RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781199|ref|YP_003065612.1| hypothetical protein
CLIBASIA_05530 [Candidatus Liberibacter asiaticus str. psy62]
(157 letters)
>gnl|CDD|31689 COG1500, COG1500, Predicted exosome subunit [Translation, ribosomal
structure and biogenesis].
Length = 234
Score = 27.5 bits (61), Expect = 1.5
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 6/75 (8%)
Query: 14 LLRFIPSGFERI---VDVVSEYLTKKQSI--EYDKLKLEMAKNDSSTQLDLAEIKAGIEE 68
L IP FER V + EY K + ++ ++K E + D S + + EI AG ++
Sbjct: 153 LRPIIPIRFERAKVAVKIPVEYAGKAYGLLRKFGEIKKEEWQEDGS-WICVLEIPAGNQD 211
Query: 69 LKIDKPIRLARIEAQ 83
+ L + E Q
Sbjct: 212 EFYELLNELTKGEVQ 226
>gnl|CDD|38081 KOG2870, KOG2870, KOG2870, NADH:ubiquinone oxidoreductase,
NDUFS2/49 kDa subunit [Energy production and
conversion].
Length = 452
Score = 27.2 bits (60), Expect = 2.1
Identities = 21/90 (23%), Positives = 43/90 (47%), Gaps = 7/90 (7%)
Query: 21 GFERIVDVVSEYLTKKQSIEY-DKLK-LEMAKNDSSTQLDLAEIKAGIEELKIDKPIRLA 78
G E+++ EY T Q++ Y D+L + M N+ + L + ++ I+ K IR+
Sbjct: 108 GTEKLI----EYKTYTQALPYFDRLDYVSMMCNEQAYSLAVEKL-LNIDVPLRAKYIRVL 162
Query: 79 RIEAQKVKSGVKWVDGFTALIRPLTTFFWI 108
E ++ + + + + +T FFW+
Sbjct: 163 FGEITRIANHIMALGTHALDVGAMTPFFWL 192
>gnl|CDD|146444 pfam03805, CLAG, Cytoadherence-linked asexual protein. Clag
(cytoadherence linked asexual gene) is a malaria
surface protein which has been shown to be involved in
the binding of Plasmodium falciparum infected
erythrocytes to host endothelial cells, a process
termed cytoadherence. The cytoadherence phenomenon is
associated with the sequestration of infected
erythrocytes in the blood vessels of the brain,
cerebral malaria. Clag is a multi-gene family in
Plasmodium falciparum with at least 9 members
identified to date. Orthologous proteins in the rodent
malaria species Plasmodium chabaudi (Lawson D Unpubl.
obs.) suggest that the gene family is found in other
malaria species and may play a more generic role in
cytoadherence.
Length = 1282
Score = 26.6 bits (59), Expect = 2.9
Identities = 12/31 (38%), Positives = 21/31 (67%)
Query: 37 QSIEYDKLKLEMAKNDSSTQLDLAEIKAGIE 67
Q++E DKLKL +A +D+ LD+++ K +
Sbjct: 28 QTLEQDKLKLPIATSDTKEYLDISKFKIINK 58
>gnl|CDD|38459 KOG3249, KOG3249, KOG3249, Uncharacterized conserved protein
[Function unknown].
Length = 181
Score = 26.6 bits (58), Expect = 3.2
Identities = 4/28 (14%), Positives = 10/28 (35%)
Query: 91 WVDGFTALIRPLTTFFWIIVYPLLVWWS 118
W+ +L + W ++ P+
Sbjct: 97 WLMFSLSLKMWVIVLLWFVLAPIAHRLD 124
>gnl|CDD|36189 KOG0971, KOG0971, KOG0971, Microtubule-associated protein dynactin
DCTN1/Glued [Cell cycle control, cell division,
chromosome partitioning, Cytoskeleton].
Length = 1243
Score = 26.2 bits (57), Expect = 4.7
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 38 SIEYDKLKLEMAKNDSST-QLDLAEIKAGIEELKIDKPIRLARIEAQ 83
+IE L EMA+ + + Q ++ +K ++EL+ D I A +E +
Sbjct: 312 AIEMATLDKEMAEERAESLQQEVEALKERVDELETDLEILKAEMEEK 358
>gnl|CDD|37825 KOG2614, KOG2614, KOG2614, Kynurenine 3-monooxygenase and related
flavoprotein monooxygenases [Energy production and
conversion, General function prediction only].
Length = 420
Score = 25.7 bits (56), Expect = 5.7
Identities = 25/121 (20%), Positives = 48/121 (39%), Gaps = 8/121 (6%)
Query: 13 FLLRFIPSGFERIVDVVSEYLTKKQSIEYDKLKLEMAKNDSSTQLDLAEIKAGIEELKID 72
FL + FE V V++E L + + + +N+S ++LA + K +
Sbjct: 303 FLGQGGNCAFEDCV-VLAECLDEAINDVSLAGEEYSRENESHAIIELA-----MYSYKEE 356
Query: 73 KPIRLARIEAQKVKSGVKWVDGFTALIRPLTTFFWIIVYPLLVWWSVKEGMFNSDPLTLL 132
+ RL R++ G+ + + + +F II L +K+ + N L
Sbjct: 357 RWRRLLRLKVDAYLVGI--LPQSFGPLYLMVSFRDIIYSEALERLGIKKKILNDGSFFLF 414
Query: 133 S 133
S
Sbjct: 415 S 415
>gnl|CDD|36641 KOG1428, KOG1428, KOG1428, Inhibitor of type V adenylyl
cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1
[Signal transduction mechanisms].
Length = 3738
Score = 25.8 bits (56), Expect = 5.8
Identities = 9/43 (20%), Positives = 21/43 (48%)
Query: 45 KLEMAKNDSSTQLDLAEIKAGIEELKIDKPIRLARIEAQKVKS 87
+E ++D LA + G + L+ + P ++ +A++ S
Sbjct: 2335 MVEFCESDEGEAWSLARDRGGNQYLRHEDPRERSKSDAKQAMS 2377
>gnl|CDD|35241 KOG0018, KOG0018, KOG0018, Structural maintenance of chromosome
protein 1 (sister chromatid cohesion complex Cohesin,
subunit SMC1) [Cell cycle control, cell division,
chromosome partitioning].
Length = 1141
Score = 25.6 bits (56), Expect = 6.2
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 16 RFIPSGFERIVDVVSEYLTKKQSIEYDKLKLEMAKNDSSTQLDLAEIKAGIEELKIDK 73
P + + +S + K EY++LK EMAK + +T + + K+ E K K
Sbjct: 139 GKNPKELTALFEEISGSIELKP--EYEELKYEMAKAEETTTGNYKKKKSIAAEKKEAK 194
>gnl|CDD|38307 KOG3097, KOG3097, KOG3097, Predicted membrane protein [Function
unknown].
Length = 390
Score = 25.7 bits (56), Expect = 6.3
Identities = 13/66 (19%), Positives = 28/66 (42%), Gaps = 7/66 (10%)
Query: 82 AQKVKSGVKWVDGFTALIRPLTTFFWIIVYPLLVWWSVKEGMFNSDPLTLLSPFTQEIIA 141
+K + V ++ F + L ++ PL ++ +++ +D FT+ +A
Sbjct: 252 GEKRLASVSGLNIFQLTFKHLRDIRLRLLVPLTIFSGLEQAFLCAD-------FTKAYVA 304
Query: 142 CILGFW 147
C LG
Sbjct: 305 CALGVS 310
>gnl|CDD|99834 cd06130, DNA_pol_III_epsilon_like, an uncharacterized bacterial
subgroup of the DEDDh 3'-5' exonuclease domain family
with similarity to the epsilon subunit of DNA polymerase
III. This subfamily is composed of uncharacterized
bacterial proteins with similarity to the epsilon
subunit of DNA polymerase III (Pol III), a multisubunit
polymerase which is the main DNA replicating enzyme in
bacteria, functioning as the chromosomal replicase. The
Pol III holoenzyme is a complex of ten different
subunits, three of which (alpha, epsilon, and theta)
compose the catalytic core. The Pol III epsilon subunit,
encoded by the dnaQ gene, is a DEDDh-type 3'-5'
exonuclease which is responsible for the proofreading
activity of the polymerase, increasing the fidelity of
DNA synthesis. It contains three conserved sequence
motifs termed ExoI, ExoII and ExoIII, with a specific
Hx(4)D conserved pattern at ExoIII. These motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. The epsilon
subunit of Pol III also functions as a stabilizer of the
holoenzyme complex.
Length = 156
Score = 25.5 bits (57), Expect = 7.2
Identities = 11/34 (32%), Positives = 15/34 (44%), Gaps = 6/34 (17%)
Query: 75 IRLARIEAQKVKSGVKWVDGFTALIRPLTTFFWI 108
I L ++ ++ VD F LIRP T F
Sbjct: 19 IGLVKVRDGQI------VDTFYTLIRPPTRFDPF 46
>gnl|CDD|173875 cd08510, PBP2_Lactococcal_OppA_like, The substrate binding
component of an ABC-type lactococcal OppA-like transport
system contains. This family represents the substrate
binding domain of an ATP-binding cassette (ABC)-type
oligopeptide import system from Lactococcus lactis and
other gram-positive bacteria, as well as its closet
homologs from gram-negative bacteria.
Oligopeptide-binding protein (OppA) from Lactococcus
lactis can bind peptides of length from 4 to at least 35
residues without sequence preference. The oligopeptide
import system OppABCDEF is consisting of five subunits:
two homologous integral membrane proteins OppB and OppF
that form the translocation pore; two homologous
nucleotide-binding domains OppD and OppF that drive the
transport process through binding and hydrolysis of ATP;
and the substrate-binding protein or receptor OppA that
determines the substrate specificity of the transport
system. The dipeptide (DppA) and oligopeptide (OppA)
binding proteins differ in several ways. The DppA binds
dipeptides and some tripeptides and also is involved in
chemotaxis toward dipeptides, whereas the OppA binds
peptides of a wide range of lengths (2-35 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 = 516
Score = 25.3 bits (56), Expect = 7.2
Identities = 14/50 (28%), Positives = 21/50 (42%), Gaps = 8/50 (16%)
Query: 62 IKAGIEELKIDKPIRLARIEAQKVKSGVKWVDGFTALIRPLTTFFWIIVY 111
+G + K+D + I +K GVKW DG +P+T Y
Sbjct: 49 TDSGAAKFKLDDKAKTVTI---TIKDGVKWSDG-----KPVTAKDLEYSY 90
>gnl|CDD|38425 KOG3215, KOG3215, KOG3215, Uncharacterized conserved protein
[Function unknown].
Length = 222
Score = 25.4 bits (55), Expect = 7.5
Identities = 7/34 (20%), Positives = 16/34 (47%)
Query: 40 EYDKLKLEMAKNDSSTQLDLAEIKAGIEELKIDK 73
+ KLE+ ++ + + +K + E KI +
Sbjct: 93 NLVQKKLEIERSIQKARNKIELLKKQLHEAKIVR 126
>gnl|CDD|36049 KOG0831, KOG0831, KOG0831, Acyl-CoA:diacylglycerol acyltransferase
(DGAT) [Lipid transport and metabolism].
Length = 334
Score = 25.2 bits (55), Expect = 7.7
Identities = 6/16 (37%), Positives = 7/16 (43%)
Query: 102 LTTFFWIIVYPLLVWW 117
L T FW + VW
Sbjct: 42 LFTRFWPLAILYAVWL 57
>gnl|CDD|99838 cd06135, Orn, DEDDh 3'-5' exonuclease domain of oligoribonuclease
and similar proteins. Oligoribonuclease (Orn) is a
DEDDh-type DnaQ-like 3'-5' exoribonuclease that is
responsible for degrading small oligoribonucleotides to
mononucleotides. It contains three conserved sequence
motifs termed ExoI, ExoII and ExoIII, with a specific
Hx(4)D conserved pattern at ExoIII. These motifs are
clustered around the active site and contain four
conserved acidic residues that serve as ligands for the
two metal ions required for catalysis. Orn is essential
for Escherichia coli survival. The human homolog, also
called Sfn (small fragment nuclease), is able to
hydrolyze short single-stranded RNA and DNA oligomers.
It plays a role in cellular nucleotide recycling.
Length = 173
Score = 25.2 bits (56), Expect = 8.8
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 11/66 (16%)
Query: 11 FRFLLRFIPSGFE----RIVDVVS--EYLTKKQSIEYDKLKLEMAKNDSSTQLDLAEIKA 64
RFL +++P E RI+DV S E + Y ++ + A T L +I+
Sbjct: 106 RRFLDKYMPELEEYLHYRILDVSSIKELARRW----YPEIYRK-APKKKGTHRALDDIRE 160
Query: 65 GIEELK 70
I ELK
Sbjct: 161 SIAELK 166
>gnl|CDD|30565 COG0216, PrfA, Protein chain release factor A [Translation,
ribosomal structure and biogenesis].
Length = 363
Score = 25.1 bits (55), Expect = 9.4
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 3/50 (6%)
Query: 23 ERIVDVVSEYLTKKQSIEYDKLKLEMAKNDS---STQLDLAEIKAGIEEL 69
E IV+ EY ++ +E K L K+ + ++ E++A IEEL
Sbjct: 46 EPIVEKYREYKKAQEDLEDAKEMLAEEKDPEMREMAEEEIKELEAKIEEL 95
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 0.141 0.425
Gapped
Lambda K H
0.267 0.0668 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,958,161
Number of extensions: 97943
Number of successful extensions: 391
Number of sequences better than 10.0: 1
Number of HSP's gapped: 391
Number of HSP's successfully gapped: 30
Length of query: 157
Length of database: 6,263,737
Length adjustment: 86
Effective length of query: 71
Effective length of database: 4,405,363
Effective search space: 312780773
Effective search space used: 312780773
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 (24.3 bits)