 PRK09203, rplP, 50S ribosomal protein L16; Reviewed.
Length = 138
Score = 30.1 bits (69), Expect = 0.079
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 24 AQEALRRAKFKFPVRQKIIV 43
A+EALR A K P++ K +
Sbjct: 114 AREALRLAAAKLPIKTKFVK 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 = 26.1 bits (58), Expect = 2.5
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 27 ALRRAKFKFPVRQKIIVSRKWGFTKFSRANYLRCKS 62
ALRRA V+ +++VS W T S +L+
Sbjct: 58 ALRRAAVDRGVKVRLLVS-NWKHTDPSMDAFLKSLQ 92
>gnl|CDD|180687 PRK06770, PRK06770, hypothetical protein; Provisional.
Length = 180
Score = 25.9 bits (57), Expect = 3.2
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 37 VRQKIIVSRKWGFTKFSRAN 56
QK+ KWGF + ++ N
Sbjct: 80 THQKVKADEKWGFIEMTQEN 99
>gnl|CDD|176985 CHL00044, rpl16, ribosomal protein L16.
Length = 135
Score = 25.2 bits (56), Expect = 4.2
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 24 AQEALRRAKFKFPVRQKIIVS 44
A+ A++ A +K P++ + I+S
Sbjct: 114 ARAAIKIAAYKMPIKTQFIIS 134
>gnl|CDD|182461 PRK10438, PRK10438, C-N hydrolase family amidase; Provisional.
Length = 256
Score = 25.5 bits (56), Expect = 5.0
Identities = 9/16 (56%), Positives = 11/16 (68%), Gaps = 1/16 (6%)
Query: 11 AGCND-GTDSNSHHAQ 25
AGCN G+D N HH +
Sbjct: 189 AGCNRVGSDGNGHHYR 204
>gnl|CDD|215379 PLN02708, PLN02708, Probable pectinesterase/pectinesterase
inhibitor.
Length = 553
Score = 25.2 bits (55), Expect = 6.9
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 27 ALRRAKFKFPVRQKIIVSRKWGFTKFSRANYLRCKSENRIVPDG 70
L R+ P K + R W ++SR ++ C E I P G
Sbjct: 454 KLYRSN---PKVHKNFLGRPW--KEYSRTVFIGCNLEALITPQG 492
>gnl|CDD|239744 cd03775, MATH_Ubp21p, Ubiquitin-specific protease 21 (Ubp21p)
family, MATH domain; composed of fungal proteins with
similarity to Ubp21p of fission yeast. Ubp21p is a
deubiquitinating enzyme that may be involved in the
regulation of the protein kinase Prp4p, which controls
the formation of active spliceosomes. Members of this
family are similar to human HAUSP
(Herpesvirus-associated ubiquitin-specific protease) in
that they contain an N-terminal MATH domain and a
C-terminal catalytic protease (C19 family) domain. HAUSP
is also an ubiquitin-specific protease that specifically
catalyzes the deubiquitylation of p53 and MDM2. The MATH
domain of HAUSP contains the binding site for p53 and
MDM2. Similarly, the MATH domain of members in this
family may be involved in substrate binding.
Length = 134
Score = 24.6 bits (54), Expect = 8.0
Identities = 7/22 (31%), Positives = 12/22 (54%)
Query: 47 WGFTKFSRANYLRCKSENRIVP 68
WGFT+F L ++ ++ P
Sbjct: 99 WGFTRFIELRKLAHRTPDKPSP 120
>gnl|CDD|177491 PHA02825, PHA02825, LAP/PHD finger-like protein; Provisional.
Length = 162
Score = 24.8 bits (54), Expect = 8.8
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 55 ANYLRCKSENRIVPD 69
NY CK+EN+IV
Sbjct: 22 TNYCNCKNENKIVHK 36
>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 = 24.4 bits (53), Expect = 9.3
Identities = 13/44 (29%), Positives = 18/44 (40%), Gaps = 15/44 (34%)
Query: 30 RAKFKF---------------PVRQKIIVSRKWGFTKFSRANYL 58
RAKFKF + + + WGF KF R ++L
Sbjct: 72 RAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFL 115
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
0.321 0.134 0.419
Gapped
Lambda K H
0.267 0.0853 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,735,781
Number of extensions: 365061
Number of successful extensions: 246
Number of sequences better than 10.0: 1
Number of HSP's gapped: 246
Number of HSP's successfully gapped: 17
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
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 (21.9 bits)
S2: 53 (24.0 bits)