RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4492
(96 letters)
>gnl|CDD|100102 cd00387, Ribosomal_L7_L12, Ribosomal protein L7/L12. Ribosomal
protein L7/L12 refers to the large ribosomal subunit
proteins L7 and L12, which are identical except that L7
is acetylated at the N terminus. It is a component of
the L7/L12 stalk, which is located at the surface of the
ribosome. The stalk base consists of a portion of the
23S rRNA and ribosomal proteins L11 and L10. An extended
C-terminal helix of L10 provides the binding site for
L7/L12. L7/L12 consists of two domains joined by a
flexible hinge, with the helical N-terminal domain (NTD)
forming pairs of homodimers that bind to the extended
helix of L10. It is the only multimeric ribosomal
component, with either four or six copies per ribosome
that occur as two or three dimers bound to the L10
helix. L7/L12 is the only ribosomal protein that does
not interact directly with rRNA, but instead has
indirect interactions through L10. The globular
C-terminal domains of L7/L12 are highly mobile. They are
exposed to the cytoplasm and contain binding sites for
other molecules. Initiation factors, elongation factors,
and release factors are known to interact with the
L7/L12 stalk during their GTP-dependent cycles. The
binding site for the factors EF-Tu and EF-G comprises
L7/L12, L10, L11, the L11-binding region of 23S rRNA,
and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12
has minimal effect on factor binding and it has been
proposed that L7/L12 induces the catalytically active
conformation of EF-Tu and EF-G, thereby stimulating the
GTPase activity of both factors. In eukaryotes, the
proteins that perform the equivalent function to L7/L12
are called P1 and P2, which do not share sequence
similarity with L7/L12. However, a bacterial L7/L12
homolog is found in some eukaryotes, in mitochondria and
chloroplasts. In archaea, the protein equivalent to
L7/L12 is called aL12 or L12p, but it is closer in
sequence to P1 and P2 than to L7/L12.
Length = 127
Score = 74.9 bits (185), Expect = 5e-19
Identities = 32/89 (35%), Positives = 49/89 (55%), Gaps = 1/89 (1%)
Query: 7 AQAPVAAAPVEEEEEKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESI 66
A A AA E ++ F V L + +K+ +IKE++ + G+ L +AK VES
Sbjct: 40 AAAAAPAAAAAAAAEAEEKTEFDVVLESFGAAKKIAVIKEVREIT-GLGLKEAKDLVESA 98
Query: 67 PAVVKTDVTKEEAEALKASLAKVGGEVSV 95
P V+K V+KEEAE +K L + G +V +
Sbjct: 99 PKVLKEGVSKEEAEEIKKKLEEAGAKVEL 127
>gnl|CDD|201294 pfam00542, Ribosomal_L12, Ribosomal protein L7/L12 C-terminal
domain.
Length = 68
Score = 54.4 bits (132), Expect = 1e-11
Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 2/69 (2%)
Query: 28 FTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLA 87
F V L DK K+ +IK ++ + G+ L +AK VE P +K V+KEEAE +K L
Sbjct: 2 FDVVLTSAGDK-KIAVIKVVREIT-GLGLKEAKDLVEGAPKTIKEGVSKEEAEEIKKKLE 59
Query: 88 KVGGEVSVE 96
+ G +V ++
Sbjct: 60 EAGAKVELK 68
>gnl|CDD|234671 PRK00157, rplL, 50S ribosomal protein L7/L12; Reviewed.
Length = 123
Score = 52.5 bits (127), Expect = 3e-10
Identities = 35/88 (39%), Positives = 49/88 (55%), Gaps = 5/88 (5%)
Query: 9 APVAAAPVEEEEEKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESIPA 68
A AAA EEK + F V L DK K+ +IK ++ + G+ L +AK VE P
Sbjct: 41 AAAAAAAAAAAEEK---TEFDVVLKSAGDK-KIAVIKAVREIT-GLGLKEAKDLVEGAPK 95
Query: 69 VVKTDVTKEEAEALKASLAKVGGEVSVE 96
VVK V+KEEAE +K L + G +V ++
Sbjct: 96 VVKEGVSKEEAEEIKKKLEEAGAKVELK 123
>gnl|CDD|223300 COG0222, RplL, Ribosomal protein L7/L12 [Translation, ribosomal
structure and biogenesis].
Length = 124
Score = 47.7 bits (114), Expect = 2e-08
Identities = 35/90 (38%), Positives = 49/90 (54%), Gaps = 5/90 (5%)
Query: 7 AQAPVAAAPVEEEEEKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESI 66
A A AA E EEK + F V L K K+ +IK ++ L G+ L +AK VE
Sbjct: 40 AAAAAGAAAAEAAEEK---TEFDVVLKSAGGK-KIAVIKVVRELT-GLGLKEAKDLVEGA 94
Query: 67 PAVVKTDVTKEEAEALKASLAKVGGEVSVE 96
P V+K V+KEEAE +K L + G +V ++
Sbjct: 95 PKVLKEGVSKEEAEEIKKKLEEAGAKVELK 124
>gnl|CDD|233152 TIGR00855, L12, ribosomal protein L7/L12. Ribosomal proteins L7
and L12 are synonymous except for post-translational
modification of the N-terminal amino acid. THis model
resembles pfam00542 but matches the full length of
prokaryotic and organellar proteins rather than just the
C-terminus [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 123
Score = 44.7 bits (106), Expect = 2e-07
Identities = 35/94 (37%), Positives = 49/94 (52%), Gaps = 5/94 (5%)
Query: 2 TISIFAQAPVAAAPVEEEEEKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKK 61
+ A A AAA EE ++ F V L D K+ +IK ++ + G+ L +AK
Sbjct: 34 AAPVAAGAAGAAAAAAAAEE---KTEFDVILKGAGDN-KIAVIKVVREI-TGLGLKEAKD 88
Query: 62 FVESIPAVVKTDVTKEEAEALKASLAKVGGEVSV 95
VE P V+K V+KEEAE LK L + G +V V
Sbjct: 89 LVEGAPKVLKEGVSKEEAEELKKKLEEAGAKVEV 122
>gnl|CDD|214358 CHL00083, rpl12, ribosomal protein L12.
Length = 131
Score = 44.6 bits (106), Expect = 4e-07
Identities = 32/89 (35%), Positives = 51/89 (57%), Gaps = 4/89 (4%)
Query: 7 AQAPVAAAPVEEEEEKIVQSLFTVKLVKYDDKQKVPLIKEIKGLLEGMNLVQAKKFVESI 66
A A AA EE EEK + F V L + +++ ++K ++ L G+ L +AK+ VES+
Sbjct: 46 APAAAAAQAAEEVEEK---TEFDVILEEVPADKRIAVLKVVRSLT-GLGLKEAKELVESL 101
Query: 67 PAVVKTDVTKEEAEALKASLAKVGGEVSV 95
P +K ++KEEAE K L + G +V +
Sbjct: 102 PKTIKEGISKEEAEEAKKQLEEAGAKVII 130
>gnl|CDD|235546 PRK05653, fabG, 3-ketoacyl-(acyl-carrier-protein) reductase;
Validated.
Length = 246
Score = 27.0 bits (61), Expect = 1.2
Identities = 15/37 (40%), Positives = 17/37 (45%)
Query: 59 AKKFVESIPAVVKTDVTKEEAEALKASLAKVGGEVSV 95
A + VV D +E AEAL A L GGE V
Sbjct: 22 ALRLAADGAKVVIYDSNEEAAEALAAELRAAGGEARV 58
>gnl|CDD|181077 PRK07677, PRK07677, short chain dehydrogenase; Provisional.
Length = 252
Score = 26.6 bits (59), Expect = 2.3
Identities = 18/49 (36%), Positives = 23/49 (46%)
Query: 47 IKGLLEGMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLAKVGGEVSV 95
I G GM AK+F E VV T TKE+ E K + + G+V
Sbjct: 6 ITGGSSGMGKAMAKRFAEEGANVVITGRTKEKLEEAKLEIEQFPGQVLT 54
>gnl|CDD|241308 cd10572, PH_RhoGEF3_XPLN, Rho guanine nucleotide exchange factor
3 Pleckstrin homology (PH) domain. RhoGEF3/XPLN, a Rho
family GEF, preferentially stimulates guanine
nucleotide exchange on RhoA and RhoB, but not RhoC,
RhoG, Rac1, or Cdc42 in vitro. It also possesses
transforming activity. RhoGEF3/XPLN contains a tandem
Dbl homology and PH domain, but lacks homology with
other known functional domains or motifs. It is
expressed in the brain, skeletal muscle, heart, kidney,
platelets, and macrophage and neuronal cell lines. PH
domains have diverse functions, but in general are
involved in targeting proteins to the appropriate
cellular location or in the interaction with a binding
partner. They share little sequence conservation, but
all have a common fold, which is electrostatically
polarized. Less than 10% of PH domains bind
phosphoinositide phosphates (PIPs) with high affinity
and specificity. PH domains are distinguished from
other PIP-binding domains by their specific
high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 143
Score = 26.1 bits (58), Expect = 2.4
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 31 KLVKYDDKQKVPLIKEIKGLL 51
+L D+KQK PLI E + LL
Sbjct: 11 RLEYLDEKQKDPLIDESRALL 31
>gnl|CDD|139037 PRK12525, PRK12525, RNA polymerase sigma factor; Provisional.
Length = 168
Score = 26.1 bits (57), Expect = 2.6
Identities = 8/28 (28%), Positives = 16/28 (57%)
Query: 3 ISIFAQAPVAAAPVEEEEEKIVQSLFTV 30
+ A+AP A P EE+ ++++L +
Sbjct: 85 LQSLAEAPEAVQPSPEEQWMVIETLLAI 112
>gnl|CDD|217812 pfam03953, Tubulin_C, Tubulin C-terminal domain. This family
includes the tubulin alpha, beta and gamma chains.
Members of this family are involved in polymer
formation. Tubulins are GTPases. FtsZ can polymerise
into tubes, sheets, and rings in vitro and is ubiquitous
in eubacteria and archaea. Tubulin is the major
component of microtubules. (The FtsZ GTPases have been
split into their won family).
Length = 126
Score = 25.6 bits (57), Expect = 2.9
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 3/37 (8%)
Query: 52 EGMNLVQAKK---FVESIPAVVKTDVTKEEAEALKAS 85
+ + +Q K FVE IP +K + L S
Sbjct: 68 KAIQRIQEKNSANFVEWIPNSIKVAICDVPPYGLPGS 104
>gnl|CDD|173871 cd08506, PBP2_clavulanate_OppA2, The substrate-binding domain of an
oligopeptide binding protein (OppA2) from the
biosynthesis pathway of the beta-lactamase inhibitor
clavulanic acid contains the type 2 periplasmic binding
fold. Clavulanic acid (CA), a clinically important
beta-lactamase inhibitor, is one of a family of clavams
produced as secondary metabolites by fermentation of
Streptomyces clavuligeru. The biosynthesis of CA
proceeds via multiple steps from the precursors,
glyceraldehyde-3-phosphate and arginine. CA possesses a
characteristic (3R,5R) stereochemistry essential for
reaction with penicillin-binding proteins and
beta-lactamases. Two genes (oppA1 and oppA2) in the
clavulanic acid gene cluster encode oligopeptide-binding
proteins that are required for CA biosynthesis. OppA1/2
is involved in the binding and transport of peptides
across the cell membrane of Streptomyces clavuligerus.
Most of other periplasmic binding proteins are comprised
of only two globular subdomains corresponding to domains
I and III of the dipeptide/oligopeptide binding
proteins. The structural topology of these domains is
most similar to that of the type 2 periplasmic binding
proteins (PBP2), which are responsible for the uptake of
a variety of substrates such as phosphate, sulfate,
polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis. Besides transport proteins, the PBP2
superfamily includes the ligand-binding domains from
ionotropic glutamate receptors, LysR-type
transcriptional regulators, and unorthodox sensor
proteins involved in signal transduction.
Length = 466
Score = 26.1 bits (58), Expect = 3.0
Identities = 13/24 (54%), Positives = 19/24 (79%)
Query: 72 TDVTKEEAEALKASLAKVGGEVSV 95
T V K+ AEAL+ASLA+ G +V++
Sbjct: 328 TAVDKKIAEALQASLARAGIDVTL 351
>gnl|CDD|184703 PRK14485, PRK14485, putative bifunctional cbb3-type cytochrome c
oxidase subunit I/II; Provisional.
Length = 712
Score = 25.8 bits (57), Expect = 4.1
Identities = 11/33 (33%), Positives = 14/33 (42%)
Query: 12 AAAPVEEEEEKIVQSLFTVKLVKYDDKQKVPLI 44
A A + E+ E I L DK+ V LI
Sbjct: 659 AQADLREQAEAIAADLAADGFKVAPDKEIVALI 691
>gnl|CDD|173882 cd08517, PBP2_NikA_DppA_OppA_like_13, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 480
Score = 25.6 bits (57), Expect = 4.2
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 73 DVTKEEAEALKASLAKVGGEVSVE 96
+ K AE +K +L +VG +V +
Sbjct: 345 EFWKRTAEYVKQALKEVGIDVELR 368
>gnl|CDD|183833 PRK12939, PRK12939, short chain dehydrogenase; Provisional.
Length = 250
Score = 25.3 bits (56), Expect = 4.9
Identities = 12/41 (29%), Positives = 16/41 (39%)
Query: 53 GMNLVQAKKFVESIPAVVKTDVTKEEAEALKASLAKVGGEV 93
G+ A+ E+ V D EA L A+L GG
Sbjct: 18 GLGAAFAEALAEAGATVAFNDGLAAEARELAAALEAAGGRA 58
>gnl|CDD|173877 cd08512, PBP2_NikA_DppA_OppA_like_7, The substrate-binding
component of an uncharacterized ABC-type
nickel/dipeptide/oligopeptide-like import system
contains the type 2 periplasmic binding fold. This CD
represents the substrate-binding domain of an
uncharacterized ATP-binding cassette (ABC) type
nickel/dipeptide/oligopeptide-like transporter. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA, the initial nickel receptor. The
DppA binds dipeptides and some tripeptides and is
involved in chemotaxis toward dipeptides, whereas the
OppA binds peptides of a wide range of lengths (2-35
amino acid residues) and plays a role in recycling of
cell wall peptides, which precludes any involvement in
chemotaxis. Most of other periplasmic binding proteins
are comprised of only two globular subdomains
corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 476
Score = 25.6 bits (57), Expect = 5.0
Identities = 9/32 (28%), Positives = 20/32 (62%)
Query: 65 SIPAVVKTDVTKEEAEALKASLAKVGGEVSVE 96
++ + ++ A+ L+ASLA++G +V +E
Sbjct: 337 TLSYNSGNEPREDIAQLLQASLAQIGIKVEIE 368
>gnl|CDD|216520 pfam01474, DAHP_synth_2, Class-II DAHP synthetase family.
Members of this family are aldolase enzymes that
catalyze the first step of the shikimate pathway.
Length = 437
Score = 25.6 bits (57), Expect = 5.5
Identities = 7/16 (43%), Positives = 7/16 (43%)
Query: 74 VTKEEAEALKASLAKV 89
V E LK LA V
Sbjct: 38 VFAGEIRRLKEQLADV 53
>gnl|CDD|131451 TIGR02398, gluc_glyc_Psyn, glucosylglycerol-phosphate synthase.
Glucosylglycerol-phosphate synthase catalyzes the key
step in the biosynthesis of the osmolyte
glucosylglycerol. It is known in several cyanobacteria
and in Pseudomonas anguilliseptica. The enzyme is
closely related to the alpha,alpha-trehalose-phosphate
synthase, likewise involved in osmolyte biosynthesis, of
E. coli and many other bacteria. A close homolog from
Xanthomonas campestris is excluded from this model and
scores between trusted and noise.
Length = 487
Score = 25.2 bits (55), Expect = 6.7
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 8 QAPVAAAPVEEEEEKIVQSLFTVKLV 33
++ +AAA + E E+I L VKL+
Sbjct: 263 RSALAAASIREMMERIRSELAGVKLI 288
>gnl|CDD|215107 PLN00220, PLN00220, tubulin beta chain; Provisional.
Length = 447
Score = 25.2 bits (55), Expect = 7.1
Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 52 EGMNLVQAKK---FVESIPAVVKTDVTKEEAEALKASLAKVGGEVSVE 96
E M VQ K FVE IP VK+ V + LK + +G S++
Sbjct: 328 EQMINVQNKNSSYFVEWIPNNVKSSVCDIPPKGLKMASTFIGNSTSIQ 375
>gnl|CDD|220081 pfam08959, DUF1872, Domain of unknown function (DUF1872). The CS
domain, found in Ubiquitin specific peptidase 19
(USP-19), has no known function.
Length = 288
Score = 24.6 bits (53), Expect = 9.7
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 8 QAPVAAAPVEEEEEKIV 24
+PV+ PVEEEEEK V
Sbjct: 270 HSPVSKEPVEEEEEKKV 286
>gnl|CDD|239545 cd03462, 1,2-CCD, chlorocatechol 1,2-dioxygenases (1,2-CCDs)
(type II enzymes) are homodimeric intradiol
dioxygenases that degrade chlorocatechols via the
addition of molecular oxygen and the subsequent
cleavage between two adjacent hydroxyl groups. This
reaction is part of the modified ortho-cleavage pathway
which is a central oxidative bacterial pathway that
channels chlorocatechols, derived from the degradation
of chlorinated benzoic acids, phenoxyacetic acids,
phenols, benzenes, and other aromatics into the
energy-generating tricarboxylic acid pathway.
Length = 247
Score = 24.6 bits (54), Expect = 9.9
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 59 AKKFVESIPAV-VKTDVTKEEAEALKASLAKVGG 91
V++I V +K +VT +E A L KVG
Sbjct: 9 VGDIVDAIRDVLLKHEVTYDEYRAGVQYLIKVGE 42
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
0.310 0.128 0.321
Gapped
Lambda K H
0.267 0.0816 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,699,702
Number of extensions: 394384
Number of successful extensions: 552
Number of sequences better than 10.0: 1
Number of HSP's gapped: 545
Number of HSP's successfully gapped: 70
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 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (24.0 bits)