RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 043998
(101 letters)
>gnl|CDD|185498 PTZ00173, PTZ00173, 60S ribosomal protein L10; Provisional.
Length = 213
Score = 74.3 bits (183), Expect = 7e-18
Identities = 28/70 (40%), Positives = 44/70 (62%), Gaps = 1/70 (1%)
Query: 27 SMGICQSRFKALQTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKIIVSRKWGFTKFSRAD 86
G C +R + Q + + ++ A EAL RAK+KFP RQKI+VS KWGFT ++R +
Sbjct: 122 PNGTC-ARVRIGQILLSIRTKEAYVPQAIEALRRAKYKFPGRQKIVVSNKWGFTNYTREE 180
Query: 87 YLRWKSENRM 96
Y + ++E ++
Sbjct: 181 YQKLRAEGKL 190
>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 = 44.1 bits (104), Expect = 1e-06
Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 33 SRFKALQTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKIIVSRKWGFTK 81
+R K Q IF ++ SN A+EAL RA KFPV KI++ + W K
Sbjct: 124 ARVKIGQKIFSVWTKPSNFDVAKEALRRAAMKFPVPCKIVIEKGWELLK 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 = 35.9 bits (84), Expect = 5e-04
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 34 RFKALQTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKII 72
R K Q +F+ A+EAL RA K P++ KI+
Sbjct: 75 RVKPGQILFE-VRGVPEEEVAKEALRRAAKKLPIKTKIV 112
>gnl|CDD|235252 PRK04199, rpl10e, 50S ribosomal protein L10e; Reviewed.
Length = 172
Score = 34.8 bits (81), Expect = 0.003
Identities = 15/48 (31%), Positives = 22/48 (45%)
Query: 34 RFKALQTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKIIVSRKWGFTK 81
R + Q IF + + A+EAL RA K P +I+V + K
Sbjct: 125 RVEKGQKIFTVRVNPEHLEAAKEALRRAAMKLPTPCRIVVEKGKELLK 172
>gnl|CDD|215820 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.
Length = 129
Score = 31.3 bits (72), Expect = 0.036
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 33 SRFKALQTIFKLFHPDSNSHHAQEALHRAKFKFPVRQKI 71
+R K Q +F++ + A+EAL RA K P++ KI
Sbjct: 93 ARVKPGQILFEI--GGVSEEVAKEALRRAASKLPIKTKI 129
>gnl|CDD|223275 COG0197, RplP, Ribosomal protein L16/L10E [Translation, ribosomal
structure and biogenesis].
Length = 146
Score = 31.0 bits (71), Expect = 0.055
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 51 SHHAQEALHRAKFKFPVRQKI-IVSRKWGFTK 81
A+EAL RA K PV+ K I K T+
Sbjct: 114 EELAREALRRAAAKLPVKTKFVIRIEKREGTE 145
>gnl|CDD|236411 PRK09203, rplP, 50S ribosomal protein L16; Reviewed.
Length = 138
Score = 26.6 bits (60), Expect = 1.6
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 54 AQEALHRAKFKFPVRQKIIV 73
A+EAL A K P++ K +
Sbjct: 114 AREALRLAAAKLPIKTKFVK 133
>gnl|CDD|197617 smart00271, DnaJ, DnaJ molecular chaperone homology domain.
Length = 60
Score = 24.9 bits (55), Expect = 3.1
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 36 KALQTIFKLFHPDSNSHHAQEALHRAK 62
KA + + +HPD N +EA + K
Sbjct: 20 KAYRKLALKYHPDKNPGDKEEAEEKFK 46
>gnl|CDD|180687 PRK06770, PRK06770, hypothetical protein; Provisional.
Length = 180
Score = 25.9 bits (57), Expect = 3.5
Identities = 9/37 (24%), Positives = 14/37 (37%), Gaps = 5/37 (13%)
Query: 47 PDSNSHHAQEALHRAKFKFPVRQKIIVSRKWGFTKFS 83
S A+H+ QK+ KWGF + +
Sbjct: 65 FKSTEEEIITAMHKM-----THQKVKADEKWGFIEMT 96
>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 = 25.6 bits (57), Expect = 4.9
Identities = 11/26 (42%), Positives = 12/26 (46%)
Query: 62 KFKFPVRQKIIVSRKWGFTKFSRADY 87
KF FP R KW + FS DY
Sbjct: 138 KFTFPGRGGKYSDFKWNWQHFSGVDY 163
>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 = 25.2 bits (55), Expect = 6.2
Identities = 14/44 (31%), Positives = 18/44 (40%), Gaps = 15/44 (34%)
Query: 60 RAKFKF---------------PVRQKIIVSRKWGFTKFSRADYL 88
RAKFKF + + + WGF KF R D+L
Sbjct: 72 RAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFL 115
>gnl|CDD|99751 cd06257, DnaJ, DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock
protein 40) proteins are highly conserved and play
crucial roles in protein translation, folding,
unfolding, translocation, and degradation. They act
primarily by stimulating the ATPase activity of Hsp70s,
an important chaperonine family. Hsp40 proteins are
characterized by the presence of a J domain, which
mediates the interaction with Hsp70. They may contain
other domains as well, and the architectures provide a
means of classification.
Length = 55
Score = 23.7 bits (52), Expect = 8.0
Identities = 9/29 (31%), Positives = 13/29 (44%), Gaps = 3/29 (10%)
Query: 36 KALQTIFKLFHPDSNSHHAQEALHRAKFK 64
KA + + +HPD N + KFK
Sbjct: 19 KAYRKLALKYHPDKNPDDPEAE---EKFK 44
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
0.322 0.129 0.401
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: 4,849,944
Number of extensions: 371595
Number of successful extensions: 414
Number of sequences better than 10.0: 1
Number of HSP's gapped: 414
Number of HSP's successfully gapped: 20
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
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: 40 (21.6 bits)
S2: 53 (24.2 bits)