RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781226|ref|YP_003065639.1| hypothetical protein
CLIBASIA_05665 [Candidatus Liberibacter asiaticus str. psy62]
(129 letters)
>gnl|CDD|99740 cd00616, AHBA_syn, 3-amino-5-hydroxybenzoic acid synthase family
(AHBA_syn). AHBA_syn family belongs to pyridoxal
phosphate (PLP)-dependent aspartate aminotransferase
superfamily (fold I). The members of this CD are
involved in various biosynthetic pathways for secondary
metabolites. Some well studied proteins in this CD are
AHBA_synthase, protein product of pleiotropic regulatory
gene degT, Arnb aminotransferase and pilin
glycosylation protein. The prototype of this family, the
AHBA_synthase, is a dimeric PLP dependent enzyme.
AHBA_syn is the terminal enzyme of
3-amino-5-hydroxybenzoic acid (AHBA) formation which is
involved in the biosynthesis of ansamycin antibiotics,
including rifamycin B. Some members of this CD are
involved in 4-amino-6-deoxy-monosaccharide D-perosamine
synthesis. Perosamine is an important element in the
glycosylation of several cell products, such as
antibiotics and lipopolysaccharides of gram-positive and
gram-negative bacteria. The pilin glycosylation protein
encoded by gene pglA, is a galactosyltransferase
involved in pilin glycosylation. Additionally, this CD
consists of ArnB (PmrH) aminotransferase, a
4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying
enzyme. This CD also consists of several predicted
pyridoxal phosphate-dependent enzymes apparently
involved in regulation of cell wall biogenesis. The
catalytic lysine which is present in all characterized
PLP dependent enzymes is replaced by histidine in some
members of this CD..
Length = 352
Score = 29.8 bits (68), Expect = 0.23
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 23/70 (32%)
Query: 24 LKNRDKILERRRRRY------LKN---------KDKIRESYHQYYLKNKDKYREYKRRYY 68
L+ D+I+ RRR L + ++ SYH Y ++ + E
Sbjct: 227 LEKLDEIIARRREIAERYKELLADLPGIRLPDVPPGVKHSYHLYVIRLDPEAGE------ 280
Query: 69 LKNRDKMREK 78
+RD++ E
Sbjct: 281 --SRDELIEA 288
>gnl|CDD|163652 cd07409, MPP_CD73_N, CD73 ecto-5'-nucleotidase and related
proteins, N-terminal metallophosphatase domain. CD73 is
a mammalian ecto-5'-nucleotidase expressed in
endothelial cells and lymphocytes that catalyzes the
conversion of 5'-AMP to adenosine in the final step of a
pathway that generates adenosine from ATP. This pathway
also includes a CD39 nucleoside triphosphate
dephosphorylase that mediates the dephosphorylation of
ATP to ADP and then to 5'-AMP. These enzymes all have
an N-terminal metallophosphatase domain and a C-terminal
5'nucleotidase domain. The N-terminal
metallophosphatase domain belongs to a large superfamily
of distantly related metallophosphatases (MPPs) that
includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA
lariat debranching enzymes, YfcE-like
phosphodiesterases, purple acid phosphatases (PAPs),
YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid
sphingomyelinases (ASMases). MPPs are functionally
diverse, but all share a conserved domain with an active
site consisting of two metal ions (usually manganese,
iron, or zinc) coordinated with octahedral geometry by a
cage of histidine, aspartate, and asparagine residues.
The conserved domain is a double beta-sheet sandwich
with a di-metal active site made up of residues located
at the C-terminal side of the sheets. This domain is
thought to allow for productive metal coordination.
Length = 281
Score = 27.5 bits (62), Expect = 1.00
Identities = 9/21 (42%), Positives = 16/21 (76%)
Query: 105 EIEALEREIARLKAKPIEELI 125
EIEA ++E +LKA+ + ++I
Sbjct: 167 EIEAAQKEADKLKAQGVNKII 187
>gnl|CDD|144201 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A.
Length = 428
Score = 27.5 bits (62), Expect = 1.00
Identities = 25/108 (23%), Positives = 53/108 (49%), Gaps = 11/108 (10%)
Query: 21 RYYLKNRDKILERRRRRYLKNKDKIRESYH--QYYLKNKDKYREYKRRYYLKNRDKMREK 78
+ +L++R ++ +RR+ L+ K+ E H + LK +K ++ + +
Sbjct: 312 KEFLEHRLEVYKRRKEYLLE---KLEERLHILEGLLKALNKIDFVIEV--IRGSIDLNKA 366
Query: 79 ARQSYRKLYSKDS-WIAPEEPMG-MTKAEIEALEREIARLKAKPIEEL 124
++ +L + ++ + + +TK EIE LE+EI L+ + I EL
Sbjct: 367 KKELIEELSEIQADYLL-DMRLRRLTKEEIEKLEKEIEELEKE-IAEL 412
>gnl|CDD|30998 COG0653, SecA, Preprotein translocase subunit SecA (ATPase, RNA
helicase) [Intracellular trafficking and secretion].
Length = 822
Score = 27.5 bits (61), Expect = 1.0
Identities = 17/81 (20%), Positives = 27/81 (33%)
Query: 36 RRYLKNKDKIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKDSWIAP 95
R +L D +RE H KD EYKR + D + + ++L+
Sbjct: 727 REHLDAMDALREGIHLRGYAQKDPLIEYKREAFELFEDMLEDIKEDVVKRLFKVQVAEVE 786
Query: 96 EEPMGMTKAEIEALEREIARL 116
EE + E +
Sbjct: 787 EEDRSLLAQEKALTQARALGK 807
>gnl|CDD|38228 KOG3018, KOG3018, KOG3018, Malonyl-CoA decarboxylase [Carbohydrate
transport and metabolism].
Length = 362
Score = 26.2 bits (57), Expect = 2.9
Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 4/71 (5%)
Query: 44 KIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKDSWIAPEEPMGMTK 103
+ L++ K E + + + NR+ +RE+ YR+ +P EP+
Sbjct: 74 DLERGTWSSPLEDLQKLLEVEAVHPVVNREDVRERVGP-YRRCLGFSHPASPREPLVFIH 132
Query: 104 AEIEALEREIA 114
AL IA
Sbjct: 133 V---ALMETIA 140
>gnl|CDD|34782 COG5183, SSM4, Protein involved in mRNA turnover and stability [RNA
processing and modification].
Length = 1175
Score = 26.2 bits (57), Expect = 2.9
Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 3/67 (4%)
Query: 33 RRRRRYLKNKDKIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKDSW 92
R RRR L N I ES + ++ R R+ R+ R+ + S + + S
Sbjct: 215 RLRRRMLMNPRAILESISR---ESAQLERNTARQQGEHARENGRDLSSDSNNNVINPVSD 271
Query: 93 IAPEEPM 99
P M
Sbjct: 272 NVPSRDM 278
>gnl|CDD|31325 COG1129, MglA, ABC-type sugar transport system, ATPase component
[Carbohydrate transport and metabolism].
Length = 500
Score = 25.9 bits (57), Expect = 3.2
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 6/56 (10%)
Query: 61 REYKRRYYLKNRDKMREKARQSYRKLYSKDSWIAPEEPMG-MTKAEIEALEREIAR 115
RE RR+ L +R MR +AR+ +L I P+ +G ++ A+ + + EIAR
Sbjct: 108 REPTRRFGLIDRKAMRRRARELLARL---GLDIDPDTLVGDLSIAQRQMV--EIAR 158
>gnl|CDD|35636 KOG0415, KOG0415, KOG0415, Predicted peptidyl prolyl cis-trans
isomerase [Posttranslational modification, protein
turnover, chaperones].
Length = 479
Score = 26.1 bits (57), Expect = 3.2
Identities = 13/78 (16%), Positives = 28/78 (35%)
Query: 7 TPEERMLCRREYKRRYYLKNRDKILERRRRRYLKNKDKIRESYHQYYLKNKDKYREYKRR 66
++R +R ER R ++ RE + + + + E + R
Sbjct: 369 NSDDRERSESAQRRSPGEGRHQHSDERDDGRRQHRREDARELDRKSRFRKERESNEDEDR 428
Query: 67 YYLKNRDKMREKARQSYR 84
+ R++ R K+ + R
Sbjct: 429 RSRRKRERTRNKSSRRER 446
>gnl|CDD|111439 pfam02538, Hydantoinase_B, Hydantoinase B/oxoprolinase. This
family includes N-methylhydaintoinase B which converts
hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase
EC:3.5.2.9 which catalyses the formation of L-glutamate
from 5-oxo-L-proline. These enzymes are part of the
oxoprolinase family and are related to pfam01968.
Length = 527
Score = 25.5 bits (56), Expect = 4.4
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 6/59 (10%)
Query: 69 LKNRDKMREKARQSYRKLYSKDSWIA--PEEPMGMTKAEIEALEREIARLKAKPIEELI 125
L + E + R+L+ ++ + + PE +G KA+I A ++ I R+ K I+E
Sbjct: 152 LVKNGEFNE---ELIRQLFVRNPYPSRNPECNIGDLKAQIAANQKGIDRIG-KLIDEYG 206
>gnl|CDD|38823 KOG3617, KOG3617, KOG3617, WD40 and TPR repeat-containing protein
[General function prediction only].
Length = 1416
Score = 25.4 bits (55), Expect = 4.5
Identities = 13/63 (20%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 20 RRYYLKNRDKILERRRRRYLKNKDKIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKA 79
+Y + RD+ L +YL++ ++ + +Y KD + + + DK A
Sbjct: 903 EQYVRRKRDESLYSWWGQYLESVGEMDAALS-FYSSAKDYFSMVRIKCIQGKTDKAARIA 961
Query: 80 RQS 82
+S
Sbjct: 962 EES 964
>gnl|CDD|30540 COG0191, Fba, Fructose/tagatose bisphosphate aldolase [Carbohydrate
transport and metabolism].
Length = 286
Score = 25.5 bits (56), Expect = 4.6
Identities = 10/48 (20%), Positives = 20/48 (41%), Gaps = 6/48 (12%)
Query: 43 DKIRESYHQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKD 90
+RE Y +N +Y R+Y + M+E ++ ++ S
Sbjct: 243 AAVRE----YLAENPKEYDP--RKYLKPAIEAMKEVVKEKIKEFGSAG 284
>gnl|CDD|32946 COG3132, COG3132, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 215
Score = 25.4 bits (55), Expect = 4.8
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 94 APEEPMGMTKAEIEALEREIARLKAK 119
AP +A +EALE+E+A L+A+
Sbjct: 182 APAAASSDLEARVEALEQEVAELRAR 207
>gnl|CDD|143419 cd07101, ALDH_SSADH2_GabD2, Mycobacterium tuberculosis
succinate-semialdehyde dehydrogenase 2-like.
Succinate-semialdehyde dehydrogenase 2 (SSADH2) and
similar proteins are in this CD. SSADH1 (GabD1,
EC=1.2.1.16) catalyzes the NADP(+)-dependent oxidation
of succinate semialdehyde to succinate. SSADH activity
in Mycobacterium tuberculosis is encoded by both gabD1
(Rv0234c) and gabD2 (Rv1731), however ,the Vmax of GabD1
was shown to be much higher than that of GabD2, and
GabD2 (SSADH2) is likely to serve physiologically as a
dehydrogenase for a different aldehyde(s).
Length = 454
Score = 25.0 bits (55), Expect = 5.7
Identities = 8/17 (47%), Positives = 13/17 (76%)
Query: 21 RYYLKNRDKILERRRRR 37
RYY + +++L+ RRRR
Sbjct: 87 RYYARRAERLLKPRRRR 103
>gnl|CDD|35965 KOG0746, KOG0746, KOG0746, 60S ribosomal protein L3 and related
proteins [Translation, ribosomal structure and
biogenesis].
Length = 384
Score = 25.0 bits (54), Expect = 5.8
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 62 EYKRRYYLKNRDKMREKARQSYRKLYSKDSWIAPEE 97
E KRR+Y KN K ++KA Y K + + E
Sbjct: 100 ECKRRFY-KNWHKSKKKAFTKYCKKWQDEDGKKQLE 134
>gnl|CDD|147119 pfam04802, SMK-1, Component of IIS longevity pathway SMK-1. SMK-1
is a component of the IIs longevity pathway which
regulates aging in C.elegans. Specifically, SMK-1
influences DAF-16-dependant regulation of the aging
process by regulating the transcriptional specificity of
DAF-16 activity. SMK-1 plays a role in longevity by
modulating the transcriptional specificity of DAF-16.
Length = 193
Score = 24.8 bits (55), Expect = 6.4
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 50 HQYYLKNKDKYREYKRRYYLKNRDKMREKARQSYRKLYSKD 90
H+ +L K++E +KN ++R+K Q+YR Y KD
Sbjct: 74 HRQFLTQNAKFKEVIP---IKN-PELRQKIHQTYRLQYLKD 110
>gnl|CDD|36758 KOG1545, KOG1545, KOG1545, Voltage-gated shaker-like K+ channel
KCNA [Inorganic ion transport and metabolism].
Length = 507
Score = 24.5 bits (53), Expect = 7.9
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 8 PEERMLCRREYKRRYYL 24
PEER L R E++R+ +L
Sbjct: 163 PEERPLPRNEFQRQVWL 179
>gnl|CDD|39002 KOG3798, KOG3798, KOG3798, Predicted Zn-dependent hydrolase
(beta-lactamase superfamily) [General function
prediction only].
Length = 343
Score = 24.6 bits (53), Expect = 9.0
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 51 QYYLKNKDKYREYKRRYYLKNRD 73
+YYL+ +DK +E LK+
Sbjct: 307 EYYLEPRDKLKELMEAEGLKDTS 329
>gnl|CDD|132756 cd07071, NR_LBD_Nurr1, The ligand binding domain of Nurr1, a
member of conserved family of nuclear receptors. The
ligand binding domain of nuclear receptor Nurr1: Nurr1
belongs to the conserved family of nuclear receptors. It
is a transcription factor that is expressed in the
embryonic ventral midbrain and is critical for the
development of dopamine (DA) neurons. Structural studies
have shown that the ligand binding pocket of Nurr1 is
filled by bulky hydrophobic residues, making it unable
to bind to ligands. Therefore, it belongs to the class
of orphan receptors. However, Nurr1 forms heterodimers
with RXR and can promote signaling via its partner, RXR.
Like other members of the nuclear receptor (NR)
superfamily of ligand-activated transcription factors,
Nurr1 has a central well conserved DNA binding domain
(DBD), a variable N-terminal domain, a flexible hinge
and a C-terminal ligand binding domain (LBD).
Length = 238
Score = 24.6 bits (53), Expect = 9.2
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 8 PEERMLCRREYKRRYYLKNRD 28
PE R LC + +R +YLK D
Sbjct: 200 PELRTLCTQGLQRIFYLKLED 220
>gnl|CDD|145880 pfam02956, TT_ORF1, TT viral orf 1. TT virus (TTV), isolated
initially from a Japanese patient with hepatitis of
unknown aetiology, has since been found to infect both
healthy and diseased individuals and numerous
prevalence studies have raised questions about its role
in unexplained hepatitis. ORF1 is a large 750 residue
protein. The N-terminal half of this protein
corresponds to the capsid protein.
Length = 525
Score = 24.5 bits (54), Expect = 9.3
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 15 RREYKRRYYLKNRDKILERRRRRY 38
R +RR ++ R + RRRRR
Sbjct: 25 ARRRRRRRRVRRRRRGRRRRRRRR 48
>gnl|CDD|33234 COG3428, COG3428, Predicted membrane protein [Function unknown].
Length = 494
Score = 24.5 bits (53), Expect = 9.9
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 96 EEPMGMTKAEIEALEREIARLKAKPIEELIYKRG 129
E G +AE E +EREIA A + E K+
Sbjct: 117 ETAGGGGEAEAELVEREIAFELAALVREARVKKL 150
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
0.320 0.136 0.389
Gapped
Lambda K H
0.267 0.0615 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,749,306
Number of extensions: 94668
Number of successful extensions: 717
Number of sequences better than 10.0: 1
Number of HSP's gapped: 680
Number of HSP's successfully gapped: 163
Length of query: 129
Length of database: 6,263,737
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,470,190
Effective search space: 205628740
Effective search space used: 205628740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.1 bits)