RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781163|ref|YP_003065576.1| hypothetical protein
CLIBASIA_05350 [Candidatus Liberibacter asiaticus str. psy62]
(214 letters)
>gnl|CDD|176858 cd07816, Bet_v1-like, Ligand-binding bet_v_1 domain of major pollen
allergen of white birch (Betula verrucosa), Bet v 1, and
related proteins. This family includes the ligand
binding domain of Bet v 1 (the major pollen allergen of
white birch, Betula verrucosa) and related proteins. In
addition to birch Bet v 1, this family includes other
plant intracellular pathogenesis-related class 10
(PR-10) proteins, norcoclaurine synthases (NCSs),
cytokinin binding proteins (CSBPs), major latex proteins
(MLPs), and ripening-related proteins. It belongs to the
SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. Members of this family binds a diverse range of
ligands. Bet v 1 can bind brassinosteroids, cytokinins,
flavonoids and fatty acids. Hyp-1, a PR-10 from
Hypericum perforatum/St. John's wort, catalyzes the
condensation of two molecules of emodin to the bioactive
naphthodianthrone hypericin. NCSs catalyze the
condensation of dopamine and 4-hydroxyphenylacetaldehyde
to (S)-norcoclaurine, the first committed step in the
biosynthesis of benzylisoquinoline alkaloids such as
morphine. The role of MLPs is unclear; however, they are
associated with fruit and flower development and in
pathogen defense responses. A number of PR-10 proteins
in this subgroup, including Bet v 1, have in vitro RNase
activity, the biological significance of which is
unclear. Bet v 1 family proteins have a conserved
glycine-rich P (phosphate-binding)-loop proximal to the
entrance of the ligand-binding pocket. However, its
conformation differs from that of the canonical P-loop
structure found in nucleotide-binding proteins. Several
PR-10 members including Bet v1 are allergenic.
Cross-reactivity of Bet v 1 with homologs from plant
foods results in birch-fruit syndrome.
Length = 148
Score = 32.9 bits (76), Expect = 0.058
Identities = 18/46 (39%), Positives = 20/46 (43%), Gaps = 7/46 (15%)
Query: 148 FTHFKEYIDEVDKILMRYG---IEGIPLTDFDHEKIKSYLTHIKIV 190
+ KE ID VD+ Y IEG L D KSY IK V
Sbjct: 61 VKYVKERIDAVDEENKTYKYTVIEGDVLKD----GYKSYKVEIKFV 102
>gnl|CDD|73095 cd04595, CBS_pair_DHH_polyA_Pol_assoc, This cd contains two tandem
repeats of the cystathionine beta-synthase (CBS pair)
domains associated with an upstream DHH domain which
performs a phosphoesterase function and a downstream
polyA polymerase domain. CBS is a small domain
originally identified in cystathionine beta-synthase and
subsequently found in a wide range of different
proteins. CBS domains usually come in tandem repeats,
which associate to form a so-called Bateman domain or a
CBS pair which is reflected in this model. The interface
between the two CBS domains forms a cleft that is a
potential ligand binding site. The CBS pair coexists
with a variety of other functional domains. It has been
proposed that the CBS domain may play a regulatory role,
although its exact function is unknown..
Length = 110
Score = 30.5 bits (69), Expect = 0.31
Identities = 7/31 (22%), Positives = 18/31 (58%), Gaps = 2/31 (6%)
Query: 155 IDEVDKILMRYGIEGIPLTDFDHEKIKSYLT 185
I+E ++L+RYG +P+ + ++ ++
Sbjct: 13 IEEARELLLRYGHTALPV--VEGGRVVGIIS 41
>gnl|CDD|32643 COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport
and metabolism].
Length = 394
Score = 30.2 bits (68), Expect = 0.44
Identities = 24/76 (31%), Positives = 33/76 (43%), Gaps = 12/76 (15%)
Query: 31 SAEQRKLWSLLRYWSVEFWELLCRTFLWLLCLGFFTLFAY--WFFGEKFSYDVSIKIVLA 88
R L LLR V L TFL+ G F L+ Y F + VS A
Sbjct: 198 PGPLRTLLRLLRRPGV--LLGLLATFLF--MTGHFALYTYIRPFLESVAGFSVS-----A 248
Query: 89 INVLLFSFVIA-LLGN 103
++++L +F IA +GN
Sbjct: 249 VSLVLLAFGIAGFIGN 264
>gnl|CDD|112133 pfam03304, Mlp, Mlp lipoprotein family. The Mlp (for Multicopy
Lipoprotein) family of lipoproteins is found in Borrelia
species. This family were previously known as 2.9
lipoprotein genes. These surface expressed genes may
represent new candidate vaccinogens for Lyme disease.
Members of this family generally are downstream of four
ORFs called A,B,C and D that are involved in hemolytic
activity.
Length = 150
Score = 30.2 bits (68), Expect = 0.49
Identities = 22/77 (28%), Positives = 28/77 (36%), Gaps = 20/77 (25%)
Query: 131 EKISQKNVEKDFFNS------KFFTHFKEYID---EVDKILMRYGIEGIPLTDFDHEKIK 181
EK K+ E+ F F KE + + K L + D KIK
Sbjct: 50 EKPKSKSDEELLFEKLSDDQKTFLDWLKEALGAFGKFYKFL-----------ESDKSKIK 98
Query: 182 SYLTHIKIVRDCLKKDN 198
S LTHIK DC +
Sbjct: 99 SALTHIKGELDCCNGNP 115
>gnl|CDD|37761 KOG2550, KOG2550, KOG2550, IMP dehydrogenase/GMP reductase
[Nucleotide transport and metabolism].
Length = 503
Score = 29.2 bits (65), Expect = 0.92
Identities = 25/88 (28%), Positives = 34/88 (38%), Gaps = 4/88 (4%)
Query: 107 EMAKDIAQL--FTLIDNIENGYGQYLEKISQKNVEKDFFNSKFFTHFKEYIDEVDKILMR 164
EMA +A L I + Q KN E F N+ + EV + +
Sbjct: 77 EMAIAMALLGGIGFIHHNCTPEDQADMVRRVKNYENGFINNPIVISPTTTVGEVKEAKEK 136
Query: 165 YGIEGIPLTDFDHEKIKSYLTHIKIVRD 192
+G GIP+T+ K S L I RD
Sbjct: 137 HGFSGIPVTEDG--KRGSKLVGIITSRD 162
>gnl|CDD|36975 KOG1764, KOG1764, KOG1764, 5'-AMP-activated protein kinase, gamma
subunit [Energy production and conversion].
Length = 381
Score = 28.8 bits (64), Expect = 1.2
Identities = 21/130 (16%), Positives = 45/130 (34%), Gaps = 20/130 (15%)
Query: 80 DVSIKIVLAINVLLFSFVIALLGNPNIEMAKDIAQLFTLID--NIENGYGQYLEKISQKN 137
D + + A N L+ + V A + + + T+ D + Y + +
Sbjct: 82 DTKLSVKKAFNALVQNGVRAAPLWDS--KKQQFVGMLTITDFITVLLRYYKSKSSLDNIE 139
Query: 138 VEKDFFNSK----------FFTHFKEYID------EVDKILMRYGIEGIPLTDFDHEKIK 181
V +D SK I + +L++ I +P+ D + ++
Sbjct: 140 VLEDSQLSKRREVECLLKETLKPPFVSISPESSLLDAVLLLIKSRIHRVPVIDPETGEVL 199
Query: 182 SYLTHIKIVR 191
LT +I++
Sbjct: 200 YILTQRRILK 209
>gnl|CDD|37313 KOG2102, KOG2102, KOG2102, Exosomal 3'-5' exoribonuclease complex,
subunit Rrp44/Dis3 [Translation, ribosomal structure and
biogenesis].
Length = 941
Score = 28.1 bits (62), Expect = 2.0
Identities = 11/59 (18%), Positives = 18/59 (30%), Gaps = 4/59 (6%)
Query: 143 FNSKFFTHF----KEYIDEVDKILMRYGIEGIPLTDFDHEKIKSYLTHIKIVRDCLKKD 197
S +THF + Y D + + T D + S + + KK
Sbjct: 775 LASPLYTHFTSPIRRYADIIVHRQLAAAFLERSPTAPDRPNLSSLAANCNERKKAAKKA 833
>gnl|CDD|39018 KOG3814, KOG3814, KOG3814, Signaling protein van gogh/strabismus
[Signal transduction mechanisms].
Length = 531
Score = 27.7 bits (61), Expect = 2.7
Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 14/85 (16%)
Query: 27 GLFDSAEQRKLWSLLRYWSVEFWEL----LCRTFLW---LLCLGFFTLFAYW-FFGEK-- 76
GL S + L L+ W++ F+ + R F+ LL L F +FAYW F+ +
Sbjct: 156 GLLISMAFKLLILLIGIWAL-FFRKAMADMPRVFVVRALLLVLVFLIVFAYWLFYIVRIL 214
Query: 77 FSYDVSIKIVLAINVLLFSFVIALL 101
+ K ++ S V ALL
Sbjct: 215 DERYRNYKGIVQYAT---SLVDALL 236
>gnl|CDD|144171 pfam00478, IMPDH, IMP dehydrogenase / GMP reductase domain. This
family is involved in biosynthesis of guanosine
nucleotide. Members of this family contain a TIM barrel
structure. In the inosine monophosphate dehydrogenases 2
CBS domains pfam00571 are inserted in the TIM barrel.
This family is a member of the common phosphate binding
site TIM barrel family.
Length = 467
Score = 27.6 bits (62), Expect = 3.0
Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 2/57 (3%)
Query: 136 KNVEKDFFNSKFFTHFKEYIDEVDKILMRYGIEGIPLTDFDHEKIKSYLTHIKIVRD 192
K E F + E ++ RYGI G+P+T + K+ L I+ RD
Sbjct: 82 KRFESGFITDPVTVSPDTTVAEALELKERYGISGVPVT--EDGKLLGGLVGIRTSRD 136
>gnl|CDD|36273 KOG1055, KOG1055, KOG1055, GABA-B ion channel receptor subunit
GABABR1 and related subunits, G-protein coupled receptor
superfamily [Inorganic ion transport and metabolism,
Amino acid transport and metabolism, Signal transduction
mechanisms].
Length = 865
Score = 26.9 bits (59), Expect = 4.0
Identities = 11/28 (39%), Positives = 13/28 (46%)
Query: 45 SVEFWELLCRTFLWLLCLGFFTLFAYWF 72
SV + LC W+L LGF F F
Sbjct: 529 SVNAFPFLCTARTWILGLGFTLAFGAMF 556
>gnl|CDD|144229 pfam00562, RNA_pol_Rpb2_6, RNA polymerase Rpb2, domain 6. RNA
polymerases catalyse the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This domain
represents the hybrid binding domain and the wall
domain. The hybrid binding domain binds the nascent RNA
strand / template DNA strand in the Pol II transcription
elongation complex. This domain contains the important
structural motifs, switch 3 and the flap loop and binds
an active site metal ion. This domain is also involved
in binding to Rpb1 and Rpb3. Many of the bacterial
members contain large insertions within this domain, as
region known as dispensable region 2 (DRII).
Length = 373
Score = 27.1 bits (61), Expect = 4.0
Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 3/52 (5%)
Query: 133 ISQKNVEKDFFNSKFFTHFKEYIDEVDKILMRYGIEGIPLTDFDHEKIKSYL 184
I++ +V++ F S H KEY E K + E E+ L
Sbjct: 92 INKSSVDRGLFTS---IHIKEYEIEARKTKLGPIEEITRDPPNVSEEAYRKL 140
>gnl|CDD|36500 KOG1286, KOG1286, KOG1286, Amino acid transporters [Amino acid
transport and metabolism].
Length = 554
Score = 26.8 bits (59), Expect = 4.8
Identities = 13/47 (27%), Positives = 22/47 (46%), Gaps = 3/47 (6%)
Query: 59 LLCLGFFTLFAYWFFGEKFSYDVSIKIVLAINVLLFSFVIALLGNPN 105
+L + F + AY +FS KI+ A+ ++ + VI G P
Sbjct: 166 ILIINLFGVLAY--GEVEFSL-AFNKILTAVGFIILAIVIIAGGGPA 209
>gnl|CDD|38951 KOG3747, KOG3747, KOG3747, Concentrative Na+-nucleoside
cotransporter CNT1/CNT2 [Nucleotide transport and
metabolism, Inorganic ion transport and metabolism].
Length = 602
Score = 26.8 bits (59), Expect = 5.0
Identities = 18/81 (22%), Positives = 26/81 (32%), Gaps = 24/81 (29%)
Query: 43 YWSVEFWELLCRTFLWLLCLGFFTLFAYWFF----------------GEKFSYDVSIK-- 84
W + L + L LL L W F G F + +I
Sbjct: 203 NWRIVTSGLGLQFLLGLLVLR--WPTGRWIFQWLGEQVQIFLEYAQAGASFVFGDNICDL 260
Query: 85 IVLAINVL----LFSFVIALL 101
V A +L FS V+++L
Sbjct: 261 AVFAFAILPIIIFFSAVVSIL 281
>gnl|CDD|153334 cd07650, F-BAR_Syp1p_like, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of yeast Syp1 protein.
F-BAR domains are dimerization modules that bind and
bend membranes and are found in proteins involved in
membrane dynamics and actin reorganization. Syp1p is
associated with septins, a family of GTP-binding
proteins that serve as elements of septin filaments,
which are required for cell morphogenesis and division.
Syp1p regulates cell-cycle dependent septin cytoskeletal
dynamics in yeast. It contains an N-terminal F-BAR
domain and a C-terminal domain of unknown function named
SAFF which is also present in FCH domain Only (FCHO)
proteins and endophilin interacting protein 1. F-BAR
domains form banana-shaped dimers with a
positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 228
Score = 26.5 bits (59), Expect = 5.2
Identities = 7/32 (21%), Positives = 15/32 (46%)
Query: 110 KDIAQLFTLIDNIENGYGQYLEKISQKNVEKD 141
++A +E Y Q L K++++N +
Sbjct: 22 TELADWLQERRRLERQYVQGLRKLARRNEPLN 53
>gnl|CDD|33694 COG3907, COG3907, PAP2 (acid phosphatase) superfamily protein
[General function prediction only].
Length = 249
Score = 26.1 bits (57), Expect = 6.6
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 55 TFLWLLCLGFFTLFAY 70
T WL+ LGFF LF
Sbjct: 224 TICWLVALGFFYLFFV 239
>gnl|CDD|73050 cd03291, ABCC_CFTR1, The CFTR subfamily domain 1. The cystic
fibrosis transmembrane regulator (CFTR), the product of
the gene mutated in patients with cystic fibrosis, has
adapted the ABC transporter structural motif to form a
tightly regulated anion channel at the apical surface of
many epithelia. Use of the term assembly of a
functional ion channel implies the coming together of
subunits, or at least smaller not-yet functional
components of the active whole. In fact, on the basis
of current knowledge only the CFTR polypeptide itself is
required to form an ATP- and protein kinase A-dependent
low-conductance chloride channel of the type present in
the apical membrane of many epithelial cells. CFTR
displays the typical organization (IM-ABC)2 and carries
a characteristic hydrophilic R-domain that separates
IM1-ABC1 from IM2-ABC2..
Length = 282
Score = 26.1 bits (57), Expect = 6.9
Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 123 ENGYGQYLEKISQKNVEKDFFN---SKFFTHFKEYIDEVDK 160
+ G+G+ LEK Q+N ++ + + FF++ V K
Sbjct: 14 DEGFGELLEKAKQENNDRKHSSDDNNLFFSNLCLVGAPVLK 54
>gnl|CDD|110588 pfam01594, UPF0118, Domain of unknown function DUF20. This
transmembrane region is found in putative permeases and
predicted transmembrane proteins it has no known
function. It is not clear what source suggested that
these proteins may be permeases and this information
should be treated with caution.
Length = 327
Score = 26.0 bits (58), Expect = 7.5
Identities = 11/83 (13%), Positives = 27/83 (32%), Gaps = 8/83 (9%)
Query: 56 FLWLLCLGFFTLFAY-----WFFGEKFSYDVSIKIVLAINVLLFSFVIALLGNPNIEMAK 110
L L + + + ++I +VL + ++ + LL I
Sbjct: 21 LLVPLLIALVLAYLLNPVVRFLKRRGIPRSLAILLVLLLFLVALVLLGLLLIPLLIIQ-- 78
Query: 111 DIAQLFTLIDNIENGYGQYLEKI 133
+ QL + + +L ++
Sbjct: 79 -LTQLIKSLPQYIDSLLNWLNEL 100
>gnl|CDD|176956 CHL00013, rpoA, RNA polymerase alpha subunit.
Length = 327
Score = 26.1 bits (58), Expect = 7.8
Identities = 20/71 (28%), Positives = 28/71 (39%), Gaps = 13/71 (18%)
Query: 141 DFFNSKFFTHFKE---YIDEVDKILMRYGIEGIPLTDFDHEKIKSYLTHIKI------VR 191
D F F H +E ++ + + LTD K + L I I VR
Sbjct: 216 DLFIP--FLHAEEENLKLENNENRVTLLFTFHDRLTDLKKNKKEIALKQIFIEQLELSVR 273
Query: 192 --DCLKKDNIH 200
+CLK+ NIH
Sbjct: 274 AYNCLKRANIH 284
>gnl|CDD|146277 pfam03552, Cellulose_synt, Cellulose synthase. Cellulose, an
aggregate of unbranched polymers of beta-1,4-linked
glucose residues, is the major component of wood and
thus paper, and is synthesized by plants, most algae,
some bacteria and fungi, and even some animals. The
genes that synthesize cellulose in higher plants differ
greatly from the well-characterized genes found in
Acetobacter and Agrobacterium sp. More correctly
designated as 'cellulose synthase catalytic subunits',
plant cellulose synthase (CesA) proteins are integral
membrane proteins, approximately 1,000 amino acids in
length. There are a number of highly conserved residues,
including several motifs shown to be necessary for
processive glycosyltransferase activity.
Length = 716
Score = 25.9 bits (57), Expect = 8.1
Identities = 27/101 (26%), Positives = 40/101 (39%), Gaps = 18/101 (17%)
Query: 113 AQLFTLIDNIENGYGQYLEKISQKNVEKDFFNSKFFTHFKEYIDEVDKILMRYGIEGIPL 172
A +F L D E + +SQ ++EK F S F + LM G G+P
Sbjct: 334 APIFNLEDIDEGDEDEKSSLMSQLSLEKRFGQSPVF---------IASTLMEEG--GVPR 382
Query: 173 TDFDHEKIKSYLTHIKIVRDCLKKDNIHYAKELRNDWI-GS 212
+ +K + I C +D + KE+ WI GS
Sbjct: 383 SPLPATLVKEAIHVIS----CGYEDKTEWGKEI--GWIYGS 417
>gnl|CDD|31481 COG1290, QcrB, Cytochrome b subunit of the bc complex [Energy
production and conversion].
Length = 381
Score = 26.0 bits (57), Expect = 8.6
Identities = 15/69 (21%), Positives = 25/69 (36%), Gaps = 5/69 (7%)
Query: 38 WSLLRYWSVEFWELLCRTFLWLLCLGFFTLFAYWFFGEKFSYDVSIKIVLAINVLLFSFV 97
W + YW L ++ T W FG D ++ A++VLL +
Sbjct: 145 WDQMSYWGATVITNLFSAIPFI-----GTWLVQWLFGGFSVSDPTLNRFFALHVLLLPAI 199
Query: 98 IALLGNPNI 106
I L ++
Sbjct: 200 ILALVGLHL 208
>gnl|CDD|48065 cd03488, Topoisomer_IB_N_htopoI_like, Topoisomer_IB_N_htopoI_like :
N-terminal DNA binding fragment found in eukaryotic DNA
topoisomerase (topo) IB proteins similar to the
monomeric yeast and human topo I. Topo I enzymes are
divided into: topo type IA (bacterial) and type IB
(eukaryotic). Topo I relaxes superhelical tension in
duplex DNA by creating a single-strand nick, the broken
strand can then rotate around the unbroken strand to
remove DNA supercoils and, the nick is religated,
liberating topo I. These enzymes regulate the
topological changes that accompany DNA replication,
transcription and other nuclear processes. Human topo I
is the target of a diverse set of anticancer drugs
including camptothecins (CPTs). CPTs bind to the topo
I-DNA complex and inhibit religation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. This family may represent more than
one structural domain..
Length = 215
Score = 25.6 bits (56), Expect = 9.2
Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 3/39 (7%)
Query: 126 YGQYLEKISQKNVEKDFFNSKFFTHFKEYIDEVDKILMR 164
Y + LE K+ F FF FK+ + + +K++++
Sbjct: 45 YAKMLE---HDYATKEIFQKNFFKDFKKVMTKEEKVIIK 80
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
0.327 0.143 0.450
Gapped
Lambda K H
0.267 0.0711 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,847,001
Number of extensions: 159493
Number of successful extensions: 850
Number of sequences better than 10.0: 1
Number of HSP's gapped: 847
Number of HSP's successfully gapped: 93
Length of query: 214
Length of database: 6,263,737
Length adjustment: 90
Effective length of query: 124
Effective length of database: 4,318,927
Effective search space: 535546948
Effective search space used: 535546948
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (25.0 bits)