RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781089|ref|YP_003065502.1| hypothetical protein
CLIBASIA_04955 [Candidatus Liberibacter asiaticus str. psy62]
(80 letters)
>gnl|CDD|30768 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 30.4 bits (68), Expect = 0.11
Identities = 7/17 (41%), Positives = 14/17 (82%), Gaps = 2/17 (11%)
Query: 6 SGKTTLLEAIF--LFGE 20
+GK+++L+AI L+G+
Sbjct: 36 AGKSSILDAITFALYGK 52
>gnl|CDD|31388 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway)
[DNA replication, recombination, and repair].
Length = 363
Score = 30.2 bits (68), Expect = 0.12
Identities = 12/28 (42%), Positives = 15/28 (53%)
Query: 2 GLSESGKTTLLEAIFLFGEALALALSND 29
G + GKT LLEAI+L + S D
Sbjct: 30 GENGQGKTNLLEAIYLLALGRSHRTSRD 57
>gnl|CDD|133369 cd04169, RF3, RF3 subfamily. Peptide chain release factor 3
(RF3) is a protein involved in the termination step of
translation in bacteria. Termination occurs when class
I release factors (RF1 or RF2) recognize the stop codon
at the A-site of the ribosome and activate the release
of the nascent polypeptide. The class II release
factor RF3 then initiates the release of the class I RF
from the ribosome. RF3 binds to the RF/ribosome
complex in the inactive (GDP-bound) state. GDP/GTP
exchange occurs, followed by the release of the class I
RF. Subsequent hydrolysis of GTP to GDP triggers the
release of RF3 from the ribosome. RF3 also enhances
the efficiency of class I RFs at less preferred stop
codons and at stop codons in weak contexts.
Length = 267
Score = 28.3 bits (64), Expect = 0.46
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 7 GKTTLLEAIFLFGEALALA 25
GKTTL E + LFG A+ A
Sbjct: 14 GKTTLTEKLLLFGGAIREA 32
>gnl|CDD|72993 cd03234, ABCG_White, The White subfamily represents ABC
transporters homologous to the Drosophila white gene,
which acts as a dimeric importer for eye pigment
precursors. The eye pigmentation of Drosophila is
developed from the synthesis and deposition in the
cells of red pigments, which are synthesized from
guanine, and brown pigments, which are synthesized from
tryptophan. The pigment precursors are encoded by the
white, brown, and scarlet genes, respectively.
Evidence from genetic and biochemical studies suggest
that the White and Brown proteins function as
heterodimers to import guanine, while the White and
Scarlet proteins function to import tryptophan.
However, a recent study also suggests that White may be
involved in the transport of a metabolite, such as
3-hydroxykynurenine, across intracellular membranes.
Mammalian ABC transporters belonging to the White
subfamily (ABCG1, ABCG5, and ABCG8) have been shown to
be involved in the regulation of lipid-trafficking
mechanisms in macrophages, hepatocytes, and intestinal
mucosa cells. ABCG1 (ABC8), the human homolog of the
Drosophila white gene is induced in monocyte-derived
macrophages during cholesterol influx mediated by
acetylated low-density lipoprotein. It is possible
that human ABCG1 forms heterodimers with several
heterologous partners..
Length = 226
Score = 28.3 bits (63), Expect = 0.54
Identities = 14/54 (25%), Positives = 20/54 (37%), Gaps = 14/54 (25%)
Query: 1 MGLSESGKTTLLEAI--------------FLFGEALALALSNDPVSVFLKSDVF 40
+G S SGKTTLL+AI G+ V+ + D+
Sbjct: 39 LGSSGSGKTTLLDAISGRVEGGGTTSGQILFNGQPRKPDQFQKCVAYVRQDDIL 92
>gnl|CDD|33865 COG4108, PrfC, Peptide chain release factor RF-3 [Translation,
ribosomal structure and biogenesis].
Length = 528
Score = 27.9 bits (62), Expect = 0.66
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 5 ESGKTTLLEAIFLFGEALALA 25
++GKTTL E + LFG A+ A
Sbjct: 22 DAGKTTLTEKLLLFGGAIQEA 42
>gnl|CDD|35284 KOG0061, KOG0061, KOG0061, Transporter, ABC superfamily (Breast
cancer resistance protein) [Secondary metabolites
biosynthesis, transport and catabolism].
Length = 613
Score = 27.6 bits (61), Expect = 0.85
Identities = 11/16 (68%), Positives = 12/16 (75%)
Query: 1 MGLSESGKTTLLEAIF 16
MG S SGKTTLL A+
Sbjct: 62 MGPSGSGKTTLLNALA 77
>gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily.
Translocation is mediated by EF-G (also called
translocase). The structure of EF-G closely resembles
that of the complex between EF-Tu and tRNA. This is an
example of molecular mimicry; a protein domain evolved
so that it mimics the shape of a tRNA molecule. EF-G
in the GTP form binds to the ribosome, primarily
through the interaction of its EF-Tu-like domain with
the 50S subunit. The binding of EF-G to the ribosome
in this manner stimulates the GTPase activity of EF-G.
On GTP hydrolysis, EF-G undergoes a conformational
change that forces its arm deeper into the A site on
the 30S subunit. To accommodate this domain, the
peptidyl-tRNA in the A site moves to the P site,
carrying the mRNA and the deacylated tRNA with it. The
ribosome may be prepared for these rearrangements by
the initial binding of EF-G as well. The dissociation
of EF-G leaves the ribosome ready to accept the next
aminoacyl-tRNA into the A site. This group contains
only bacterial members.
Length = 268
Score = 27.1 bits (61), Expect = 1.0
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 1 MGLSESGKTTLLEAI 15
+G S SGKTTL EA+
Sbjct: 5 VGHSGSGKTTLAEAL 19
>gnl|CDD|33915 COG4175, ProV, ABC-type proline/glycine betaine transport system,
ATPase component [Amino acid transport and metabolism].
Length = 386
Score = 26.9 bits (59), Expect = 1.1
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 1 MGLSESGKTTLLEAI 15
MGLS SGK+TL+ +
Sbjct: 60 MGLSGSGKSTLVRLL 74
>gnl|CDD|48380 cd03116, MobB, Molybdenum is an essential trace element in the
form of molybdenum cofactor (Moco) which is associated
with the metabolism of nitrogen, carbon and sulfur by
redox active enzymes. In E. coli, the synthesis of Moco
involves genes from several loci: moa, mob, mod, moe
and mog. The mob locus contains mobA and mobB genes.
MobB catalyzes the attachment of the guanine
dinucleotide to molybdopterin..
Length = 159
Score = 26.7 bits (59), Expect = 1.5
Identities = 10/14 (71%), Positives = 11/14 (78%)
Query: 2 GLSESGKTTLLEAI 15
G S SGKTTLLE +
Sbjct: 8 GYSGSGKTTLLEKL 21
>gnl|CDD|72999 cd03240, ABC_Rad50, The catalytic domains of Rad50 are similar to
the ATP-binding cassette of ABC transporters, but are
not associated with membrane-spanning domains. The
conserved ATP-binding motifs common to Rad50 and the
ABC transporter family include the Walker A and Walker
B motifs, the Q loop, a histidine residue in the switch
region, a D-loop, and a conserved LSGG sequence. This
conserved sequence, LSGG, is the most specific and
characteristic motif of this family and is thus known
as the ABC signature sequence..
Length = 204
Score = 26.3 bits (58), Expect = 1.8
Identities = 10/22 (45%), Positives = 15/22 (68%), Gaps = 2/22 (9%)
Query: 2 GLSESGKTTLLEAIF--LFGEA 21
G + +GKTT++EA+ L GE
Sbjct: 29 GQNGAGKTTIIEALKYALTGEL 50
>gnl|CDD|30194 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl
transfer from ATP to gluconate. The resulting product
gluconate-6-phoshate is an important precursor of
gluconate metabolism. GntK acts as a dimmer composed of
two identical subunits..
Length = 150
Score = 26.4 bits (58), Expect = 1.9
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 11/40 (27%)
Query: 1 MGLSESGKTTLLEAIFLFGEALALALSNDPVSVFLKSDVF 40
MG+S SGK+T+ G+ALA L + F+ D
Sbjct: 5 MGVSGSGKSTV-------GKALAERLG----APFIDGDDL 33
>gnl|CDD|145545 pfam02463, SMC_N, RecF/RecN/SMC N terminal domain. This domain
is found at the N terminus of SMC proteins. The SMC
(structural maintenance of chromosomes) superfamily
proteins have ATP-binding domains at the N- and
C-termini, and two extended coiled-coil domains
separated by a hinge in the middle. The eukaryotic SMC
proteins form two kind of heterodimers: the SMC1/SMC3
and the SMC2/SMC4 types. These heterodimers constitute
an essential part of higher order complexes, which are
involved in chromatin and DNA dynamics. This family
also includes the RecF and RecN proteins that are
involved in DNA metabolism and recombination.
Length = 1162
Score = 26.1 bits (57), Expect = 2.0
Identities = 11/22 (50%), Positives = 16/22 (72%), Gaps = 1/22 (4%)
Query: 6 SGKTTLLEAI-FLFGEALALAL 26
SGK+ +L+AI F+ GE A +L
Sbjct: 34 SGKSNILDAILFVLGERSAKSL 55
>gnl|CDD|99964 cd03789, GT1_LPS_heptosyltransferase, Lipopolysaccharide
heptosyltransferase is involved in the biosynthesis of
lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a
major component of the outer membrane of gram-negative
bacteria. LPS heptosyltransferase transfers heptose
molecules from ADP-heptose to
3-deoxy-D-manno-octulosonic acid (KDO), a part of the
inner core component of LPS. This family belongs to the
GT-B structural superfamily of glycoslytransferases,
which have characteristic N- and C-terminal domains each
containing a typical Rossmann fold. The two domains have
high structural homology despite minimal sequence
homology. The large cleft that separates the two
domains includes the catalytic center and permits a high
degree of flexibility..
Length = 279
Score = 26.1 bits (58), Expect = 2.1
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 7 GKTTLLEAIFLFGEALALALSND 29
GKT+L E L A L ++ND
Sbjct: 185 GKTSLRELAALLARA-DLVVTND 206
>gnl|CDD|73053 cd03294, ABC_Pro_Gly_Bertaine, This family comprises the glycine
betaine/L-proline ATP binding subunit in bacteria and
its equivalents in archaea. This transport system
belong to the larger ATP-Binding Cassette (ABC)
transporter superfamily. The characteristic feature of
these transporters is the obligatory coupling of ATP
hydrolysis to substrate translocation. ABC
transporters are a subset of nucleotide hydrolases that
contain a signature motif, Q-loop, and H-loop/switch
region, in addition to, the Walker A motif/P-loop and
Walker B motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins..
Length = 269
Score = 25.9 bits (57), Expect = 2.2
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 1 MGLSESGKTTLLEAI 15
MGLS SGK+TLL I
Sbjct: 56 MGLSGSGKSTLLRCI 70
>gnl|CDD|35745 KOG0525, KOG0525, KOG0525, Branched chain alpha-keto acid
dehydrogenase E1, beta subunit [Energy production and
conversion].
Length = 362
Score = 26.1 bits (57), Expect = 2.4
Identities = 13/41 (31%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 4 SESGKTTLLEAIFLFGEALALALSNDPVSVFLKSDV-FDGI 43
E+G+ + +AL +AL DP +V DV F G+
Sbjct: 33 LEAGEKKKMNLYQSVNQALHIALETDPRAVVFGEDVAFGGV 73
>gnl|CDD|72972 cd03213, ABCG_EPDR, ABCG transporters are involved in eye pigment
(EP) precursor transport, regulation of
lipid-trafficking mechanisms, and pleiotropic drug
resistance (DR). DR is a well-described phenomenon
occurring in fungi and shares several similarities with
processes in bacteria and higher eukaryotes. Compared
to other members of the ABC transporter subfamilies,
the ABCG transporter family is composed of proteins
that have an ATP-binding cassette domain at the
N-terminus and a TM (transmembrane) domain at the
C-terminus..
Length = 194
Score = 25.9 bits (57), Expect = 2.5
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 1 MGLSESGKTTLLEAI 15
MG S +GK+TLL A+
Sbjct: 41 MGPSGAGKSTLLNAL 55
>gnl|CDD|133360 cd04160, Arfrp1, Arfrp1 subfamily. Arfrp1 (Arf-related protein
1), formerly known as ARP, is a membrane-associated Arf
family member that lacks the N-terminal myristoylation
motif. Arfrp1 is mainly associated with the
trans-Golgi compartment and the trans-Golgi network,
where it regulates the targeting of Arl1 and the GRIP
domain-containing proteins, golgin-97 and golgin-245,
onto Golgi membranes. It is also involved in the
anterograde transport of the vesicular stomatitis virus
G protein from the Golgi to the plasma membrane, and in
the retrograde transport of TGN38 and Shiga toxin from
endosomes to the trans-Golgi network. Arfrp1 also
inhibits Arf/Sec7-dependent activation of phospholipase
D. Deletion of Arfrp1 in mice causes embryonic
lethality at the gastrulation stage and apoptosis of
mesodermal cells, indicating its importance in
development.
Length = 167
Score = 25.7 bits (57), Expect = 2.7
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 1 MGLSESGKTTLLEAI 15
+GL +GKTT LE +
Sbjct: 5 LGLDNAGKTTFLEQL 19
>gnl|CDD|31949 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis
protein [Coenzyme metabolism].
Length = 161
Score = 25.3 bits (55), Expect = 3.6
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 2 GLSESGKTTLLEAI 15
G SGKTTL+E +
Sbjct: 9 GYKNSGKTTLIEKL 22
>gnl|CDD|73038 cd03279, ABC_sbcCD, SbcCD and other Mre11/Rad50 (MR) complexes
are implicated in the metabolism of DNA ends. They
cleave ends sealed by hairpin structures and are
thought to play a role in removing protein bound to DNA
termini..
Length = 213
Score = 25.2 bits (55), Expect = 3.7
Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 6 SGKTTLLEAIF--LFGEALALALSNDPVSVF 34
+GK+T+L+AI L+G+ + SVF
Sbjct: 39 AGKSTILDAITYALYGKTPRYGRQENLRSVF 69
>gnl|CDD|147030 pfam04670, Gtr1_RagA, Gtr1/RagA G protein conserved region. GTR1
was first identified in S. cerevisiae as a suppressor
of a mutation in RCC1. Biochemical analysis revealed
that Gtr1 is in fact a G protein of the Ras family. The
RagA/B proteins are the human homologues of Gtr1.
Included in this family is the human Rag C, a novel
protein that has been shown to interact with RagA/B.
Length = 230
Score = 25.2 bits (56), Expect = 4.1
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 1 MGLSESGKTTLLEAIF 16
MGL SGK+++ IF
Sbjct: 5 MGLRGSGKSSMRSIIF 20
>gnl|CDD|72971 cd00267, ABC_ATPase, ABC (ATP-binding cassette) transporter
nucleotide-binding domain; ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters
are a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and
GTP-binding and hydrolyzing proteins..
Length = 157
Score = 24.9 bits (54), Expect = 4.5
Identities = 9/18 (50%), Positives = 12/18 (66%)
Query: 1 MGLSESGKTTLLEAIFLF 18
+G + SGK+TLL AI
Sbjct: 31 VGPNGSGKSTLLRAIAGL 48
>gnl|CDD|31331 COG1136, SalX, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 226
Score = 24.7 bits (54), Expect = 5.2
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 1 MGLSESGKTTLLEAI 15
+G S SGK+TLL +
Sbjct: 37 VGPSGSGKSTLLNLL 51
>gnl|CDD|31303 COG1106, COG1106, Predicted ATPases [General function prediction
only].
Length = 371
Score = 24.6 bits (53), Expect = 5.8
Identities = 12/57 (21%), Positives = 21/57 (36%), Gaps = 7/57 (12%)
Query: 2 GLSESGKTTLLEAIFLFGEAL-ALALSNDPVSVFLKSDVFDGISKNQYGFFTGKIKV 57
G + +GK+ LLEA++ + + S P I YG + +
Sbjct: 29 GANGAGKSNLLEALYFLKGLISPGSESPIPFE------REINIWNGSYGKEESNLDI 79
>gnl|CDD|33393 COG3593, COG3593, Predicted ATP-dependent endonuclease of the OLD
family [DNA replication, recombination, and repair].
Length = 581
Score = 24.5 bits (53), Expect = 6.0
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 8/45 (17%)
Query: 2 GLSESGKTTLLEAIFLFGEALALALSNDPVS-VFLKSDVFDGISK 45
G + SGK++LL +AL L L + F D IS+
Sbjct: 30 GENNSGKSSLL-------DALRLLLDPESDLYSFTLDDFHFPISE 67
>gnl|CDD|73014 cd03255, ABC_MJ0796_Lo1CDE_FtsE, This family is comprised of
MJ0796 ATP-binding cassette, macrolide-specific
ABC-type efflux carrier (MacAB), and proteins involved
in cell division (FtsE), and release of liporoteins
from the cytoplasmic membrane (LolCDE). They are
clustered together phylogenetically. MacAB is an
exporter that confers resistance to macrolides, while
the LolCDE system is not a transporter at all. An FtsE
null mutants showed filamentous growth and appeared
viable on high salt medium only, indicating a role for
FtsE in cell division and/or salt transport. The
LolCDE complex catalyses the release of lipoproteins
from the cytoplasmic membrane prior to their targeting
to the outer membrane..
Length = 218
Score = 24.7 bits (54), Expect = 6.5
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 1 MGLSESGKTTLLEAI 15
+G S SGK+TLL +
Sbjct: 36 VGPSGSGKSTLLNIL 50
>gnl|CDD|37962 KOG2751, KOG2751, KOG2751, Beclin-like protein [Signal
transduction mechanisms].
Length = 447
Score = 24.6 bits (53), Expect = 6.7
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 53 GKIKVDAQFILSEKMDIPHVFLPMVHFP 80
I +D + S++MDI + LP+ P
Sbjct: 23 QPIHLDNSLLGSDRMDISELVLPLHKPP 50
>gnl|CDD|35296 KOG0073, KOG0073, KOG0073, GTP-binding ADP-ribosylation
factor-like protein ARL2 [Intracellular trafficking,
secretion, and vesicular transport, Cytoskeleton].
Length = 185
Score = 24.5 bits (53), Expect = 7.0
Identities = 7/15 (46%), Positives = 12/15 (80%)
Query: 1 MGLSESGKTTLLEAI 15
+GL SGKTT+++ +
Sbjct: 22 LGLDNSGKTTIVKKL 36
>gnl|CDD|29996 cd01130, VirB11-like_ATPase, Type IV secretory pathway component
VirB11, and related ATPases. The homohexamer, VirB11 is
one of eleven Vir proteins, which are required for
T-pilus biogenesis and virulence in the transfer of
T-DNA from the Ti (tumor-inducing) plasmid of bacterial
to plant cells. The pilus is a fibrous cell surface
organelle, which mediates adhesion between bacteria
during conjugative transfer or between bacteria and
host eukaryotic cells during infection. VirB11- related
ATPases include the archaeal flagella biosynthesis
protein and the pilus assembly proteins CpaF/TadA and
TrbB. This alignment contains the C-terminal domain,
which is the ATPase..
Length = 186
Score = 24.4 bits (53), Expect = 7.0
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 1 MGLSESGKTTLLEAIFLF 18
G + SGKTTLL A+ F
Sbjct: 31 SGGTGSGKTTLLNALLAF 48
>gnl|CDD|145956 pfam03081, Exo70, Exo70 exocyst complex subunit. The Exo70
protein forms one subunit of the exocyst complex. First
discovered in S. cerevisiae, Exo70 and other exocyst
proteins have been observed in several other
eukaryotes, including humans. In S. cerevisiae, the
exocyst complex is involved in the late stages of
exocytosis, and is localized at the tip of the bud, the
major site of exocytosis in yeast. Exo70 interacts with
the Rho3 GTPase. This interaction mediates one of the
three known functions of Rho3 in cell polarity: vesicle
docking and fusion with the plasma membrane (the other
two functions are regulation of actin polarity and
transport of exocytic vesicles from the mother cell to
the bud). In humans, the functions of Exo70 and the
exocyst complex are less well characterized: Exo70 is
expressed in several tissues and is thought to also be
involved in exocytosis.
Length = 356
Score = 24.2 bits (53), Expect = 7.0
Identities = 9/35 (25%), Positives = 18/35 (51%)
Query: 12 LEAIFLFGEALALALSNDPVSVFLKSDVFDGISKN 46
+ + FGEA+A P +F D+++ +S+
Sbjct: 40 ILQLLNFGEAVASKNKRSPEKLFELLDMYEALSEL 74
>gnl|CDD|111395 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This
domain is found in HypB, a hydrogenase expression /
formation protein, and UreG a urease accessory protein.
Both these proteins contain a P-loop nucleotide binding
motif. HypB has GTPase activity and is a guanine
nucleotide binding protein. It is not known whether
UreG binds GTP or some other nucleotide. Both enzymes
are involved in nickel binding. HypB can store nickel
and is required for nickel dependent hydrogenase
expression. UreG is required for functional
incorporation of the urease nickel metallocenter. GTP
hydrolysis may required by these proteins for nickel
incorporation into other nickel proteins. This family
of domains also contains P47K, a Pseudomonas
chlororaphis protein needed for nitrile hydratase
expression, and the cobW gene product, which may be
involved in cobalamin biosynthesis in Pseudomonas
denitrificans.
Length = 174
Score = 24.5 bits (54), Expect = 7.1
Identities = 8/10 (80%), Positives = 9/10 (90%)
Query: 6 SGKTTLLEAI 15
SGKTTLLE +
Sbjct: 11 SGKTTLLEHL 20
>gnl|CDD|33633 COG3842, PotA, ABC-type spermidine/putrescine transport systems,
ATPase components [Amino acid transport and
metabolism].
Length = 352
Score = 24.1 bits (52), Expect = 8.0
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 1 MGLSESGKTTLLEAI 15
+G S GKTTLL I
Sbjct: 37 LGPSGCGKTTLLRMI 51
>gnl|CDD|133305 cd04105, SR_beta, Signal recognition particle receptor, beta
subunit (SR-beta). SR-beta and SR-alpha form the
heterodimeric signal recognition particle (SRP or SR)
receptor that binds SRP to regulate protein
translocation across the ER membrane. Nascent
polypeptide chains are synthesized with an N-terminal
hydrophobic signal sequence that binds SRP54, a
component of the SRP. SRP directs targeting of the
ribosome-nascent chain complex (RNC) to the ER membrane
via interaction with the SR, which is localized to the
ER membrane. The RNC is then transferred to the
protein-conducting channel, or translocon, which
facilitates polypeptide translation across the ER
membrane or integration into the ER membrane. SR-beta
is found only in eukaryotes; it is believed to control
the release of the signal sequence from SRP54 upon
binding of the ribosome to the translocon. High
expression of SR-beta has been observed in human colon
cancer, suggesting it may play a role in the
development of this type of cancer.
Length = 203
Score = 24.2 bits (53), Expect = 8.0
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 2 GLSESGKTTLL 12
G S+SGKT L
Sbjct: 7 GPSDSGKTALF 17
>gnl|CDD|33076 COG3265, GntK, Gluconate kinase [Carbohydrate transport and
metabolism].
Length = 161
Score = 24.1 bits (52), Expect = 8.3
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 7/27 (25%)
Query: 1 MGLSESGKTTLLEAIFLFGEALALALS 27
MG+S SGK+T+ G ALA L
Sbjct: 1 MGVSGSGKSTV-------GSALAERLG 20
>gnl|CDD|30200 cd02027, APSK, Adenosine 5'-phosphosulfate kinase (APSK)
catalyzes the phosphorylation of adenosine
5'-phosphosulfate to form 3'-phosphoadenosine
5'-phosphosulfate (PAPS). The end-product PAPS is a
biologically "activated" sulfate form important for the
assimilation of inorganic sulfate..
Length = 149
Score = 24.3 bits (53), Expect = 8.4
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 10/51 (19%)
Query: 2 GLSESGKTTLLEAIFLFGEALALALSND--PVSVFLKSDVFDGISKNQYGF 50
GLS SGK+T+ AL L PV V +V G++K+ GF
Sbjct: 6 GLSGSGKSTI-------ARALEEKLFQRGRPVYVLDGDNVRHGLNKD-LGF 48
>gnl|CDD|35288 KOG0065, KOG0065, KOG0065, Pleiotropic drug resistance proteins
(PDR1-15), ABC superfamily [Secondary metabolites
biosynthesis, transport and catabolism].
Length = 1391
Score = 24.1 bits (52), Expect = 8.9
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 1 MGLSESGKTTLL 12
MG S +GKTTLL
Sbjct: 823 MGESGAGKTTLL 834
>gnl|CDD|33631 COG3839, MalK, ABC-type sugar transport systems, ATPase
components [Carbohydrate transport and metabolism].
Length = 338
Score = 24.1 bits (52), Expect = 9.9
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 1 MGLSESGKTTLLEAI 15
+G S GK+TLL I
Sbjct: 35 LGPSGCGKSTLLRMI 49
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.324 0.142 0.407
Gapped
Lambda K H
0.267 0.0787 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 947,497
Number of extensions: 41968
Number of successful extensions: 308
Number of sequences better than 10.0: 1
Number of HSP's gapped: 308
Number of HSP's successfully gapped: 61
Length of query: 80
Length of database: 6,263,737
Length adjustment: 50
Effective length of query: 30
Effective length of database: 5,183,287
Effective search space: 155498610
Effective search space used: 155498610
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: 41 (22.0 bits)
S2: 51 (23.3 bits)