RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 033447
(119 letters)
>gnl|CDD|185498 PTZ00173, PTZ00173, 60S ribosomal protein L10; Provisional.
Length = 213
Score = 195 bits (497), Expect = 6e-65
Identities = 70/110 (63%), Positives = 88/110 (80%)
Query: 1 MLSCAGADRLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSHHAQEALRRAKFKFPG 60
MLSCAGADRLQTGMRGAFGKP GTCARV IGQ+LLS+R K++ A EALRRAK+KFPG
Sbjct: 102 MLSCAGADRLQTGMRGAFGKPNGTCARVRIGQILLSIRTKEAYVPQAIEALRRAKYKFPG 161
Query: 61 RQKIIVSRKWGFTKFSRADYLRWKSENRIVPDGVNAKLLGCHGPLAQRQP 110
RQKI+VS KWGFT ++R +Y + ++E +++ DGV+ KL+ GPL + P
Sbjct: 162 RQKIVVSNKWGFTNYTREEYQKLRAEGKLIQDGVHVKLISPKGPLTKVNP 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 = 101 bits (254), Expect = 1e-28
Identities = 43/74 (58%), Positives = 50/74 (67%)
Query: 1 MLSCAGADRLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSHHAQEALRRAKFKFPG 60
M + AGADR+Q GMRGAFGKP GT ARV IGQ + SV K SN A+EALRRA KFP
Sbjct: 99 MATGAGADRIQQGMRGAFGKPVGTAARVKIGQKIFSVWTKPSNFDVAKEALRRAAMKFPV 158
Query: 61 RQKIIVSRKWGFTK 74
KI++ + W K
Sbjct: 159 PCKIVIEKGWELLK 172
>gnl|CDD|235252 PRK04199, rpl10e, 50S ribosomal protein L10e; Reviewed.
Length = 172
Score = 91.4 bits (228), Expect = 1e-24
Identities = 35/74 (47%), Positives = 44/74 (59%)
Query: 1 MLSCAGADRLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSHHAQEALRRAKFKFPG 60
M + AGADR+ GMR AFGKP GT ARV GQ + +VR + A+EALRRA K P
Sbjct: 99 MATGAGADRVSDGMRLAFGKPVGTAARVEKGQKIFTVRVNPEHLEAAKEALRRAAMKLPT 158
Query: 61 RQKIIVSRKWGFTK 74
+I+V + K
Sbjct: 159 PCRIVVEKGKELLK 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 = 77.5 bits (192), Expect = 7e-20
Identities = 26/56 (46%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 10 LQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSHHAQEALRRAKFKFPGRQKII 65
L+T M GKP+G ARV GQ+L VR A+EALRRA K P + KI+
Sbjct: 58 LETRMGKGKGKPEGWVARVKPGQILFEVRGVPEE-EVAKEALRRAAKKLPIKTKIV 112
>gnl|CDD|223275 COG0197, RplP, Ribosomal protein L16/L10E [Translation, ribosomal
structure and biogenesis].
Length = 146
Score = 65.7 bits (161), Expect = 8e-15
Identities = 27/70 (38%), Positives = 34/70 (48%), Gaps = 7/70 (10%)
Query: 6 GADRLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSHHAQEALRRAKFKFPGRQKI- 64
G DR+ G GKP+G ARV G+VL + A+EALRRA K P + K
Sbjct: 82 GEDRMGKGK----GKPEGWAARVKPGRVLFEIAGVP--EELAREALRRAAAKLPVKTKFV 135
Query: 65 IVSRKWGFTK 74
I K T+
Sbjct: 136 IRIEKREGTE 145
>gnl|CDD|215820 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.
Length = 129
Score = 55.6 bits (135), Expect = 4e-11
Identities = 22/64 (34%), Positives = 30/64 (46%), Gaps = 11/64 (17%)
Query: 1 MLSCAGADRLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSHHAQEALRRAKFKFPG 60
+ G + GKP+G ARV GQ+L + + A+EALRRA K P
Sbjct: 77 AETRMGKGK---------GKPEGWVARVKPGQILFEI--GGVSEEVAKEALRRAASKLPI 125
Query: 61 RQKI 64
+ KI
Sbjct: 126 KTKI 129
>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 = 0.12
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 55 KFKFPGRQKIIVSRKWGFTKFSRADYLRWKSENRI 89
KF FPGR KW + FS DY + + I
Sbjct: 138 KFTFPGRGGKYSDFKWNWQHFSGVDYDQKTKKKGI 172
>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 = 26.9 bits (59), Expect = 2.9
Identities = 10/31 (32%), Positives = 15/31 (48%), Gaps = 3/31 (9%)
Query: 55 KFKFPGRQKIIVSR---KWGFTKFSRADYLR 82
+KFPG I++ + KW F + R R
Sbjct: 270 DYKFPGANTILIEKEIPKWDFDEMKRETQFR 300
>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 = 26.4 bits (58), Expect = 2.9
Identities = 14/44 (31%), Positives = 18/44 (40%), Gaps = 15/44 (34%)
Query: 53 RAKFKF---------------PGRQKIIVSRKWGFTKFSRADYL 81
RAKFKF + + + WGF KF R D+L
Sbjct: 72 RAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFL 115
>gnl|CDD|213240 cd03273, ABC_SMC2_euk, ATP-binding cassette domain of eukaryotic
SMC2 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 251
Score = 26.5 bits (59), Expect = 3.4
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 46 HAQEALRRAKFKFPGRQKIIVSRKWGFTKFSRADYL 81
H Q R K F G Q I+VS K G F+ A+ L
Sbjct: 205 HTQNIGRMIKTHFKGSQFIVVSLKEGM--FNNANVL 238
>gnl|CDD|236518 PRK09441, PRK09441, cytoplasmic alpha-amylase; Reviewed.
Length = 479
Score = 26.0 bits (58), Expect = 5.4
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 55 KFKFPGRQKIIVSRKWGFTKFSRADYLRWKSENRI 89
+F FPGR KW + FS DY E+ I
Sbjct: 140 RFTFPGRGGKYSDFKWHWYHFSGTDYDENPDESGI 174
>gnl|CDD|236411 PRK09203, rplP, 50S ribosomal protein L16; Reviewed.
Length = 138
Score = 25.4 bits (57), Expect = 6.8
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 47 AQEALRRAKFKFPGRQKIIV 66
A+EALR A K P + K +
Sbjct: 114 AREALRLAAAKLPIKTKFVK 133
>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 = 25.4 bits (56), Expect = 6.9
Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 10 LQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSHHAQEALRRAKFKFPG 60
L+T M G P+ A V G++L + A+EA R A K P
Sbjct: 78 LETRMGKGKGNPEYWVAVVKPGKILFEIAGVPEEV--AREAFRLAASKLPI 126
>gnl|CDD|166698 PLN03059, PLN03059, beta-galactosidase; Provisional.
Length = 840
Score = 25.7 bits (56), Expect = 8.8
Identities = 17/66 (25%), Positives = 26/66 (39%), Gaps = 12/66 (18%)
Query: 2 LSCAGADRLQTGMRGAFGKPQGTCARVAIGQVLLSVRCKDSNSHHAQEALRRAKFKFPGR 61
L C ++ +FG PQGTC S R ++H + +A R G+
Sbjct: 762 LWCPPGQKISKIKFASFGVPQGTCG---------SFREGSCHAHKSYDAFER---NCIGK 809
Query: 62 QKIIVS 67
Q V+
Sbjct: 810 QSCSVT 815
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 0.136 0.427
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: 5,962,632
Number of extensions: 496093
Number of successful extensions: 503
Number of sequences better than 10.0: 1
Number of HSP's gapped: 499
Number of HSP's successfully gapped: 17
Length of query: 119
Length of database: 10,937,602
Length adjustment: 82
Effective length of query: 37
Effective length of database: 7,300,574
Effective search space: 270121238
Effective search space used: 270121238
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: 53 (24.6 bits)