RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 030082
(183 letters)
>gnl|CDD|185498 PTZ00173, PTZ00173, 60S ribosomal protein L10; Provisional.
Length = 213
Score = 317 bits (815), Expect = e-112
Identities = 119/173 (68%), Positives = 140/173 (80%)
Query: 2 KKKGVDEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLR 61
KK VDEFP CVH+VS E E +SSEALEAARI+ NKYM K AGKD FHLR+RVHPFHVLR
Sbjct: 39 KKATVDEFPVCVHIVSDEYEQISSEALEAARISANKYMVKRAGKDGFHLRIRVHPFHVLR 98
Query: 62 INKMLSCAGADRLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFK 121
INKMLSCAGADRLQTGMRGAFGKP GTCARV IGQ+LLS+R K++ A EALRRAK+K
Sbjct: 99 INKMLSCAGADRLQTGMRGAFGKPNGTCARVRIGQILLSIRTKEAYVPQAIEALRRAKYK 158
Query: 122 FPGRQKIIVSRKWGFTKFSRSDYLRFKSENRIVPDGVNAKLLGCHGPLASRQP 174
FPGRQKI+VS KWGFT ++R +Y + ++E +++ DGV+ KL+ GPL P
Sbjct: 159 FPGRQKIVVSNKWGFTNYTREEYQKLRAEGKLIQDGVHVKLISPKGPLTKVNP 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 = 186 bits (473), Expect = 9e-61
Identities = 77/133 (57%), Positives = 93/133 (69%)
Query: 6 VDEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKM 65
EFP CVHLV+ E E + ALEAARIA NKYM + AG+ +HL++RV+P H+LR NKM
Sbjct: 40 SAEFPVCVHLVAKEPEQIRHNALEAARIAANKYMTRRAGRMGYHLKIRVYPHHILRENKM 99
Query: 66 LSCAGADRLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGR 125
+ AGADR+Q GMRGAFGKP GT ARV IGQ + SV K SN A+EALRRA KFP
Sbjct: 100 ATGAGADRIQQGMRGAFGKPVGTAARVKIGQKIFSVWTKPSNFDVAKEALRRAAMKFPVP 159
Query: 126 QKIIVSRKWGFTK 138
KI++ + W K
Sbjct: 160 CKIVIEKGWELLK 172
>gnl|CDD|235252 PRK04199, rpl10e, 50S ribosomal protein L10e; Reviewed.
Length = 172
Score = 160 bits (408), Expect = 1e-50
Identities = 65/132 (49%), Positives = 82/132 (62%)
Query: 7 DEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKML 66
+FP V LV E + ALEAARIA NKY+ K G+ +HL++RV+P HVLR NKM
Sbjct: 41 GDFPVEVSLVVEEPCQIRHNALEAARIAANKYLTKTVGRSNYHLKIRVYPHHVLRENKMA 100
Query: 67 SCAGADRLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQ 126
+ AGADR+ GMR AFGKP GT ARV GQ + +VR + A+EALRRA K P
Sbjct: 101 TGAGADRVSDGMRLAFGKPVGTAARVEKGQKIFTVRVNPEHLEAAKEALRRAAMKLPTPC 160
Query: 127 KIIVSRKWGFTK 138
+I+V + K
Sbjct: 161 RIVVEKGKELLK 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 = 140 bits (355), Expect = 2e-43
Identities = 48/126 (38%), Positives = 62/126 (49%), Gaps = 14/126 (11%)
Query: 4 KGVDEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRIN 63
KG F LV+ E +++E LEAARIA N+Y+ K L +RV P H +
Sbjct: 1 KGNKLFFGEYGLVALEPGRITAEQLEAARIAINRYL----KKKGGKLWIRVFPDHPVTKK 56
Query: 64 KMLSCAGADRLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFP 123
L+T M GKP+G ARV GQ+L VR A+EALRRA K P
Sbjct: 57 P---------LETRMGKGKGKPEGWVARVKPGQILFEVRGVPEEE-VAKEALRRAAKKLP 106
Query: 124 GRQKII 129
+ KI+
Sbjct: 107 IKTKIV 112
>gnl|CDD|223275 COG0197, RplP, Ribosomal protein L16/L10E [Translation, ribosomal
structure and biogenesis].
Length = 146
Score = 117 bits (296), Expect = 3e-34
Identities = 47/137 (34%), Positives = 63/137 (45%), Gaps = 17/137 (12%)
Query: 3 KKGVDEFPFCVHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRI 62
K G F LV+ E +++ +EAARIA N+Y+ + G L +RV P L
Sbjct: 25 KGGNKVFFGEYGLVALEPGQITARQIEAARIAANRYLKRGGG-----LWIRVFPDKPLTE 79
Query: 63 NKMLSCAGADRLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKF 122
G DR+ G GKP+G ARV G+VL + A+EALRRA K
Sbjct: 80 KP-----GEDRMGKGK----GKPEGWAARVKPGRVLFEIAGVPEEL--AREALRRAAAKL 128
Query: 123 PGRQKI-IVSRKWGFTK 138
P + K I K T+
Sbjct: 129 PVKTKFVIRIEKREGTE 145
>gnl|CDD|215820 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.
Length = 129
Score = 101 bits (255), Expect = 3e-28
Identities = 37/116 (31%), Positives = 54/116 (46%), Gaps = 16/116 (13%)
Query: 13 VHLVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGAD 72
L + E +++ +EAARIA N+Y+ K L +RV P + + G
Sbjct: 30 YGLKALEPGRITARQIEAARIAINRYL-----KRGGKLWIRVFPDKPVTKKPAETRMGKG 84
Query: 73 RLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKI 128
+ GKP+G ARV GQ+L + + A+EALRRA K P + KI
Sbjct: 85 K---------GKPEGWVARVKPGQILFEI--GGVSEEVAKEALRRAASKLPIKTKI 129
>gnl|CDD|211627 TIGR01164, rplP_bact, ribosomal protein L16, bacterial/organelle.
This model describes bacterial and organellar ribosomal
protein L16. The homologous protein of the eukaryotic
cytosol is designated L10 [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 126
Score = 36.2 bits (84), Expect = 0.002
Identities = 28/113 (24%), Positives = 47/113 (41%), Gaps = 22/113 (19%)
Query: 15 LVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRL 74
L + E +++ +EAAR+A +Y+ K L +R+ P +K +
Sbjct: 33 LQALEPGWITARQIEAARVAMTRYV-----KRGGKLWIRIFP------DKPYTKKPL--- 78
Query: 75 QTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSLH---AQEALRRAKFKFPG 124
+T M G P+ A V G++L + + A+EA R A K P
Sbjct: 79 ETRMGKGKGNPEYWVAVVKPGKILFEI-----AGVPEEVAREAFRLAASKLPI 126
>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 = 30.9 bits (71), Expect = 0.31
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 119 KFKFPGRQKIIVSRKWGFTKFSRSDYLRFKSENRI 153
KF FPGR KW + FS DY + + I
Sbjct: 138 KFTFPGRGGKYSDFKWNWQHFSGVDYDQKTKKKGI 172
>gnl|CDD|236411 PRK09203, rplP, 50S ribosomal protein L16; Reviewed.
Length = 138
Score = 27.8 bits (63), Expect = 1.8
Identities = 31/117 (26%), Positives = 53/117 (45%), Gaps = 18/117 (15%)
Query: 15 LVSWEKENVSSEALEAARIACNKYMAKFAGKDAFHLRVRVHPFHVLRINKMLSCAGADRL 74
L + E +++ +EAARIA +++ K GK + +R+ P +K ++
Sbjct: 34 LKALEPGWITARQIEAARIAMTRHI-KRGGK----VWIRIFP------DKPVT---KKPA 79
Query: 75 QTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSLH-AQEALRRAKFKFPGRQKIIV 130
+ M G P+ A V G++L + S A+EALR A K P + K +
Sbjct: 80 EVRMGKGKGSPEYWVAVVKPGRILFEI---AGVSEELAREALRLAAAKLPIKTKFVK 133
>gnl|CDD|239572 cd03490, Topoisomer_IB_N_1, Topoisomer_IB_N_1: A subgroup of the
N-terminal DNA binding fragment found in eukaryotic DNA
topoisomerase (topo) IB. Topo IB proteins include the
monomeric yeast and human topo I and heterodimeric topo
I from Leishmania donvanni. Topo I enzymes are divided
into: topo type IA (bacterial) and type IB
(eukaryotic). Topo I relaxes superhelical tension in
duplex DNA by creating a single-strand nick, the broken
strand can then rotate around the unbroken strand to
remove DNA supercoils and, the nick is religated,
liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit religation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topos I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I have putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain.
Length = 217
Score = 28.3 bits (63), Expect = 1.9
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 2 KKKGVDEFPFCVHLVSWEKENVSSEALE 29
K++ E+PF LV W +E VSS LE
Sbjct: 113 KERAKREYPFNYALVDWIREKVSSNKLE 140
>gnl|CDD|218099 pfam04465, DUF499, Protein of unknown function (DUF499). Family of
uncharacterized hypothetical prokaryotic proteins.
Length = 1025
Score = 28.3 bits (63), Expect = 2.7
Identities = 12/41 (29%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 95 GQVLLSVRCKDSNSLHAQEALRRAKFKFPGRQKIIVSRKWG 135
G+ VR D L +EALRR + +K + + G
Sbjct: 720 GKPPAKVREDDV-ILPREEALRRQVCELLKEEKDEIKERNG 759
>gnl|CDD|114908 pfam06216, RTBV_P46, Rice tungro bacilliform virus P46 protein.
This family consists of several Rice tungro bacilliform
virus P46 proteins. The function of this family is
unknown.
Length = 392
Score = 27.7 bits (61), Expect = 4.1
Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 3/31 (9%)
Query: 119 KFKFPGRQKIIVSR---KWGFTKFSRSDYLR 146
+KFPG I++ + KW F + R R
Sbjct: 270 DYKFPGANTILIEKEIPKWDFDEMKRETQFR 300
>gnl|CDD|227032 COG4688, COG4688, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 665
Score = 27.3 bits (60), Expect = 5.6
Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 104 KDSNSLHAQEALRRAKFKFPGRQKIIVSRKWGFTKFSRSDYLRFKSENRIVPDGV 158
K + + E +R+ K P R+ + + G T+ S +L N + V
Sbjct: 123 KSEDEIRDSEEIRKRAEKLPERR----AFRIGMTEPKLSRFLC---LNSMTVTAV 170
>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 = 26.7 bits (59), Expect = 5.6
Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 16/55 (29%)
Query: 117 RAKFKF---------------PGRQKIIVSRKWGFTKFSRSDYLRFKSENRIVPD 156
RAKFKF + + + WGF KF R D+L N ++PD
Sbjct: 72 RAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFL-LDEANGLLPD 125
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
0.325 0.136 0.422
Gapped
Lambda K H
0.267 0.0550 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,205,264
Number of extensions: 819420
Number of successful extensions: 725
Number of sequences better than 10.0: 1
Number of HSP's gapped: 712
Number of HSP's successfully gapped: 19
Length of query: 183
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 92
Effective length of database: 6,901,388
Effective search space: 634927696
Effective search space used: 634927696
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 (21.6 bits)
S2: 56 (25.8 bits)