RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1816
(122 letters)
>gnl|CDD|185498 PTZ00173, PTZ00173, 60S ribosomal protein L10; Provisional.
Length = 213
Score = 139 bits (352), Expect = 7e-43
Identities = 48/75 (64%), Positives = 59/75 (78%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKP GT ARV IGQ ++S+R+ + + P IEALRRAK+KFPGRQKI VS KWGFT
Sbjct: 115 MRGAFGKPNGTCARVRIGQILLSIRTKEAYVPQAIEALRRAKYKFPGRQKIVVSNKWGFT 174
Query: 61 KYDREEYETLRDQNR 75
Y REEY+ LR + +
Sbjct: 175 NYTREEYQKLRAEGK 189
>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 = 82.6 bits (204), Expect = 5e-21
Identities = 32/61 (52%), Positives = 35/61 (57%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MRGA+GKP GT ARV IGQ I SV + EALRRA KFP KI + K W
Sbjct: 112 MRGAFGKPVGTAARVKIGQKIFSVWTKPSNFDVAKEALRRAAMKFPVPCKIVIEKGWELL 171
Query: 61 K 61
K
Sbjct: 172 K 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 = 69.8 bits (172), Expect = 1e-16
Identities = 24/52 (46%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIY 52
M GKP+G VARV GQ + VR + + A EALRRA K P + KI
Sbjct: 62 MGKGKGKPEGWVARVKPGQILFEVRGVPEEEVA-KEALRRAAKKLPIKTKIV 112
>gnl|CDD|235252 PRK04199, rpl10e, 50S ribosomal protein L10e; Reviewed.
Length = 172
Score = 64.9 bits (159), Expect = 2e-14
Identities = 29/61 (47%), Positives = 34/61 (55%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFT 60
MR A+GKP GT ARV GQ I +VR + + A EALRRA K P +I V K
Sbjct: 112 MRLAFGKPVGTAARVEKGQKIFTVRVNPEHLEAAKEALRRAAMKLPTPCRIVVEKGKELL 171
Query: 61 K 61
K
Sbjct: 172 K 172
>gnl|CDD|215820 pfam00252, Ribosomal_L16, Ribosomal protein L16p/L10e.
Length = 129
Score = 51.7 bits (125), Expect = 1e-09
Identities = 20/46 (43%), Positives = 25/46 (54%), Gaps = 2/46 (4%)
Query: 6 GKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKI 51
GKP+G VARV GQ + + + EALRRA K P + KI
Sbjct: 86 GKPEGWVARVKPGQILFEIGGVS--EEVAKEALRRAASKLPIKTKI 129
>gnl|CDD|223275 COG0197, RplP, Ribosomal protein L16/L10E [Translation, ribosomal
structure and biogenesis].
Length = 146
Score = 50.3 bits (121), Expect = 5e-09
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 6 GKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPG--RQKIYVSKK 56
GKP+G ARV G+ + + + EALRRA K P + I + K+
Sbjct: 91 GKPEGWAARVKPGRVLFEIAGVPEEL--AREALRRAAAKLPVKTKFVIRIEKR 141
>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 = 28.6 bits (65), Expect = 0.66
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 25 RSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYETLRDQNR 75
R+ + +P IEA KF FPGR Y KW + + +Y+ +
Sbjct: 123 RNKEISEPYEIEAW--TKFTFPGRGGKYSDFKWNWQHFSGVDYDQKTKKKG 171
>gnl|CDD|227565 COG5240, SEC21, Vesicle coat complex COPI, gamma subunit
[Intracellular trafficking and secretion].
Length = 898
Score = 28.8 bits (64), Expect = 0.76
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 27 SDKFKPAVIEALRRAKFKFPGRQKIYVS 54
SD FK I+ALR FP ++ Y+
Sbjct: 388 SDGFKIIAIDALRSLSLLFPSKKLSYLD 415
>gnl|CDD|214925 smart00941, PYNP_C, Pyrimidine nucleoside phosphorylase
C-terminal domain. This domain is found at the
C-terminal end of the large alpha/beta domain making up
various pyrimidine nucleoside phosphorylases. It has
slightly different conformations in different members
of this family. For example, in pyrimidine nucleoside
phosphorylase (PYNP) there is an added three-stranded
anti-parallel beta sheet as compared to other members
of the family, such as E. coli thymidine phosphorylase
(TP). The domain contains an alpha/ beta hammerhead
fold and residues in this domain seem to be important
in formation of the homodimer.
Length = 75
Score = 26.0 bits (58), Expect = 2.0
Identities = 10/29 (34%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 14 RVNIGQPIMSVRSSDKFKPA-VIEALRRA 41
RV G+P+ ++ ++D+ + EALR A
Sbjct: 43 RVKKGEPLATIHANDEAELEEAAEALRAA 71
>gnl|CDD|184620 PRK14323, glmM, phosphoglucosamine mutase; Provisional.
Length = 440
Score = 27.5 bits (61), Expect = 2.3
Identities = 15/39 (38%), Positives = 24/39 (61%), Gaps = 4/39 (10%)
Query: 19 QPIMSVRSSDKFK----PAVIEALRRAKFKFPGRQKIYV 53
Q +++VR SDK K P V EA+R A+ + GR ++ +
Sbjct: 365 QTLLNVRVSDKAKVAADPRVQEAVREAEARLGGRGRVNL 403
>gnl|CDD|213607 TIGR01352, tonB_Cterm, TonB family C-terminal domain. This model
represents the C-terminal of TonB and is homologs. TonB
is an energy-transducer for TonB-dependent receptors of
Gram-negative bacteria. Most members are designated as
TonB or TonB-related proteins, but a few represent the
paralogous TolA protein. Several bacteria have up to
four TonB paralogs. In nearly every case, a
proline-rich repetive region is found N-terminal to
this domain; these low-complexity regions are highly
divergent and cannot readily be aligned. The region is
suggested to help span the periplasm [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 74
Score = 25.3 bits (56), Expect = 4.6
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 8/41 (19%)
Query: 8 PQGTVARVNIGQPIMSVRSSDK--FKPAVIEALRRAKFKFP 46
P G V V++ ++SS A +EA+R+A+F+ P
Sbjct: 20 PSGRVTSVSV------LKSSGDEALDRAALEAVRKARFEPP 54
>gnl|CDD|205193 pfam13012, MitMem_reg, Maintenance of mitochondrial structure and
function. This is C-terminal to the Mov24 region of the
yeast proteasomal subunit Rpn11 and seems likely to
regulate the mitochondrial fission and tubulation
processes, ie the outer mitochondrial membrane proteins.
This function appears to be unrelated to the proteasome
activity of the N-terminal region.
Length = 115
Score = 25.6 bits (57), Expect = 4.6
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 89 IFQGSPTLSEEEIIESSNNETNDE 112
+ P +E E N ETND+
Sbjct: 69 LLNLLPNYDNKEFEEEFNVETNDQ 92
>gnl|CDD|180276 PRK05820, deoA, thymidine phosphorylase; Reviewed.
Length = 440
Score = 26.3 bits (59), Expect = 5.1
Identities = 9/31 (29%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 13 ARVNIGQPIMSVRSSD--KFKPAVIEALRRA 41
RV+ G+P+ ++ + D +F AL+ A
Sbjct: 391 DRVDAGEPLATLHADDEERF-QEAAAALKAA 420
>gnl|CDD|197201 cd09102, PLDc_CDP-OH_P_transf_II_1, Catalytic domain, repeat 1, of
CDP-alcohol phosphatidyltransferase class-II family
members. Catalytic domain, repeat 1, of CDP-alcohol
phosphatidyltransferase class-II family members, which
mainly include gram-negative bacterial
phosphatidylserine synthases (PSS;
CDP-diacylglycerol--serine O-phosphatidyltransferase, EC
2.7.8.8), yeast phosphatidylglycerophosphate synthase
(PGP synthase; CDP-diacylglycerol--glycerol-3-phosphate
3-phosphatidyltransferase, EC 2.7.8.5), and metazoan PGP
synthase 1. All members in this subfamily have two HKD
motifs (H-x-K-x(4)-D, where x represents any amino acid
residue) that characterize the phospholipase D (PLD)
superfamily. They may utilize a common two-step
ping-pong catalytic mechanism, involving a
substrate-enzyme intermediate, to cleave phosphodiester
bonds. The two motifs are suggested to constitute the
active site involving phosphatidyl group transfer.
Phosphatidylserine synthases from gram-positive bacteria
and eukaryotes, and prokaryotic
phosphatidylglycerophosphate synthases are not members
of this subfamily.
Length = 168
Score = 26.0 bits (57), Expect = 5.1
Identities = 23/96 (23%), Positives = 37/96 (38%), Gaps = 12/96 (12%)
Query: 24 VRSSDKFKPAVIEALRRAKFKFPGRQKIYV-SKKWGFTKYDREEYETLRDQNRTS--IIS 80
+ S +FK +IE +R AK +++YV S WG D E L + +
Sbjct: 5 LGSPAEFKTQIIELIRNAK------RRVYVASLYWG---KDEAGQEILDEIYSVKQENPN 55
Query: 81 TPKSVFFPIFQGSPTLSEEEIIESSNNETNDEENNT 116
SV + L E ++N + E+ T
Sbjct: 56 LDVSVLIDWHRAQRNLLGSETKSATNADWYCEQRQT 91
>gnl|CDD|180687 PRK06770, PRK06770, hypothetical protein; Provisional.
Length = 180
Score = 25.9 bits (57), Expect = 5.2
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 49 QKIYVSKKWGFTKYDREEYETLRD 72
QK+ +KWGF + +E E L+D
Sbjct: 82 QKVKADEKWGFIEMTQENIEKLKD 105
>gnl|CDD|236298 PRK08574, PRK08574, cystathionine gamma-synthase; Provisional.
Length = 385
Score = 26.2 bits (58), Expect = 5.8
Identities = 16/56 (28%), Positives = 21/56 (37%), Gaps = 2/56 (3%)
Query: 16 NIGQPIMSVRSSDKFKPAVIEALRRAKFKFPGRQKIYVSKKWGFTKYDREEYETLR 71
+ R SD + A F+ G + Y S + KY REE TLR
Sbjct: 3 RGTDAVRGYRGSDPYGSLQPPIYLTALFRQEG--EAYPSDRGFDLKYSREENPTLR 56
>gnl|CDD|182134 PRK09897, PRK09897, hypothetical protein; Provisional.
Length = 534
Score = 25.9 bits (57), Expect = 6.1
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 65 EEYETLRDQNRTSIISTPKSVFFPIF 90
E+YE +++RT I + S F +F
Sbjct: 414 EDYEMEINESRTVIKTEDNSYSFDVF 439
>gnl|CDD|132143 TIGR03099, dCO2ase_PEP1, pyridoxal-dependent decarboxylase,
exosortase A system-associated. The sequences in this
family contain the pyridoxal binding domain (pfam02784)
and C-terminal sheet domain (pfam00278) of a family of
Pyridoxal-dependent decarboxylases. Characterized
enzymes in this family decarboxylate substrates such as
ornithine, diaminopimelate and arginine. The genes of
the family modeled here, with the exception of those
observed in certain Burkholderia species, are all found
in the context of exopolysaccharide biosynthesis loci
containing the exosortase/PEP-CTERM protein sorting
system. More specifically, these are characteristic of
the type 1 exosortase system represented by the Genome
Property GenProp0652. The substrate of these enzymes may
be a precursor of the carrier or linker which is
hypothesized to release the PEP-CTERM protein from the
exosortase enzyme. These enzymes are apparently most
closely related to the diaminopimelate decarboxylase
modeled by TIGR01048 which may suggest a similarity (or
identity) of substrate.
Length = 398
Score = 25.9 bits (57), Expect = 6.2
Identities = 10/21 (47%), Positives = 12/21 (57%)
Query: 87 FPIFQGSPTLSEEEIIESSNN 107
F IF GS L+ E IIE+
Sbjct: 190 FHIFAGSQNLNAEAIIEAQAK 210
>gnl|CDD|239233 cd02905, Macro_GDAP2_like, Macro domain, GDAP2_like family. The
macro domain is a high-affinity ADP-ribose binding
module found in a variety of proteins as a stand-alone
domain or in combination with other domains like in
histone macroH2A and some PARPs (poly ADP-ribose
polymerases). Some macro domains recognize poly
ADP-ribose as a ligand. Previously identified as
displaying an Appr-1"-p (ADP-ribose-1"-monophosphate)
processing activity, the macro domain may play roles in
distinct ADP-ribose pathways, such as the
ADP-ribosylation of proteins, an important
post-translational modification which occurs in DNA
repair, transcription, chromatin biology, and long-term
memory formation, among other processes. This family
contains proteins similar to human GDAP2, the
ganglioside induced differentiation associated protein
2, whose gene is expressed at a higher level in
differentiated Neuro2a cells compared with
non-differentiated cells. GDAP2 contains an N-terminal
macro domain and a C-terminal Sec14p-like lipid binding
domain. It is specifically expressed in brain and
testis.
Length = 140
Score = 25.4 bits (56), Expect = 7.8
Identities = 9/36 (25%), Positives = 16/36 (44%)
Query: 87 FPIFQGSPTLSEEEIIESSNNETNDEENNTEDVFFV 122
+++G + I +S NET ++N D F
Sbjct: 3 IVLWEGDICNLNVDAIVNSTNETLTDKNPISDKIFA 38
>gnl|CDD|132014 TIGR02969, mam_aldehyde_ox, aldehyde oxidase. Members of this
family are mammalian aldehyde oxidase (EC 1.2.3.1)
isozymes, closely related to xanthine
dehydrogenase/oxidase.
Length = 1330
Score = 25.7 bits (56), Expect = 8.5
Identities = 16/47 (34%), Positives = 22/47 (46%), Gaps = 8/47 (17%)
Query: 1 MRGAYGKPQGTVARVNIGQPIMSVRSSDKFKPAVIEALRRAKFKFPG 47
MR A +PQ T RV + +M P ++ L AKFK+P
Sbjct: 219 MRMAEKQPQRT--RVFYSERMMW------ISPVTLKELLEAKFKYPQ 257
>gnl|CDD|163693 cd08062, MPN_RPN7_8, Mpr1p, Pad1p N-terminal (MPN) domains without
catalytic isopeptidase activity, found in 19S
proteasomal subunits Rpn7 and Rpn8. This family
includes lid subunits of the 26 S proteasome regulatory
particles, Rpn7 (PSMD7; proteasome 26S non-ATPase
subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S
non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be
critical for the integrity of the 26 S proteasome
complex by establishing a correct lid structure. It is
necessary for the incorporation/anchoring of Rpn3 and
Rpn12 to the lid and essential for viability and normal
mitosis. Rpn7 and Rpn8 are ATP-independent components of
the 19S regulator subunit, and contain the MPN
structural motif on its N-terminal region. However,
while they show a typical MPN metalloprotease fold, they
lack the canonical JAMM motif, and therefore do not show
catalytic isopeptidase activity. It is suggested that
Rpn7 function is primarily structural.
Length = 280
Score = 25.6 bits (57), Expect = 8.7
Identities = 8/24 (33%), Positives = 15/24 (62%)
Query: 89 IFQGSPTLSEEEIIESSNNETNDE 112
IF P L+ E++++ +TND+
Sbjct: 226 IFNLLPNLNLPELVKAFAVKTNDQ 249
>gnl|CDD|237890 PRK15055, PRK15055, anaerobic sulfite reductase subunit A;
Provisional.
Length = 344
Score = 25.3 bits (56), Expect = 9.7
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 6/32 (18%)
Query: 82 PKSVFFPIFQGSPTL---SEEEIIESSNNETN 110
PK V PI Q TL +E+EI E+ +E
Sbjct: 62 PKEVILPITQ---TLFYFTEDEIKEAKTDEKK 90
>gnl|CDD|233412 TIGR01438, TGR, thioredoxin and glutathione reductase
selenoprotein. This homodimeric, FAD-containing member
of the pyridine nucleotide disulfide oxidoreductase
family contains a C-terminal motif Cys-SeCys-Gly, where
SeCys is selenocysteine encoded by TGA (in some sequence
reports interpreted as a stop codon). In some members of
this subfamily, Cys-SeCys-Gly is replaced by
Cys-Cys-Gly. The reach of the selenium atom at the
C-term arm of the protein is proposed to allow broad
substrate specificity.
Length = 484
Score = 25.6 bits (56), Expect = 10.0
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 82 PKSVFFPIFQGSPTLSEEEIIE 103
P +VF P+ G+ LSEE+ +E
Sbjct: 355 PTTVFTPLEYGACGLSEEKAVE 376
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
0.314 0.132 0.374
Gapped
Lambda K H
0.267 0.0814 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,163,754
Number of extensions: 528656
Number of successful extensions: 459
Number of sequences better than 10.0: 1
Number of HSP's gapped: 456
Number of HSP's successfully gapped: 36
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 53 (24.0 bits)