RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781207|ref|YP_003065620.1| hypothetical protein
CLIBASIA_05570 [Candidatus Liberibacter asiaticus str. psy62]
(80 letters)
>gnl|CDD|34980 COG5421, COG5421, Transposase [DNA replication, recombination, and
repair].
Length = 480
Score = 28.7 bits (64), Expect = 0.35
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 53 LAMHKMREQEEEEKKLLKKGLKKRQKN 79
+ ++R + EEEK+L+ K KK+ K
Sbjct: 423 ILEWELRTKLEEEKELIPKLKKKKTKR 449
>gnl|CDD|147748 pfam05764, YL1, YL1 nuclear protein. The proteins in this family
are designated YL1. These proteins have been shown to be
DNA-binding and may be a transcription factor.
Length = 238
Score = 27.7 bits (62), Expect = 0.68
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 56 HKMREQEEEEKKLLKKGLKKRQKN 79
+ EQEEE+KK + LKKR+
Sbjct: 204 ERYEEQEEEKKKAKIQALKKRRLY 227
>gnl|CDD|32643 COG2814, AraJ, Arabinose efflux permease [Carbohydrate transport
and metabolism].
Length = 394
Score = 26.7 bits (59), Expect = 1.4
Identities = 11/50 (22%), Positives = 20/50 (40%)
Query: 1 MGFWNSITSIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGA 50
+ ++ +GA +G + A GWVGAA+ + + A
Sbjct: 337 GSLNVAAFNLGIALGAALGGLVLDALGYAATGWVGAALLLLALLLALLSA 386
>gnl|CDD|110170 pfam01148, CTP_transf_1, Cytidylyltransferase family. The members
of this family are integral membrane protein
cytidylyltransferases. The family includes phosphatidate
cytidylyltransferase EC:2.7.7.41 as well as Sec59 from
yeast. Sec59 is a dolichol kinase EC:2.7.1.108.
Length = 259
Score = 26.2 bits (58), Expect = 1.8
Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 1/47 (2%)
Query: 9 SIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGASDLAM 55
+ V AV+ + + L + A + G+ A++VG DL
Sbjct: 171 FLGGFVAAVLVGLLFSLLLGPYPSPLHALLLGLLASLVGQ-FGDLVE 216
>gnl|CDD|145855 pfam02919, Topoisom_I_N, Eukaryotic DNA topoisomerase I, DNA
binding fragment. Topoisomerase I promotes the
relaxation of DNA superhelical tension by introducing a
transient single-stranded break in duplex DNA and are
vital for the processes of replication, transcription,
and recombination. This family may be more than one
structural domain.
Length = 215
Score = 26.4 bits (59), Expect = 2.0
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 55 MHKMREQEEEEKKLLKKGLKKRQK 78
+++ E E+E+KK + K KK K
Sbjct: 91 IYEYFEAEKEKKKAMSKEEKKALK 114
>gnl|CDD|145052 pfam01698, FLO_LFY, Floricaula / Leafy protein. This family
consists of various plant development proteins which are
homologues of floricaula (FLO) and Leafy (LFY) proteins
which are floral meristem identity proteins. Mutations
in the sequences of these proteins affect flower and
leaf development.
Length = 382
Score = 26.1 bits (58), Expect = 2.3
Identities = 12/39 (30%), Positives = 16/39 (41%)
Query: 40 GVGAAVVGAGASDLAMHKMREQEEEEKKLLKKGLKKRQK 78
G+ G G L + E+KK KK +KR K
Sbjct: 158 AAGSGGGGGGTWGLVGVPGHSSDSEKKKQRKKQRRKRSK 196
>gnl|CDD|34302 COG4685, COG4685, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 571
Score = 25.8 bits (56), Expect = 2.5
Identities = 10/40 (25%), Positives = 14/40 (35%)
Query: 9 SIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGA 48
A + V + L W+G A VGAA +
Sbjct: 2 GGACSGFPAVLPKHPSMKLTRKKIWIGVAALAVGAAAIVQ 41
>gnl|CDD|144619 pfam01093, Clusterin, Clusterin.
Length = 460
Score = 25.8 bits (57), Expect = 2.8
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 55 MHKMREQEEEEKKLLKKGLKKRQKN 79
M + E+ EEE K L L+K +K
Sbjct: 54 MKTLMERTEEEHKNLMSTLEKTKKE 78
>gnl|CDD|144263 pfam00606, Glycoprotein_B, Herpesvirus Glycoprotein B. This family
of proteins contains a transmembrane region.
Length = 711
Score = 25.6 bits (57), Expect = 3.3
Identities = 14/54 (25%), Positives = 21/54 (38%), Gaps = 12/54 (22%)
Query: 3 FWNSITSIAATVGAVVGTVATAAA---------LATPIGWVG---AAVAGVGAA 44
F+ + ++ VG VV VA A L P G + +AG+ A
Sbjct: 628 FFQGLGAVGKAVGNVVSGVAGAVGSIVSGVVSFLKNPFGGLLIILLVLAGLVAV 681
>gnl|CDD|146537 pfam03956, DUF340, Membrane protein of unknown function (DUF340).
Members of this family contain a conserved core of
four predicted transmembrane segments. Some members
have an additional pair of N-terminal transmembrane
helices. The functions of the proteins in this family
are unknown.
Length = 191
Score = 25.6 bits (57), Expect = 3.3
Identities = 8/36 (22%), Positives = 17/36 (47%)
Query: 7 ITSIAATVGAVVGTVATAAALATPIGWVGAAVAGVG 42
+ + +G+++G + A L P+ A +G G
Sbjct: 60 LIPLVTILGSLLGGLIAALILGIPLKQGLAVASGFG 95
>gnl|CDD|176857 cd07815, SRPBCC_PITP, Lipid-binding SRPBCC domain of Class I and
Class II Phosphatidylinositol Transfer Proteins. This
family includes the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of the
phosphatidylinositol transfer protein (PITP) family of
lipid transfer proteins. This family of proteins
includes Class 1 PITPs (PITPNA/PITPalpha and
PITPNB/PITPbeta, Drosophila vibrator and related
proteins), Class IIA PITPs (PITPNM1/PITPalphaI/Nir2,
PITPNM2/PITPalphaII/Nir3, Drosophila RdgB, and related
proteins), and Class IIB PITPs (PITPNC1/RdgBbeta and
related proteins). The PITP family belongs to the SRPBCC
domain superfamily of proteins that bind hydrophobic
ligands. SRPBCC domains have a deep hydrophobic
ligand-binding pocket. In vitro, PITPs bind
phosphatidylinositol (PtdIns), as well as
phosphatidylcholine (PtdCho) but with a lower affinity.
They transfer these lipids from one membrane compartment
to another. The cellular roles of PITPs include inositol
lipid signaling, PtdIns metabolism, and membrane
trafficking. Class III PITPs, exemplified by the Sec14p
family, are found in yeast and plants but are unrelated
in sequence and structure to Class I and II PITPs and
belong to a different superfamily.
Length = 251
Score = 25.4 bits (56), Expect = 3.9
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 52 DLAMHKMREQEEEEKKLLKKGLK 74
DL M +RE EEE K+LL K
Sbjct: 229 DLTMEDIREFEEETKELLDAKRK 251
>gnl|CDD|147010 pfam04641, Rtf2, Replication termination factor 2. It is vital for
effective cell-replication that replication is not
stalled at any point by, for instance, damaged bases.
Rtf2 stabilizes the replication fork stalled at the
site-specific replication barrier RTS1 by preventing
replication restart until completion of DNA synthesis by
a converging replication fork initiated at a flanking
origin. The RTS1 element terminates replication forks
that are moving in the cen2-distal direction while
allowing forks moving in the cen2-proximal direction to
pass through the region. Rtf2 contains a C2HC2 motif
related to the C3HC4 RING-finger motif, and would appear
to fold up, creating a RING finger-like structure but
forming only one functional Zn2+ ion-binding site.
Length = 254
Score = 25.4 bits (56), Expect = 4.0
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 52 DLAMHKMREQEEEEKKLLKKGLKKRQKN 79
++ + K R +EE KK KK KKR+KN
Sbjct: 168 EVELLKARLEEERAKKKKKKKKKKRKKN 195
>gnl|CDD|31474 COG1283, NptA, Na+/phosphate symporter [Inorganic ion transport and
metabolism].
Length = 533
Score = 25.2 bits (55), Expect = 4.1
Identities = 12/43 (27%), Positives = 21/43 (48%)
Query: 2 GFWNSITSIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAA 44
G + +I +GA +GT TA +A + W+ + +GA
Sbjct: 78 GLLSLKQAIGVILGANIGTTVTAWIVALDLSWLSPPLLAIGAI 120
>gnl|CDD|37807 KOG2596, KOG2596, KOG2596, Aminopeptidase I zinc metalloprotease
(M18) [Amino acid transport and metabolism].
Length = 479
Score = 24.9 bits (54), Expect = 4.4
Identities = 7/22 (31%), Positives = 11/22 (50%)
Query: 39 AGVGAAVVGAGASDLAMHKMRE 60
+ G + G L+MH +RE
Sbjct: 427 SKTGIRTLDLGIPQLSMHSIRE 448
>gnl|CDD|119321 cd06579, TM_PBP1_transp_AraH_like, Transmembrane subunit (TM) of
Escherichia coli AraH and related proteins. E. coli
AraH is the TM of a Periplasmic Binding Protein
(PBP)-dependent ATP-Binding Cassette (ABC) transporter
involved in the uptake of the monosaccharide arabinose.
This group also contains E. coli RbsC, AlsC, and MglC,
which are TMs of other monosaccharide transporters, the
ribose transporter, the D-allose transporter and the
galactose transporter, respectively. The D-allose
transporter may also be involved in low affinity ribose
transport. These transporters generally bind type 1
PBPs. PBP-dependent ABC transporters consist of a PBP,
two TMs, and two cytoplasmic ABCs, and are mainly
involved in importing solutes from the environment. The
solute is captured by the PBP, which delivers it to a
gated translocation pathway formed by the two TMs. The
two ABCs bind and hydrolyze ATP and drive the transport
reaction. Proteins in this subgroup have a single TM
which homodimerizes to generate the transmembrane
pore..
Length = 263
Score = 25.1 bits (56), Expect = 4.8
Identities = 12/37 (32%), Positives = 16/37 (43%)
Query: 14 VGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGA 50
VG+V A AAL + +A + A VGA
Sbjct: 24 VGSVAALSAVVAALLLVNAGLPIPLAILAALAVGALI 60
Score = 23.9 bits (53), Expect = 8.7
Identities = 10/43 (23%), Positives = 16/43 (37%), Gaps = 3/43 (6%)
Query: 6 SITSIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGA 48
S+ S+AA V + A L + A A++G
Sbjct: 23 SVGSVAALSAVVAALLLVNAGLPI---PLAILAALAVGALIGL 62
>gnl|CDD|30730 COG0381, WecB, UDP-N-acetylglucosamine 2-epimerase [Cell envelope
biogenesis, outer membrane].
Length = 383
Score = 24.8 bits (54), Expect = 5.0
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 45 VVGAGASDLAMHKMREQEEEEKKLLKKGLKKRQKNY 80
V G D A+ R++ E+ K+L KGL + K Y
Sbjct: 172 VTGNTVID-ALLNTRDRVLEDSKILAKGLDDKDKKY 206
>gnl|CDD|35064 COG5505, COG5505, Predicted integral membrane protein [Function
unknown].
Length = 384
Score = 24.5 bits (53), Expect = 6.3
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 4 WNSITSIAAT-VGAVVGTVATAAALATPIGWVGAAVA 39
W + I+ + G A AAL P + A +A
Sbjct: 119 WKAGGMISGSYTGGSANMAAMQAALEVPGEYFSATLA 155
>gnl|CDD|35631 KOG0410, KOG0410, KOG0410, Predicted GTP binding protein [General
function prediction only].
Length = 410
Score = 24.6 bits (53), Expect = 6.5
Identities = 12/41 (29%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 40 GVGAAVVGAGASDLAMHK---MREQEEEEKKLLKKGLKKRQ 77
G V G+G S + +R +E + +K L++ +KRQ
Sbjct: 128 QSGGQVKGSGESIIDRDIRRLLRIKEAQLRKELQRVRRKRQ 168
>gnl|CDD|146981 pfam04600, DUF571, Protein of unknown function (DUF571). Family of
hypothetical bacterial proteins.
Length = 426
Score = 24.6 bits (54), Expect = 6.6
Identities = 12/52 (23%), Positives = 14/52 (26%)
Query: 4 WNSITSIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGASDLAM 55
W + A AA LA P + AAV G A
Sbjct: 79 WGPTAARRVAGLAAAAVALAAAGLALPARGATGWLTAAVAAVAGVLLLAAAA 130
>gnl|CDD|30901 COG0555, CysU, ABC-type sulfate transport system, permease
component [Posttranslational modification, protein
turnover, chaperones].
Length = 274
Score = 24.4 bits (53), Expect = 6.8
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 8/54 (14%)
Query: 2 GFWNSITSIAATVGAVVGTVATAAA-------LATPIGWVGAAVAGVGAAVVGA 48
GFW+++TS + A+ T+ TA A P+ WV G +V A
Sbjct: 45 GFWSALTS-PRVLAALKLTLLTAFAATLLNLVFGLPLAWVLVRYDFPGKRLVDA 97
>gnl|CDD|146478 pfam03866, HAP, Hydrophobic abundant protein (HAP). Expression of
HAP is thought to be developmentally regulated and
possibly involved in spherule cell wall formation.
Length = 167
Score = 24.5 bits (53), Expect = 6.8
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 14 VGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGA 50
+G V+G VAT AALA + VG +V G+ + A
Sbjct: 75 IGTVLGLVATLAALALDL--VGGSVGGICNDFLDFDA 109
>gnl|CDD|34339 COG4723, COG4723, Phage-related protein, tail component [Function
unknown].
Length = 198
Score = 24.5 bits (53), Expect = 7.5
Identities = 10/45 (22%), Positives = 14/45 (31%)
Query: 7 ITSIAATVGAVVGTVATAAALATPIGWVGAAVAGVGAAVVGAGAS 51
+ V+G A+ T A G A + GAS
Sbjct: 86 AGAKKGGFQTVLGAALIVASFFTAGWGAALAAGGFSAMLFSLGAS 130
>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 = 24.5 bits (53), Expect = 7.6
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 54 AMHKMREQEEEEKKLLKKGLKKRQKN 79
M + ++EEKK + K KK K
Sbjct: 89 QMFAYFKAQKEEKKAMSKEEKKAIKA 114
>gnl|CDD|145336 pfam02127, Peptidase_M18, Aminopeptidase I zinc metalloprotease
(M18).
Length = 425
Score = 24.3 bits (53), Expect = 7.7
Identities = 8/22 (36%), Positives = 12/22 (54%)
Query: 39 AGVGAAVVGAGASDLAMHKMRE 60
A G + G + L+MH +RE
Sbjct: 386 ARTGIRTIDLGPAQLSMHSIRE 407
>gnl|CDD|37213 KOG2002, KOG2002, KOG2002, TPR-containing nuclear phosphoprotein
that regulates K(+) uptake [Inorganic ion transport and
metabolism].
Length = 1018
Score = 24.2 bits (52), Expect = 8.2
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 57 KMREQEEEEKKLLKKGLKKRQ 77
+ R +EEEEK +K K+R+
Sbjct: 855 EARRKEEEEKARREKLEKQRE 875
>gnl|CDD|48064 cd00660, Topoisomer_IB_N, Topoisomer_IB_N: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the monomeric yeast and human topo I
and heterodimeric topo I from Leishmania donvanni. 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 re-ligation of the
single-strand nick, resulting in the accumulation of
topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topos I play putative roles
in organizing the kinetoplast DNA network unique to
these parasites. This family may represent more than
one structural domain..
Length = 215
Score = 24.0 bits (52), Expect = 8.7
Identities = 9/26 (34%), Positives = 16/26 (61%)
Query: 54 AMHKMREQEEEEKKLLKKGLKKRQKN 79
+++ E+E+E+KK + K KK K
Sbjct: 89 PIYQYFEEEKEKKKAMSKEEKKAIKE 114
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
0.313 0.126 0.355
Gapped
Lambda K H
0.267 0.0700 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 872,309
Number of extensions: 39544
Number of successful extensions: 449
Number of sequences better than 10.0: 1
Number of HSP's gapped: 432
Number of HSP's successfully gapped: 136
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: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (23.5 bits)