RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780996|ref|YP_003065409.1| hypothetical protein
CLIBASIA_04485 [Candidatus Liberibacter asiaticus str. psy62]
(109 letters)
>gnl|CDD|33631 COG3839, MalK, ABC-type sugar transport systems, ATPase
components [Carbohydrate transport and metabolism].
Length = 338
Score = 30.2 bits (68), Expect = 0.13
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 6/55 (10%)
Query: 11 SGCGKNPVWDSMKGCLNFSSYDDNSGNIDTDESDINTAIAIRKDVARVLQVSYPL 65
SGCGK+ + + G + SG I D D+ ++ +A V Q +Y L
Sbjct: 38 SGCGKSTLLRMIAGLE-----EPTSGEILIDGRDVTDLPPEKRGIAMVFQ-NYAL 86
>gnl|CDD|32727 COG2902, COG2902, NAD-specific glutamate dehydrogenase [Amino acid
transport and metabolism].
Length = 1592
Score = 27.2 bits (60), Expect = 1.1
Identities = 8/31 (25%), Positives = 16/31 (51%)
Query: 21 SMKGCLNFSSYDDNSGNIDTDESDINTAIAI 51
++ G + DNS +D + ++N IA+
Sbjct: 1135 ALAGGRINTDAIDNSAGVDCSDHEVNIKIAL 1165
>gnl|CDD|33953 COG4228, COG4228, Mu-like prophage DNA circulation protein [General
function prediction only].
Length = 451
Score = 26.9 bits (59), Expect = 1.2
Identities = 10/52 (19%), Positives = 18/52 (34%), Gaps = 2/52 (3%)
Query: 11 SGCG--KNPVWDSMKGCLNFSSYDDNSGNIDTDESDINTAIAIRKDVARVLQ 60
SG G +P + +M +N DD++ IN + +
Sbjct: 80 SGAGTLVHPDYGTMNVLINAFERDDSAAEQRVFRFTINATPVFDRTAPEITF 131
>gnl|CDD|34408 COG4799, COG4799, Acetyl-CoA carboxylase, carboxyltransferase
component (subunits alpha and beta) [Lipid metabolism].
Length = 526
Score = 26.7 bits (59), Expect = 1.3
Identities = 16/66 (24%), Positives = 23/66 (34%)
Query: 33 DNSGNIDTDESDINTAIAIRKDVARVLQVSYPLPAPQEITPRMGNRKTVELLIEIDDQKV 92
SG D D AI + + + L + P P TP +R EL + D
Sbjct: 226 RKSGVADLLAEDDEDAIELVRRLLSYLPSNNREPPPVVPTPDEPDRDDEELDSIVPDDPR 285
Query: 93 WLLNVH 98
+V
Sbjct: 286 KPYDVR 291
>gnl|CDD|107386 cd06391, PBP1_iGluR_delta_2, N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the delta2 receptor of an orphan glutamate
receptor family. N-terminal
leucine/isoleucine/valine-binding protein (LIVBP)-like
domain of the delta2 receptor of an orphan glutamate
receptor family. While this N-terminal domain belongs to
the periplasmic-binding fold type I superfamily, the
glutamate-binding domain of the iGluR is structurally
homologous to the periplasmic-binding fold type II. The
LIVBP-like domain of iGluRs is thought to play a role in
the initial assembly of iGluR subunits, but it is not
well understood how this domain is arranged and
functions in intact iGluR. Although the delta receptors
are a member of the ionotropic glutamate receptor
family, they cannot be activated by AMPA, kainate, NMDA,
glutamate, or any other ligands. Phylogenetic analysis
shows that both GluRdelta1 and GluRalpha2 are closer
related to non-NMDA receptors. GluRdelta2 was shown to
function as an AMPA-like receptor by mutation analysis.
Moreover, targeted disruption of GluRdelta2 gene caused
motor coordination impairment, Purkinje cell maturation,
and long-term depression of synaptic transmission. It
has been suggested that GluRdelta2 is the receptor for
cerebellin 1, a glycoprotein of the Clq and tumor
necrosis factor family that is secreted from cerebellar
granule cells.
Length = 400
Score = 26.1 bits (57), Expect = 2.0
Identities = 16/73 (21%), Positives = 34/73 (46%), Gaps = 2/73 (2%)
Query: 27 NFSSYDDNSGNIDTDESDINTAIAIRKDVARVLQVSYPLPAPQEITPR--MGNRKTVELL 84
N ++D + I+ + SD++ +R+ + R+ + P PQ I+ R GN + L
Sbjct: 223 NLVAFDCHWIIINEEISDMDVQELVRRSIGRLTIIRQTFPLPQNISQRCFRGNHRISSSL 282
Query: 85 IEIDDQKVWLLNV 97
+ D ++ +
Sbjct: 283 CDPKDPFAQMMEI 295
>gnl|CDD|73012 cd03253, ABCC_ATM1_transporter, ATM1 is an ABC transporter that
is expressed in the mitochondria. Although the
specific function of ATM1 is unknown, its disruption
results in the accumulation of excess mitochondrial
iron, loss of mitochondrial cytochromes, oxidative
damage to mitochondrial DNA, and decreased levels of
cytosolic heme proteins. 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 = 236
Score = 25.9 bits (57), Expect = 2.3
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 7/52 (13%)
Query: 11 SGCGKNPVWDSMKGCLNFSSYDDNSGNIDTDESDIN--TAIAIRKDVARVLQ 60
SG GK+ + ++ L F YD +SG+I D DI T ++R+ + V Q
Sbjct: 36 SGSGKSTI---LR--LLFRFYDVSSGSILIDGQDIREVTLDSLRRAIGVVPQ 82
>gnl|CDD|36850 KOG1637, KOG1637, KOG1637, Threonyl-tRNA synthetase [Translation,
ribosomal structure and biogenesis].
Length = 560
Score = 26.1 bits (57), Expect = 2.5
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 3/29 (10%)
Query: 3 EDKWYIFYSGCGKNPVWDSMKGCLNFSSY 31
+D +IF C + V + +KGCL+F Y
Sbjct: 302 QDDAHIF---CTPDQVKEEIKGCLDFLDY 327
>gnl|CDD|35260 KOG0037, KOG0037, KOG0037, Ca2+-binding protein, EF-Hand protein
superfamily [Signal transduction mechanisms].
Length = 221
Score = 24.9 bits (54), Expect = 4.6
Identities = 11/27 (40%), Positives = 15/27 (55%), Gaps = 2/27 (7%)
Query: 18 VWDSMKGCLN-FSSYD-DNSGNIDTDE 42
+W + N F +YD D SG ID+ E
Sbjct: 119 LWKYINQWRNVFRTYDRDRSGTIDSSE 145
>gnl|CDD|34862 COG5265, ATM1, ABC-type transport system involved in Fe-S cluster
assembly, permease and ATPase components
[Posttranslational modification, protein turnover,
chaperones].
Length = 497
Score = 24.8 bits (54), Expect = 5.0
Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 7/52 (13%)
Query: 11 SGCGKNPVWDSMKGCLNFSSYDDNSGNIDTDESDIN--TAIAIRKDVARVLQ 60
SG GK+ + L F YD NSG+I D DI T ++R+ + V Q
Sbjct: 298 SGAGKSTILR-----LLFRFYDVNSGSITIDGQDIRDVTQQSLRRAIGIVPQ 344
>gnl|CDD|73060 cd03301, ABC_MalK_N, The N-terminal ATPase domain of the maltose
transporter, MalK. ATP binding cassette (ABC) proteins
function from bacteria to human, mediating the
translocation of substances into and out of cells or
organelles. ABC transporters contain two
transmembrane-spanning domains (TMDs) or subunits and
two nucleotide binding domains (NBDs) or subunits that
couple transport to the hydrolysis of ATP. In the
maltose transport system, the periplasmic maltose
binding protein (MBP) stimulates the ATPase activity of
the membrane-associated transporter, which consists of
two transmembrane subunits, MalF and MalG, and two
copies of the ATP binding subunit, MalK, and becomes
tightly bound to the transporter in the catalytic
transition state, ensuring that maltose is passed to
the transporter as ATP is hydrolyzed..
Length = 213
Score = 24.7 bits (54), Expect = 5.6
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 6/55 (10%)
Query: 11 SGCGKNPVWDSMKGCLNFSSYDDNSGNIDTDESDINTAIAIRKDVARVLQVSYPL 65
SGCGK + G + SG I D+ +D+A V Q +Y L
Sbjct: 35 SGCGKTTTLRMIAGL-----EEPTSGRIYIGGRDVTDLPPKDRDIAMVFQ-NYAL 83
>gnl|CDD|32824 COG3007, COG3007, Uncharacterized paraquat-inducible protein B
[Function unknown].
Length = 398
Score = 24.5 bits (53), Expect = 6.0
Identities = 13/42 (30%), Positives = 21/42 (50%)
Query: 36 GNIDTDESDINTAIAIRKDVARVLQVSYPLPAPQEITPRMGN 77
G+ +DE AI++D +V V Y L +P+ P+ G
Sbjct: 110 GDAFSDEMKQKVIEAIKQDFGKVDLVVYSLASPRRKHPKTGE 151
>gnl|CDD|39604 KOG4403, KOG4403, KOG4403, Cell surface glycoprotein STIM,
contains SAM domain [General function prediction only].
Length = 575
Score = 24.7 bits (53), Expect = 6.5
Identities = 8/13 (61%), Positives = 12/13 (92%)
Query: 32 DDNSGNIDTDESD 44
DD++G+ID +ESD
Sbjct: 79 DDHNGSIDVEESD 91
>gnl|CDD|173856 cd08491, PBP2_NikA_DppA_OppA_like_12, 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 = 473
Score = 24.3 bits (53), Expect = 7.0
Identities = 6/27 (22%), Positives = 14/27 (51%)
Query: 38 IDTDESDINTAIAIRKDVARVLQVSYP 64
++T E+D+ +IA++ +Y
Sbjct: 202 VETGEADLAPSIAVQDATNPDTDFAYL 228
>gnl|CDD|39350 KOG4147, KOG4147, KOG4147, Uncharacterized conserved protein
[Function unknown].
Length = 127
Score = 23.8 bits (51), Expect = 9.9
Identities = 8/18 (44%), Positives = 10/18 (55%)
Query: 79 KTVELLIEIDDQKVWLLN 96
KT L+I +D WLL
Sbjct: 74 KTNNLVINLDHDDRWLLK 91
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
0.317 0.135 0.417
Gapped
Lambda K H
0.267 0.0520 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,356,936
Number of extensions: 59216
Number of successful extensions: 153
Number of sequences better than 10.0: 1
Number of HSP's gapped: 153
Number of HSP's successfully gapped: 14
Length of query: 109
Length of database: 6,263,737
Length adjustment: 75
Effective length of query: 34
Effective length of database: 4,643,062
Effective search space: 157864108
Effective search space used: 157864108
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: 41 (21.7 bits)
S2: 51 (23.9 bits)